Inhibition of dUTPase induces synthetic lethality with thymidylate synthase-targeted therapies in non-small cell lung cancer

Chemotherapies that target thymidylate synthase (TS) continue to see considerable clinical expansion in non-small cell lung cancer (NSCLC). One drawback to TS-targeted therapies is drug resistance and subsequent treatment failure. Novel therapeutic and biomarker-driven strategies are urgently needed. The enzyme deoxyuridine triphosphate nucleotidohydrolase (dUTPase) is reported to protect tumor cells from aberrant misincorporation of uracil during TS inhibition. The goal of this study was to investigate the expression and significance of dUTPase in mediating response to TS-targeted agents in NSCLC. The expression of dUTPase in NSCLC cell lines and clinical specimens was measured by quantitative real-time reverse transcriptase PCR and immunohistochemistry. Using a validated RNA interference approach, dUTPase was effectively silenced in a panel of NSCLC cell lines and response to the fluoropyrimidine fluorodeoxyuridine (FUdR) and the antifolate pemetrexed was analyzed using growth inhibition and clonogenic assays. Apoptosis was analyzed by flow cytometry. Significant variation in the quantity and cellular expression of dUTPase was observed, including clear evidence of overexpression in NSCLC cell line models and tumor specimens at the mRNA and protein level. RNA interference-mediated silencing of dUTPase significantly sensitized NSCLC cells to growth inhibition induced by FUdR and pemetrexed. This sensitization was accompanied by a significant expansion of intracellular dUTP pools and significant decreases in NSCLC cell viability evaluated by clonogenicity and apoptotic analyses. Together, these results strongly suggest that uracil misincorporation is a potent determinant of cytotoxicity to TS inhibition in NSCLC and that inhibition of dUTPase is a mechanism-based therapeutic approach to significantly enhance the efficacy of TS-targeted chemotherapeutic agents.

A novel fluorescence-based assay for the rapid detection and quantification of cellular deoxyribonucleoside triphosphates

Current methods for measuring deoxyribonucleoside triphosphates (dNTPs) employ reagent and labor-intensive assays utilizing radioisotopes in DNA polymerase-based assays and/or chromatography-based approaches. We have developed a rapid and sensitive 96-well fluorescence-based assay to quantify cellular dNTPs utilizing a standard real-time PCR thermocycler. This assay relies on the principle that incorporation of a limiting dNTP is required for primer-extension and Taq polymerase-mediated 5-3' exonuclease hydrolysis of a dual-quenched fluorophore-labeled probe resulting in fluorescence. The concentration of limiting dNTP is directly proportional to the fluorescence generated. The assay demonstrated excellent linearity (R(2) > 0.99) and can be modified to detect between ∼0.5 and 100 pmol of dNTP. The limits of detection (LOD) and quantification (LOQ) for all dNTPs were defined as <0.77 and <1.3 pmol, respectively. The intra-assay and inter-assay variation coefficients were determined to be <4.6% and <10%, respectively with an accuracy of 100 ± 15% for all dNTPs. The assay quantified intracellular dNTPs with similar results obtained from a validated LC-MS/MS approach and successfully measured quantitative differences in dNTP pools in human cancer cells treated with inhibitors of thymidylate metabolism. This assay has important application in research that investigates the influence of pathological conditions or pharmacological agents on dNTP biosynthesis and regulation.

Regulation of human dUTPase gene expression and p53-mediated transcriptional repression in response to oxaliplatin-induced DNA damage

Deoxyuridine triphosphate nucleotidohydrolase (dUTPase) catalyzes the hydrolysis of dUTP to dUMP and PPi. Although dUTP is a normal intermediate in DNA synthesis, its accumulation and misincorporation into DNA is lethal. Importantly, uracil misincorporation is a mechanism of cytotoxicity induced by fluoropyrimidine chemotherapeutic agents including 5-fluorouracil (5-FU) and elevated expression of dUTPase is negatively correlated with clinical response to 5-FU-therapy. In this study we performed the first functional characterization of the dUTPase promoter and demonstrate a role for E2F-1 and Sp1 in driving dUTPase expression. We establish a direct role for both mutant and wild-type forms of p53 in modulating dUTPase promoter activity. Treatment of HCT116 p53(+/+) cells with the DNA-damaging agent oxaliplatin induced a p53-dependent transcriptional downregulation of dUTPase not observed in the isogenic null cell line. Oxaliplatin treatment induced enrichment of p53 at the dUTPase promoter with a concomitant reduction in Sp1. The suppression of dUTPase by oxaliplatin promoted increased levels of dUTP that was enhanced by subsequent addition of fluoropyrimidines. The novel observation that oxaliplatin downregulates dUTPase expression may provide a mechanistic basis contributing to the synergy observed between 5-FU and oxaliplatin in the clinic. Furthermore, these studies provide the first evidence of a direct transcriptional link between the essential enzyme dUTPase and the tumor suppressor p53.

Differences in the levels of aminoacylation and contents of modified nucleotides between total tRNAs from N2- and NH4+-grown Azospirillum lipoferum cells

Total tRNAs isolated from N2- and NH4(+)-grown Azospirillum lipoferum cells were compared with respect to amino acid acceptance, isoacceptor tRNA species levels and extent of nucleotide modifications. Amino-acylation of these two tRNA preparations with ten different amino acids indicated differences in the relative acceptor activities. Comparison of aminoacyl-tRNA patterns by RPC-5 column chromatography revealed no qualitative differences in the elution profiles. However, quantitative differences in the relative amounts of some isoacceptors were observed. These results indicate that alterations of relative amounts of functional tRNA species occur to match cellular requirements of the bacterial cells using N2 or NH4+ as nitrogen source. In addition, the content of modified nucleotides in total tRNAs of N2- and NH4(+)-grown cells was determined. In the NH4(+)-grown cells, content of most of the modified nucleotides decreased significantly. Based upon these results, the relationship of chargeability of tRNAs to base modifications is discussed.

Interaction of metal ions with 6-oxopurine nucleotides. Part 1. X-Ray structures of ternary cobalt(III) complexes with inosine 5'-monophosphate or guanosine 5'-monophosphate

The crystal structures of two ternary metal nucleotide complexes of cobalt, [Co(en)2(H2O)2]-[Co(5?-IMP)2(H2O)4]Cl2·4H2O (1) and [Co(en)2(H2O)2][Co(5?-GMP)2(H2O)4]Cl2·4H2O (2), have been analysed by X-ray diffraction (en = ethylenediamine, 5?-IMP = inosine 5?-monophosphate, and 5?-GMP = guanosine 5?-monophosphate). Both complexes crystallize in the orthorhombic space group C2221 with a= 8.725(1), b= 25.891(5), c= 21.212(5)Å, Z= 4 for (1) and a= 8.733(2), b= 26.169(4), c= 21.288(4)Å, Z= 4 for (2). The structure of (1) was solved by the heavy-atom method, while that of (2) was deduced from (1). The structures were refined to R values of 0.09 and 0.10 for 1 546 and 1 572 reflections for (1) and (2) respectively. The two structures are isomorphous. A novel feature is that the chelate ligand en and the nucleotide are not co-ordinated to the same metal ion. One of the metal ions lying on the two-fold a axis is octahedrally co-ordinated by two chelating en molecules and two water oxygens, while the other on the two-fold b axis is octahedrally co-ordinated by two N(7) atoms of symmetry-related nucleotides in a cis position and four water oxygens. The conformations of the nucleotides are C(2?)-endo, anti, and gauche�gauche. In both (1) and (2) the charge-neutralising chloride ions are disordered in the vacant space between the molecules. These structures bear similarities to the mode of nucleotide co-ordination to PtII complexes of 6-oxopurine nucleotides, which are the proposed models for intrastrand cross-linking in DNA by a metal complex.

Interaction of metal ions with 6-oxopurine nucleotides. Part 2. X-Ray structures of ternary nickel(II) complexes with 2'-deoxyguanosine 5'-monophosphate or guanosine 5'-monophosphate

The ternary metal nucleotide complexes [Ni(en)1.3(H2O)1.4(H2O)2][Ni(5?-dGMP)2(en)0.7-(H2O)0.6(H2O)2]·7H2O (1) and [Ni(en)2(H2O)2][Ni(5?-GMP)2(H2O)4]·6H2O (2)(en = ethylenediamine, 5?-dGMP = 2?-deoxyguanosine 5?-monophosphate, 5?-GMP = guanosine 5?-monophosphate) have been prepared and their structures analyzed by X-ray diffraction methods. Both compounds crystallise in the space group C2221 with a= 8.810(1), b= 25.090(4), c= 21.084(1)Å, and Z= 4 for (1) and a= 8.730(1), b= 25.691(4), c= 21.313(5)Å, and Z= 4 for (2). The structures were deduced from the analogous CoIII complexes and refined by full-matrix least-squares methods to final R values of 0.087 and 0.131 for 1 211 and 954 reflections for (1) and (2) respectively. An interesting feature of the deoxyribonucleotide complex (1) is that en is not totally labilized from the metal centre on nucleotide co-ordination, as observed in corresponding ribonucleotide complexes. Apart from extensive intra- and inter-molecular hydrogen bonding, the structures are stabilized by significant intracomplex base�base and base�sugar interactions. The nucleotides in both complexes have an anti base, C(2?)-endo sugar pucker, and gauche�gauche conformation about the C(4?)�C(5?) bond.

Regulation of the activity of mung bean (Phaseolus aureus) glutamine synthetase by amino acids and nucleotides

The activity of glutamine synthetase isolated from the germinated seedlings of Phaseolus aureus was regulated by feedback inhibition by alanine, glycine, histidine, AMP, and ADP. When glutamate was the varied substrate, alanine, histidine, and glycine were partial noncompetitive, competitive, and mixed-type inhibitors, respectively. The type of inhibition by these amino acids was confirmed by fractional inhibition analysis. The adenine nucleotides, AMP and ADP, completely inhibited the enzyme activity and were competitive with respect to ATP. Multiple inhibition analyses revealed the presence of separate and nonexclusive binding sites for the amino acids and mutually exclusive sites for adenine nucleotides. Cumulative inhibition was observed with these end products.

Interactions of tris buffer with nucleotides: the crystal structure of tris(hydroxymethyl)methylammonium adenosine 5'-diphosphate dihydrate

The crystal and molecular structures of the Tris salt of adenosine 5'-diphosphate were determined from X-ray diffraction data. The crystals are monoclinic, space P21, and Z = 2 with a=9.198 (2) A, b=6.894 (1) A, c=18.440 (4) A, and beta = 92.55 (2) degrees. Intensity data were collected on an automated diffractometer. The structure was solved by the heavy-atom technique and refined by least squares to R = 0.047. The ADP molecule adopts a folded conformation. The conformation about the glycosidic bond is anti. The conformation of the ribose ring is close to a perfect C(2')-endo-C-(3')-exo puckering. The conformation about C(4')-C(5') is gauche-gauche, similar to other nucleotide structures. The pyrophosphate chain displays a nearly eclipsed geometry when viewed down the P-P vector, unlike the staggered conformation observed in crystal structures of other pyrophosphates. The less favorable eclipsed conformation probably results from the observed association of Tris molecules with the polar diphosphate chain through electrostatic interactions and hydrogen bonds. Such interactions may play an important role in Tris-buffered aqueous solutions of nucleotides and metal ions.

Preliminary observations on changes in nucleotides in oil sardine and certain Penaeid prawns during chill storage

Preliminary study has been made of the changes in common 5' nucleotides in oil sardine (Sardinella longiceps) and two Penaeid prawns of Indian waters during chill storage. The course of nucleotide degradation has been followed in the fresh fish and shell fish during ice storage. The level of inosine monophosphate (IMP) in prawns showed significant but steady decrease during ice storage and this appears to serve as useful indication of length of storage. Comparison has been made on the pattern of nucleotide changes in block frozen fish and individually quick frozen fish stored at -23°C.

Cleavage of nucleotides by Ce4+ and the lanthanide metal complexes

The cleavage of adenosine-5'-monophosphate (5'-AMP) and guanosine-5'-monophosphate (S-GMP) by Ce4+ and lanthanide complex of 2-carboxyethylgermanium sesquioxide (Ge-132) in acidic and near neutral conditions was investigated by NMR, HPLC and measuring the liberated inorganic phosphate at 37 degrees C and 50 degrees C, The results showed that 5'-GMP and 5'-AMP was converted to guanine (G), 5'-monophosphate (depurination of 5'-GMP), ribose (depurination and dephosphorylation of 5'-GMP), phosphate and adenine (A), 5'-monophosphate (depurination of 5'-AMP), ribose (depurination and dephosphorylation of 5'-AMP), phosphate respectively by Ce4+. In presence of lanthanide complexes, 5'-GMP and 5'-AMP were converted to guanosine (Guo) and phosphate and adenosine (Ado) and phosphate respectively. The mechanism of cleaving 5'-GMP and 5'-AMP is hydrolytic scission.