Fluoropyrimidine-mediated changes in small nuclear RNA

A novel view on an old drug, 5-fluorouracil: an unexpected RNA modifier with intriguing impact on cancer cell fate

5-Fluorouracil (5-FU) is a chemotherapeutic drug widely used to treat patients with solid tumours, such as colorectal and pancreatic cancers. Colorectal cancer (CRC) is the second leading cause of cancer-related death and half of patients experience tumour recurrence. Used for over 60 years, 5-FU was long thought to exert its cytotoxic effects by altering DNA metabolism. However, 5-FU mode of action is more complex than previously anticipated since 5-FU is an extrinsic source of RNA modifications through its ability to be incorporated into most classes of RNA. In particular, a recent report highlighted that, by its integration into the most abundant RNA, namely ribosomal RNA (rRNA), 5-FU creates fluorinated active ribosomes and induces translational reprogramming. Here, we review the historical knowledge of 5-FU mode of action and discuss progress in the field of 5-FU-induced RNA modifications. The case of rRNA, the essential component of ribosome and translational activity, and the plasticity of which was recently associated with cancer, is highlighted. We propose that translational reprogramming, induced by 5-FU integration in ribosomes, contributes to 5-FU-driven cell plasticity and ultimately to relapse.

Early 5-Fluorouracil-Induced Changes of Poly(A) Polymerase in Hela and Wish Cells

5-Fluorouracil (5-FU), a drug with numerous mechanisms of action which has a long-term suppressive effect on human cancer cell proliferation, mediates both partial dephosphorylation and inactivation of poly(A) polymerase (PAP) [EC. 2.7.7.19] as detected by immunoblotting analysis and non-specific enzyme assay, respectively, in human carcinoma HeLa and diploid WISH cells at a concentration of 100 μM. When the same experiment is done in the presence of phosphatase inhibitors, 5-FU-induced partial PAP dephosphorylation is abolished. Moreover, a cell type-modulated, differential response of HeLa cells (5-FU chemosensitive cells) versus WISH cells (drug-resistant diploid cells) is observed. These results suggest that 5-FU induces early direct or indirect changes in the structure and function of PAP and may regulate premRNA cleavage-polyadenylation.

Data-driven assessment of the association of polymorphisms in 5-Fluorouracil metabolism genes with outcome in adjuvant treatment of colorectal cancer

A major challenge in the assessment of medicines, treatment options, etc., is to establish a framework for the comparison of risks and benefits of many different types and magnitudes, a framework that at the same time allows a clear distinction between the roles played by the statistical analyses of data and by judgements based on personal experience and expertise. The purpose of this study was to demonstrate how clinical data can be weighted, scored and presented by the use of an eight-step data-driven benefit-risk assessment method, where two genetic profiles are compared. Our aim was to present a comprehensive approach that is simple to apply, allows direct comparison of different types of risks and benefits, quantifies the clinical relevance of data and is tailored for the comparison of different options. We analysed a cohort of 302 patients with colorectal cancer treated with 5-Fluorouracil (5-FU). Endpoints were cure rate, survival rate, time-to-death (TTD), time-to-relapse (TTR) and main adverse drug reactions. Multifactor dimensionality reduction (MDR) was used to identify genetic interaction profiles associated with outcome. We have been able to demonstrate that a specific MDR-derived combination (the MDR-1 group) of dihydropyrimidine dehydrogenase and thymidylate synthase polymorphisms is associated with increased and clinically significant difference for cure and survival rates, TTD and probably also for TTR, which are seen as the most important endpoints. An inferior profile was observed for severe myocardial ischaemia. A probably inferior profile was seen for severe arthralgia/myalgia and severe infections. A clear superior profile was seen for severe mucositis/stomatitis. The proposed approach offers comprehensive, data-driven assessment that can facilitate decision processes, for example, in a clinical setting. It employs descriptive statistical methods to highlight the clinically relevant differences between options.

The association of polymorphisms in 5-fluorouracil metabolism genes with outcome in adjuvant treatment of colorectal cancer

AIM

The purpose of this study was to investigate whether specific combinations of polymorphisms in 5-fluorouracil (5-FU) metabolism-related genes were associated with outcome in 5-FU-based adjuvant treatment of colorectal cancer.

METHODS

We analyzed two cohorts of 302 and 290 patients, respectively, one cohort for exploratory analyses and another cohort for validating the exploratory analyses. A total of ten polymorphisms in genes involved in 5-FU pharmacodynamics and pharmacokinetics were studied. End points were disease-free survival (DFS) and overall survival. Multifactor dimensionality reduction was used to identify genetic interaction profiles associated with outcome.

RESULTS

Low-expression alleles in thymidylate synthase (TYMS) were associated with decreased DFS and overall survival (DFS:hazard ratio [HR] exploration 2.65 [1.40-4.65]; p = 0.004, HR validation 1.69 [1.03-2.66]; p = 0.03). A specific multifactor dimensionality reduction derived combination of dihydropyrimidine dehydrogenase and TYMS polymorphisms was associated with increased DFS (HR exploration 0.69 [0.49-0.98]; p = 0.04, HR validation 0.66 [0.45-0.95]; p = 0.03). Specific combinations of functional polymorphisms in DPYD and TYMS were demonstrated to be associated with DFS and overall survival in patients receiving adjuvant 5-FU-based treatment. Specifically high TYMS expression alleles seem to be associated with decreased DFS.

Influence of halogenation on the properties of uracil and its noncovalent interactions with alkali metal ions. Threshold collision-induced dissociation and theoretical studies

The influence of halogenation on the properties of uracil and its noncovalent interactions with alkali metal ions is investigated both experimentally and theoretically. Bond dissociation energies of alkali metal ion-halouracil complexes, M+(XU), are determined using threshold collision-induced dissociation techniques in a guided ion beam mass spectrometer, where M+ = Li+, Na+, and K+ and XU = 5-fluorouracil, 5-chlorouracil, 6-chlorouracil, 5-bromouracil, and 5-iodouracil. The structures and theoretical bond dissociation energies of these complexes are determined from ab initio calculations. Theoretical calculations are also performed to examine the influence of halogenation on the acidities, proton affinities, and Watson-Crick base pairing energies. Halogenation of uracil is found to produce a decrease in the proton affinity, an increase in the alkali metal ion binding affinities, an increase in the acidity, and stabilization of the A::U base pair. In addition, alkali metal ion binding is expected to lead to an increase in the stability of nucleic acids by reducing the charge on the nucleic acid in a zwitterion effect as well as through additional noncovalent interactions between the alkali metal ion and the nucleobases.

Effect of 5-FU substitution and mutation on Sm protein binding to human U4 snRNA

The effects of native and non-native nucleotide substitution on the binding of Sm proteins to human U4 snRNA were investigated to determine if the Sm site was a likely target for the RNA-mediated effects of the anticancer drug 5-FU, and other nucleoside analogues. The Sm binding site of human U4 snRNA was prepared by in vitro transcription, and Sm protein binding was assessed using gel mobility shift assays. The U4:Sm RNA:protein complex was identified by immunoprecipitation with the Sm-specific Y12 antibody. The effects of 5-FU substitution were assessed by including FUTP in the in vitro transcription reactions. The effects of native nucleotide substitution were assessed by mutagenesis. Deletion mutants were used to assess the relative importance of the two stem-loops that flank the Sm binding site for protein binding. Point mutation (U-->G) to the 5'-Urd in the Sm site reduced Sm protein binding while similar point mutation to the 3'-Urd had a lesser effect. Mutation (U-->G) of all Urd in the Sm site completely inhibited Sm protein binding. The central stem-loop contributed significantly to Sm protein complex formation but the 3' stem-loop had little effect. Substitution of Urd by 5-fluorourdine (FUrd) did not inhibit Sm protein binding, but reduced the stability of the resulting complex. The results indicate that 5-FU, or other Uracil analogues, are unlikely to exert RNA-mediated effects through inhibition of Sm protein binding.

The structure and dynamics of the U4/U6 snRNP: implications for pre-mRNA splicing and use as a model system to investigate the RNA-mediated effects of (5F)Ura

Pre-mRNA splicing is one of the most complex and intricate processes in eukaryotic cell biology. Over the past decade, my laboratory has been interested in determining the structures of RNA components of the spliceosome, and in investigating how the structure, stability and dynamics of these RNA components are perturbed by nucleoside analog substitution. In particular, we have investigated the U4/U6 snRNA complex as a model system for understanding the biophysical basis for the RNA-mediated effects of the widely-used anticancer drug 5-fluorouracil ((5F)Ura). In this review, our studies that have provided novel information concerning the structure of U4 snRNA and its interactions with U6 snRNA and the Sm (or common) snRNA binding proteins are summarized. These studies have also quantified the structural and thermodynamic consequences of (5F)Ura in this model system. Our work to date provides the foundation on which future studies investigating the biophysical basis for spliceosomal assembly and for clarifying the mechanisms of anticancer drugs targeted at nucleic acid-mediated processes will be developed.

Naturally occurring antisense RNA

Within the last few years a number of mammalian genes have been found for which there exist naturally occurring "antisense" RNA species with complementarity to mRNAs. Effects of antisense RNA on "sense" RNA have yet to be established. Nevertheless, it is apparent that mammalian cells have devoted genetic information and machinery to processing RNA:RNA hybrids, and it is becoming clear that there may be many more genes than previously suspected to which natural antisense RNAs exist. If naturally occurring antisense RNAs are mediators of alterations in gene expression, the question arises as to whether these pathways can be exploited pharmacologically.

Role of the lung in accumulation and metabolism of xenobiotic compounds--implications for chemically induced toxicity

The mammalian lung is exposed to and affected by many airborne and bloodborne foreign compounds. This review summarizes the role of lung in accumulation and metabolism of xenobiotics, some of which are spontaneously reactive or are metabolically activated to toxic intermediates. The specific architectural arrangement of mammalian lung favors that so-called pneumophilic drugs are filtered out of the blood and are retained within the tissue as shown in particular for amphetamine, chlorphentermine, amiodarone, imipramine, chlorpromazine, propranolol, local anaesthetics, and some miscellaneous therapeutics. There is strong evidence that intrapulmonary distribution activity and regulation of drug-metabolizing enzymes in lung is distinct from liver. This review focuses on the metabolic rate of selected compounds in lung such as 5-fluoro-2'-deoxyuridine, local anesthetics, nicotine, benzo(alpha)pyrene, ipomeanol, 4-methylnitrosamino-1-(3-pyridyl)-1-butanone. It is widely accepted that the formation of radical species is a key event in the pneumotoxic mechanisms induced by bleomycin, paraquat, 3-methylindole, butylhydroxytoluene, or nitrofurantoin. Finally, methodological approaches to assess the capacity of lung to eliminate foreign compounds as well as biochemical features of the pulmonary tissue are evaluated briefly.

Altered RNA turnover in carcinogenesis. The diagnostic potential of modified base excretion

Excretion of urinary modified nucleosides is frequently elevated in patients with oncogenic disease. Increases of urinary pseudouridine excretion are now demonstrated in patients with a variety of brain tumors. The potential use of urinary modified base excretion as a cancer marker is discussed and possible sources of the elevated nucleosides are detailed. The specific steps in RNA metabolism that result in increased levels of RNA nucleoside excretion are poorly understood. This knowledge will be necessary to understand the molecular mechanism and the clinical significance of urinary nucleoside excretion in treatment and diagnosis of oncogenic disease.

Ribonucleoprotein particle assembly and modification of U2 small nuclear RNA containing 5-fluorouridine

An in vitro assembly/modification system was used to study the effect of 5-fluorouridine (5-FU) incorporation on the biosynthesis of the U2 small nuclear ribonucleoprotein particle (U2 snRNP). Labeled U2 RNAs were transcribed in vitro with 5-fluoro-UTP either partially supplementing or completely replacing UTP during synthesis. The resulting U2 RNAs have levels of 5-fluorouridine that range from 0 to 100% of the uridine content. When incubated in reactions containing extracts from HeLa cells, these 5-FU U2 RNAs are assembled into RNPs that are recognized by anti-Sm monoclonal antibody even when there is a complete replacement of uridine with 5-FU. However, when the in vitro assembled U2 snRNPs are subjected to buoyant density gradient centrifugation, the particles that contain 100% 5-FU are not resistant to salt dissociation. When the in vitro assembled U2 snRNPs were analyzed by velocity sedimentation gradient centrifugation, 5-FU incorporation correlated with a shift in the sedimentation rate of the particles. With 100% 5-FU incorporation, the peak of radioactivity shifted to approximately 15 S (control U2 RNA was at approximately 12 S). This peak from 5-FU U2 snRNPs was not resistant to dissociation on cesium sulfate gradients. The amount of pseudouridine (psi) found in the RNA from snRNP assembled in vitro on control and 5-FU-containing U2 RNAs was determined, and even at very low levels of 5-FU incorporation (5% replacement), the formation of psi was severely inhibited (36% of control). At higher levels of 5-FU incorporation, there was essentially no psi formed.

The genetic toxicology of 5-fluoropyrimidines and 5-chlorouracil

The halogenated pyrimidines were synthesized in the 1950s as potential anti-tumor agents after the discovery that certain tumors preferentially incorporated uracil rather than thymine into the DNA. The fluorinated derivatives are widely recognized today as effective treatment modalities, especially with tumors of the head, neck and breast. Mechanistically, efficacy of the fluorinated pyrimidines results from the ability of these compounds to incorporate into RNA and inhibit its maturation to those forms necessary for cellular metabolism and from the inhibition of the enzyme, thymidylate synthetase, which controls the biosynthesis of thymine and DNA synthesis. The 5-fluoropyrimidines can incorporate into DNA, but the contribution of this phenomenon to the overall efficacy of this class of chemotherapeutic agents is not totally resolved. Evidence exists that this class of compounds possesses the properties to induce genotoxic effects, both in bacterial and eukaryotic cells. Most notably, these effects include the induction of cellular toxicity and the induction of chromosome aberrations. The biology and chemistry of the chlorinated pyrimidines were first explored as a possible means of sensitizing the DNA to ionizing radiation in a manner similar to the sensitization observed when DNA incorporates bromodeoxyuridine. This approach was not utilized clinically. The genetic toxicology of this compound became important with the discovery of the ribonucleoside in the effluents of sewage treatment plants. Evidence is now available that the chlorinated pyrimidines, upon conversion to deoxyribonucleosides, are effective mutagens, clastogens and toxicants, as well as extremely effective inducers of sister-chromatid exchanges.

Effects of 5-fluorouracil on mRNA

Currently, there are a number of studies which suggest that FU can have pronounced effects on mRNA and its metabolism. However, the relevance of these changes to the antitumor effect of FU are still not clear. Generally, the mRNAs which have been studied to date involve those genes which are associated with the TS-directed effects of FU and have generally been limited to the changes in mRNA levels. The recent development of PCR methodology to investigate changes in pre-mRNA and splicing provides the tool to study a number of RNA effects of FU simultaneously. The major question is which mRNAs are important for study. DHFR mRNA has a half life of 11.5 in KB1BT cells (Will and Dolnick, 1989) and is thus, on a kinetic basis alone, unlikely to provide a significant RNA target for RNA-directed effects of FU. There is a greater likelihood that shorter lived mRNAs which not only turnover rapidly, but are important to cell proliferation will eventually be shown to be key targets for the effects of FU at the RNA level. Interestingly, many of the growth factors are encoded by short-lived and tightly regulated mRNAs (e.g. GM-CSF, Shaw and Kamen, 1986). In fact the half-lives of some of these mRNAs are regulated by U-rich sequences in their 3'-noncoding regions. The presence of U-rich sequences in these growth factor mRNAs and the small nuclear RNAs suggests these are worthwhile targets for studies, which could now be performed on clinical samples. Laboratory data which shows alterations in the small nuclear RNAs, under conditions which only provide for very low-level substitution of U residues by FU also suggest that RNA effects of FU may be a much more tightly related to cytotoxicity in vivo than previously thought.

Metabolism and RNA incorporation of cyclopentenyl cytosine in human colorectal cancer cells

We studied the cytotoxicity and metabolism of the investigational cytidine analogue cyclopentenyl cytosine (CPE-C) in three human colorectal cancer cell lines: HCT 116, SNU-C4, and NCI-H630. CPE-C potently inhibited cell growth and decreased clonogenic capacity at concentrations achieved in murine and primate pharmacologic studies. CPE-C produced a concentration-dependent depletion of CTP, accompanied by changes in the dCTP pools. CPE-C exposure was associated with an accumulation of cells in the S phase at 48 hr. [3H]CPE-C was metabolized predominantly to the triphosphate (CPE-CTP) form. Saturation of phosphorylation to the monophosphate form occurred above 5-10 microM. Plateau CPE-CTP pools were of a magnitude similar to that of the physiologic ribonucleotide triphosphate pools. The intracellular half-life of CPE-CTP was 24 hr. After a 24-hr exposure to 0.5 microM CPE-C, CPE-CTP was detected for up to 96 hr post-drug removal, accompanied by persistent depletion of the CTP pools. Cesium sulfate density centrifugation of purified nucleic acids indicated that [3H]CPE-C incorporated into RNA, but was not detected in DNA. Agarose-gel electrophoresis of RNA from [3H]CPE-C-treated cells indicated that it localized predominantly in low molecular weight (4-8 S) RNA species. When CPE-C was administered concurrently with [3H]adenosine (Ado), the proportion of [3H]Ado migrating with low molecular weight RNA species increased. Concurrent exposure to 10 microM cytidine (Cyd), sufficient to replete CTP pools, provided essentially complete protection against lethality resulting from a 24-hr exposure to less than or equal to 0.5 microM CPE-C. While 10 microM Cyd substantially decreased CPE-CTP formation and CPE-C-RNA incorporation during the initial 3 hr of exposure compared to CPE-C alone, after 24 hr the levels were not significantly different. Cyd rescue did not affect the accumulation of [3H]CPE-C or [3H]Ado into low molecular weight RNA species after a 24-hr exposure to CPE-C. Our results indicate that depletion of CTP and dCTP pools is an important component of CPE-C cytotoxicity. While CPE-C incorporation into RNA may not be the critical cytotoxic event during a 24-hr exposure to CPE-C, it may play a role during prolonged exposure to CPE-C. CPE-C is a highly potent new agent and merits clinical evaluation in the treatment of colorectal cancer.

Biochemical pharmacology and analysis of fluoropyrimidines alone and in combination with modulators

After more than three decades since their introduction, fluoropyrimidines, especially FUra, are still a mainstay in the treatment of various solid malignancies. The antitumor effects of fluoropyrimidines are dependent upon metabolic activation. FdUMP, FUTP and FdUTP were identified as the key cytotoxic metabolites that interfere with the proper function of thymidylate synthase and nucleic acids. The relevance of these metabolites is cell-type specific. Recently, fluorouridine diphospho sugars have been detected, but the precise function of this class of metabolites is currently unknown. In mammalian systems fluoropyrimidines and their natural counterparts share the same metabolic pathways since the substrate properties in enzyme-catalyzed reactions are frequently comparable. Ongoing studies indicate that the metabolism and action of fluoropyrimidines exhibit circadian rhythms, which appear to be due to variations in the activity of metabolizing enzymes. Essential for the expanding knowledge of the pathways and effects of fluoropyrimidines has been the constant improvement of analytical methods. These include ligand binding techniques, numerous dedicated HPLC systems and 19F-NMR. Because the overall response rates achieved with fluoropyrimidines are modest, strategies based on biochemical modulation have been devised to enhance their therapeutic index. Biochemical modulators include a wide range of various compounds with different modes of action. In recently completed clinical trials, combinations of FUra with leucovorin, a precursor for 5,10-methylene tetrahydrofolate, or with levamisole, an anthelminthic with immunomodulatory activity, appeared to be superior to FUra alone. At the preclinical level combinations of fluoropyrimidines with, e.g. interferons or L-histidinol were demonstrated to be interesting candidates for further testing. The future therapeutic utility of fluoropyrimidines will depend on both the improvement of combination regimens currently used in the treatment of cancer patients and the judicious clinical implementation of promising experimental modulation strategies. Moreover, novel fluoropyrimidines with superior pharmacological properties may become important as part of or instead of modulation approaches.

Metabolism and mechanism of action of 5-fluorouracil

This is a review on the mechanism of action of FUra. Three main areas are addressed: metabolism, RNA-directed actions of FUra, and DNA-directed actions of FUra. Key words for bibliographic purposes: metabolism, RNA, rRNA, mRNA, tRNA, DNA primase, DNA, thymidylate synthetase, uracil N-glycosylase, FUra, FUrd, FdUrd, FdUMP, RNA splicing, 5,10-methylene tetrahydrofolate, FUTP.

Correlation between ribosomal RNA production and RNA-directed fluoropyrimidine cytotoxicity

The relationship between cytotoxicity and fluoropyrimidine effects on the production of mature cytoplasmic 28S and 18S ribosomal RNA was studied in S-180 cells for the fluoropyrimidines: 5-fluorouracil (FUra), 5-fluorouridine (FUrd), 5-fluorodeoxyuridine (FdUrd), and 5'-deoxy-5-fluorouridine (5'-dFUrd). After a 6-hr drug exposure, the total cytotoxicity in the absence of added thymidine (dThd) was determined by soft-agar cloning and resulted in LC90 (lethal concentration to 90% of cells) values of 0.6 microM FdUrd, 0.7 microM FUrd, 5.3 microM FUra and 93 microM 5'-dFUrd. The RNA-directed (dThd-nonreversible) cytotoxicity was assessed by cloning the cells in the presence of 10 microM dThd. This resulted in an altered order of potency and increased LC90 values to 5.5 microM FUrd, 20 microM FUra, 265 microM FdUrd and 870 microM 5'-dFUrd. The production of mature cytoplasmic rRNA was determined by measuring the amount of [3H]cytidine incorporated into the 28S and 18S rANA species following their separation by agarose gel electrophoresis, compared with the level of [3H]cytidine incorporated into the nuclear rRNA. When all four fluoropyrimidines were compared together, the degree of inhibition of cytoplasmic rRNA production was poorly predictive of the total cytotoxicity in the absence of dThd (correlation coefficient, r = 0.77). FdUrd, in particular, had a very minor effect on rRNA production even at very toxic drug concentrations. When toxicity was assessed in the presence of dThd, however, there was a strong and significant correlation between rRNA production and RNA-directed cytotoxicity (r = 0.95, P less than 0.001), for all the fluoropyrimidines tested, including FdUrd. Thus, when the inhibition of thymidylate formation was eliminated as a site of drug action and only RNA-directed cytotoxicity was assessed, the impaired production of cytoplasmic rRNA was strongly associated with cytotoxicity. These results demonstrate that the inhibition of mature cytoplasmic rRNA production may be an important common mechanism of RNA-directed cytotoxicity for all the fluoropyrimidines, and not limited to FUrd or FUra.