The possibility of early diagnosis of colorectal cancer through expression of Lncrna UCA1, Lncrna LINC00970, and Wnt genes; an in-vitro study

Colorectal cancer is the 4thcause of cancer death; with considering the growth process of this cancer and the necessity of early diagnosis, the purpose of the research is to state the LncRNA 00970, LncRNA UCAI,and the Wntgene before and after the treatment by 5-Azacytidine epigenetic medicine, to reach the biomarker in the very first steps of colorectal cancer. In this experiment, the human colon cancer cell line (HT29) treated with different concentrations of 5-aza-2'-deoxycytidine (5-aza-dC) was utilized to induce DNA demethylation; Quantitative PCR (qPCR) was used to measure LncRNA UCA1and LncRNA LINC00970 and Wntexpression. There was a significant relationship between the expression of LncRNA 00970, LncRNA UCAI,and the Wntgene and its effects on colorectal (p < 0.05). The Wntgene was treated by 1 and 10 of 5-Azacytidine epigenetic medicine, which then experienced decreases. In LncRNA UCAI and LncRNA00970 in dose 1 micromolar of 5-Azacytidine had decrement and increment of expressionrespectively that explains their efficiency but in treatment by dose 10 mM of this medicine, no significant LncRNA expression difference was detected, 5-azacitidine has a direct impact on its target genes and LncRNAs.Therefore, it can be used in the early diagnosis of colorectal cancer.

Simultaneous quantitative determination of 5-aza-2'-deoxycytidine genomic incorporation and DNA demethylation by liquid chromatography tandem mass spectrometry as exposure-response measures of nucleoside analog DNA methyltransferase inhibitors.

The epigenetic and anti-cancer activities of the nucleoside analog DNA methyltransferase (DNMT) inhibitors decitabine (5-aza-2'-deoxycytidine, DAC), azacitidine, and guadecitabine are thought to require cellular uptake, metabolism to 5-aza-2'-deoxycytidine triphosphate, and incorporation into DNA. This genomic incorporation can then lead to trapping and degradation of DNMT enzymes, and ultimately, passive loss of DNA methylation. To facilitate measurement of critical exposure-response relationships of nucleoside analog DNMT inhibitors, a sensitive and reliable method was developed to simultaneously quantitate 5-aza-2'-deoxycytidine genomic incorporation and genomic 5-methylcytosine content using LC-MS/MS. Genomic DNA was extracted and digested into single nucleosides. Chromatographic separation was achieved with a Thermo Hyperpcarb porous graphite column (100mm×2.1mm, 5µm) and isocratic elution with a 10mM ammonium acetate:acetonitrile with 0.1% formic acid (70:30, v/v) mobile phase over a 5min total analytical run time. An AB Sciex 5500 triple quadrupole mass spectrometer operated in positive electrospray ionization mode was used for the detection of 5-aza-2'-deoxycytidine, 2'-deoxycytidine, and 5-methyl-2'-deoxycytidine. The assay range was 2-400ng/mL for 5-aza-2'-deoxycytidine, 50-10,000ng/mL for 2'-deoxycytidine, and was 5-1000ng/mL for 5-methyl-2'-deoxycytidine. The assay proved to be accurate (93.0-102.2%) and precise (CV≤6.3%) across all analytes. All analytes exhibited long-term frozen digest matrix stability at -70°C for at least 117 days. The method was applied for the measurement of genomic 5-aza-2'-deoxycytidine and 5-methyl-2'-deoxycytidine content following exposure of in vitro cell culture and in vivo animal models to decitabine.

Quantitative determination of decitabine incorporation into DNA and its effect on mutation rates in human cancer cells.

Decitabine (5-aza-2'-deoxycytidine) is a DNA methyltransferase inhibitor and an archetypal epigenetic drug for the therapy of myeloid leukemias. The mode of action of decitabine strictly depends on the incorporation of the drug into DNA. However, DNA incorporation and ensuing genotoxic effects of decitabine have not yet been investigated in human cancer cell lines or in models related to the approved indication of the drug. Here we describe a robust assay for the quantitative determination of decitabine incorporation rates into DNA from human cancer cells. Using a panel of human myeloid leukemia cell lines we show appreciable amounts of decitabine incorporation that closely correlated with cellular drug uptake. Decitabine incorporation was also detectable in primary cells from myeloid leukemia patients, indicating that the assay is suitable for biomarker analyses to predict drug responses in patients. Finally, we also used next-generation sequencing to comprehensively analyze the effects of decitabine incorporation on the DNA sequence level. Interestingly, this approach failed to reveal significant changes in the rates of point mutations and genome rearrangements in myeloid leukemia cell lines. These results indicate that standard rates of decitabine incorporation are not genotoxic in myeloid leukemia cells.

Quantitative determination of azacitidine triphosphate in peripheral blood mononuclear cells using liquid chromatography coupled with high-resolution mass spectrometry.

Azacitidine is a cytidine analog used in the treatment of myelodysplastic syndromes, chronic myelomonocytic leukemia and acute myeloid leukemia. The pharmacological effect of azacitidine arises after incorporation into the DNA and RNA. To this end, the drug first has to be converted into its triphosphate forms. This paper describes the development of an assay for quantitative determination of azacitidine triphosphate (aza-CTP) in peripheral blood mononuclear cells (PBMCs). To quantify aza-CTP, separation from the endogenous nucleotides cytidine triphosphate (CTP) and uridine triphosphate (UTP) is required. This was a challenge as the structures of these nucleotides are highly similar and the monoisotopic molecular masses of aza-CTP, UTP and the naturally occurring [(13)C]- and [(15)N]-isotopes of CTP differ less than 0.02 Da. Efforts to select a specific MS(2)-fragment for aza-CTP using a triple quadrupole mass spectrometer remained without success. Therefore, we investigated the feasibility to separate these highly resembling nucleotides based on accurate mass spectrometry using a linear trap quadrupole (LTQ) coupled with an Orbitrap. The LTQ-Orbitrap was able to differentiate between aza-CTP and the endogenous nucleotides UTP and [(13)C]-CTP. There was no baseline resolution between aza-CTP and [(15)N]-CTP, but the [(15)N]-CTP interference was low. For quantification, extracted ion chromatograms were obtained for the accurate m/z window of the aza-CTP product ion. The assay was able to determine aza-CTP concentrations in PBMC lysate from 40.7 to 281 nM. Assuming that an average cell suspension extracted from 16 mL blood contains 10 to 42 million PBMCs per mL, this range corresponds with 2.58/10.9-17.8/74.9 pmol aza-CTP per million PBMCs. Intra-assay accuracies were between -1.1 and 9.5% deviation and coefficient of variation values were ≤13.2%. The assay was successfully applied to quantify aza-CTP in samples from two patients treated with azacitidine. Aza-CTP concentrations up to 19.0 pmol per million PBMCs were measured. This is the first time that aza-CTP concentrations were quantified in PBMCs from patients treated with azacitidine.

Ultra-performance liquid chromatography/tandem mass spectrometry for accurate quantification of global DNA methylation in human sperms.

Aberrant DNA methylation in human sperms has been proposed to be a possible mechanism associated with male infertility. We developed an ultra-performance liquid chromatography/tandem mass spectrometry (UPLC-MS/MS) method for rapid, sensitive, and specific detection of global DNA methylation level in human sperms. Multiple-reaction monitoring (MRM) mode was used in MS/MS detection for accurate quantification of DNA methylation. The intra-day and inter-day precision values of this method were within 1.50-5.70%. By using 2-deoxyguanosine as an internal standard, UPLC-MS/MS method was applied for the detection of global DNA methylation levels in three cultured cell lines. DNA methyltransferases inhibitor 5-aza-2'-deoxycytidine can significantly reduce global DNA methylation levels in treated cell lines, showing the reliability of our method. We further examined global DNA methylation levels in human sperms, and found that global methylation values varied from 3.79% to 4.65%. The average global DNA methylation level of sperm samples washed only by PBS (4.03%) was relatively lower than that of sperm samples in which abnormal and dead sperm cells were removed by density gradient centrifugation (4.25%), indicating the possible aberrant DNA methylation level in abnormal sperm cells. Clinical application of UPLC-MS/MS method in global DNA methylation detection of human sperms will be useful in human sperm quality evaluation and the study of epigenetic mechanisms responsible for male infertility.

Simultaneous determination of decitabine and vorinostat (Suberoylanalide hydroxamic acid, SAHA) by liquid chromatography tandem mass spectrometry for clinical studies.

A reverse-phase high-performance liquid chromatography method with electrospray ionization and detection by tandem mass spectrometry is described for the simultaneous quantitative determination of decitabine (5-aza-2'-deoxycytidine) and vorinostat (Suberoylanalide hydroxamic acid, SAHA) in human plasma. The method involves a simple acetonitrile precipitation step and centrifugation followed by injection of the supernatant onto a C18 150mmx2.1mm I.D., 3microm HPLC column at 36 degrees C. Separation of decitabine, SAHA and their respective internal standards was achieved with a gradient elution and detection was via the mass spectrometer operated in selected reaction monitoring mode. The method was within the defined validation parameters for linearity, repeatability, reproducibility and stability. The limit of detection was determined as 1.0 and 0.125ngml(-1) and lower limits of quantitation were 10 and 1ngml(-1) for decitabine and SAHA, respectively. Effects of sample preparation on stability were also evaluated in human plasma. For clinical sample handling tetrahydrouridine, an inhibitor of cytidine deaminase was found to help prevent decitabine degradation. The method is currently being used in clinical pharmacokinetic studies for the evaluation of decitabine and SAHA combination therapies.

Characterization of acid-base properties of unstable drugs using a continuous-flow system with UV-vis spectrophotometric detection.

In this paper, we propose a continuous-flow system for the study of the acid-base characteristics of unstable drugs. 5-Azacytidine has been selected as a first model of unstable compound, which progressively decomposes in aqueous solutions. Besides, other compounds undergoing hydrolysis and oxidation side reactions have been also analyzed to explore the performance of the method. In comparison with conventional batch titrations, the drug decomposition can be minimized by the continuous renewal of the analyte solution. The composition of the buffer mixture is varied on-line during the process from successive changes in the flow rates of acid and basic stock solutions. As a result, the pH value of the test solution is varied in a controlled manner in the range of 1-13. Multivariate curve resolution based on alternating least squares has been used to extract relevant information concerning the acid-base properties of analytes. Results from the continuous-flow system have been compared with those obtained, using batch spectrophotometric titrations, and in the case of fast degradations, the performance of the proposed procedure has been superior.

Apoptosis of terminal hypertrophic chondrocytes in an in vitro model of endochondral ossification.

It is widely accepted that growth plate chondrocytes undergo apoptosis when they reach the terminal hypertrophic stage of their differentiation during the process of endochondral ossification in vivo. In this report, an established chondrocyte cell culture model of mammalian endochondral ossification was utilized to investigate the fate of chondrocytes after they had entered hypertrophy in vitro. Fetal bovine epiphyseal chondrocytes were treated with the demethylating agent, 5-azacytidine, for 48 h and then cultured under azacytidine-depleted conditions. There was evidence for apoptosis in azacytidine-treated cells, as demonstrated by nuclear condensation and fragmentation (days 27 and 35) using transmission electron microscopy, and the detection of exposed phosphatidylserine on the plasma membrane surface of apoptotic chondrocytes (day 27) using fluorescence-labelled annexin V. Treated cultures on days 10 and 20 and untreated cultures at all corresponding time-points showed no morphological characteristics of apoptosis. In situ hybridization studies of treated cultures revealed that expression of the apoptotic suppressor, bcl-2, remained consistently high throughout the culture period, whilst the apoptotic inducer, bax, was not expressed until day 23. Quantification of these data showed a gradual shift in the ratio of the expression level of bcl-2 and bax in favour of bax with time in culture, particularly from day 23 onwards. Taken together, the results indicate that azacytidine-treated epiphyseal chondrocytes entered terminal hypertrophy from day 23 onwards in culture and died by apoptosis. This study confirms this culture system as a successful recapitulation of the entire mammalian chondrocyte differentiation pathway, including apoptosis. The culture model will prove valuable for studies of the apoptotic fate of terminally differentiated chondrocytes in the growth plate with a view to providing a better understanding of the underlying mechanisms of skeletal malformations and other pathological disorders such as osteoarthritis.

Flow cytometric detection of drugs altering the DNA methylation pattern.

We have developed a model system for assessing the demethylating potential of external agents. Disruption in the DNA methylation pattern was evaluated at the translational level of the Escherichia coli beta-galactosidase coding gene (lacZ). We have constructed a clonal cell line (A4/4 cells) derived from the adenovirus-transformed human embryonic kidney 293 strain. The A4/4 cells contain the E. coli lacZ gene under the control of the mouse metallothionein 1 promoter which is down-regulated by a natural DNA methylation pattern. Furthermore, the lacZ transcription is also regulated by the E. coli lac operator/repressor system and by mouse metallothionein 1 metal responsiveness offering a wide range in lacZ expression. In this system, the beta-galactosidase activity was only recovered in the presence of a demethylating agent such as 5-azacytidine. The demethylating potential of 5-azacytidine, 5-aza 2'-deoxycytidine and sodium butyrate was rapidly assessed by a flow cytometric method using fluorescein di-beta-D galactopyranoside as a fluorescent probe. A tremendous induction of lacZ expression was triggered by these drugs. Analysis of cell cycles showed little disruptions with 5-azacytidine and sodium butyrate, but an important blockage in the S-phase following 5-aza 2'-deoxycytidine treatment was observed. This approach allows a rapid identification and study of environmental demethylating agents.

Stability of azacitidine in lactated Ringer's injection frozen in polypropylene syringes.

The stability of azacitidine diluted in lactated Ringer's injection was studied. Azacitidine was reconstituted with ice-cold lactated Ringer's injection to concentrations of 2.0 and 0.5 mg/mL and stored in polypropylene syringes at -20 degrees C. On days 1, 3, 7, and 14, the solutions were thawed over 30-45 minutes and the azacitidine concentration was determined by high-performance liquid chromatography immediately after thawing and one, three, and six hours later. Other studies were conducted at 37, 20, and 0-4 degrees C to determine decomposition rate constants for azacitidine at both concentrations. Hydrolysis of azacitidine resulted in a biphasic decline when the log of the percentage of drug remaining was plotted against time. No substantial decomposition occurred during storage at -20 degrees C. In thawed samples, azacitidine concentrations decreased to 90% of the initial concentrations within three hours after reaching room temperature; similar decreases in concentration were seen in nonfrozen samples stored at room temperature. The results of these studies indicate that azacitidine solutions in lactated Ringer's injection can be stored in polypropylene syringes at -20 degrees C for two weeks without decomposition. The thawed solutions should be used within three hours.

Determination of the antileukemia agents cytarabine and azacitidine and their respective degradation products by high-performance liquid chromatography.

A reversed-phase high-performance liquid chromatography (HPLC) system was developed for the determination of the antineoplastic agents cytarabine and azacitidine. Separations were performed on an octadecylsilane column with a mobile phase of methanol-phosphate buffer pH 7.0 (5:95). The assay methods are suitable for bulk drugs and sterile powder formulations of the agents. Specificity in the presence of analogues and decomposition products was demonstrated. UV spectra of the components of interest were obtained in the HPLC effluent, and appropriate wavelengths were employed for the various analytes. Samples of azacitidine in various solutions were analyzed as a function of time by HPLC to determine the three first-order constants associated with its decomposition.

Stability of azacitidine in infusion fluids.

The stability of azacitidine in four infusion fluids was studied. Azacitidine was reconstituted and diluted to final concentrations of 0.2 mg/ml and 2.0 mg/ml in glass bottles and plastic i.v. bags containing 0.9% sodium chloride injection, 5% dextrose injection, lactated Ringer's injection, or Normosol -R. All admixtures containing azacitidine 2.0 mg/ml and both drug concentrations in Normosol -R were prepared in glass bottles only. The pH of each solution was measured before mixing, immediately after mixing, and after six hours. Duplicate samples of each solution were removed for assay by high-performance liquid chromatography at zero time, then at hourly intervals for six hours, and again at 25 hours. Three experimental runs were performed for each combination of drug concentration, infusion fluid, and type of container. The percentage of initial (zero time) concentration remaining was determined and plotted versus time. This plot was used to calculate the t90 (time at which 90% of the initial concentration remained) for each solution. The t90 values did not exceed three hours for any of the solutions studied. At the 0.2 mg/ml concentration, the t90 value in 5% dextrose injection (0.8 hours) was much smaller than that of the other solutions, which had t90 values of about two hours. In plastic bags, the percentage of initial azacitidine concentration remaining after six hours was less in 5% dextrose injection than in any other solution. The t90 values for all solutions containing azacitidine 2.0 mg/ml were similar, ranging from 2.4 to 3.0 hours.(ABSTRACT TRUNCATED AT 250 WORDS)

High-performance liquid chromatographic analysis of chemical stability of 5-aza-2'-deoxycytidine.

The chemical stability of 5-aza-2'-deoxycytidine (I) in acidic, neutral, and alkaline solutions was analyzed by high-performance liquid chromatography. In alkaline solution, I underwent rapid reversible decomposition to N-(formylamidino)-N'-beta-D-2-deoxyribofuranosylurea (II), which decomposed irreversibly to form 1-beta-D-2'-deoxyribofuranosyl-3-guanylurea (III). The pseudo-first-order rate constants for this reaction were determined. The decomposition of I in alkaline solution was identical to that reported previously for the related analog, 5-aza-cytidine. However, in neutral solution (or water), there was a marked difference in the decomposition of I and 5-azacytidine. The same decomposition products were formed from 5-azacytidine in neutral solution as in alkaline solution. However, in neutral solution, I decomposed to II and three unknown compounds that were chromophoric at 254 nm. Compound I was most stable when stored in neutral solution at low temperature.

5-Azacytidine hydrolysis kinetics measured by high-pressure liquid chromatography and 13C-NMR spectroscopy.

Hydrolysis of 5-azacytidine, an experimental anticancer drug, in aqueous buffers was measured using a high-pressure liquid chromatographic (HPLC) procedure and a 13C-NMR method. The former utilized a 17.5-micron Aminex A-6 strong cation-exchanger column eluted with 0.4 M, pH 4.6 ammonium formate buffer at a flow rate of 0.4 ml/min. The hydrolysis sequence as well as the existence of a labile intermediate, N-formylguanylribosylurea, was unequivocally established using 6-13C-5-azacytidine and NMR spectral techniques. A reversible ring opening step to the N-formylguanylribosylurea with an equilibrium constant of 0.58 +/- 0.03 between pH 5.6 and 8.5, followed by an irreversible formation of guanylribosylurea, was found by HPLC. The data confirm previous assumptions on the hydrolytic kinetics. The pH dependency of hydrolysis was examined, and the hydrolysis profile gave a normal V shape with the most stable pH at 7.0. Rather stable intravenous dosage forms can be formulated.

Stabilization of 5-azacytidine by nucleophilic addition of bisulfite ion.

5-Azacytidine (I) stability was increased approximately 10-fold over its stability in water or lactated Ringer injection by the addition of excess sodium bisulfite and the maintenance of pH approximately 2.5. The increased stability in the presence of bisulfite at pH 2.5 was attributed to the addition of bisulfite across the 5-6 protonated imine bond of I, which prevented the hydrolytic attack on this labile double bond. However, above pH 4, bisulfite increased I degradation. At higher pH, the compound was no longer protonated and bisulfite did not form the stable addition product. The addition compound quickly decomposed above pH 6 to give back the parent compound and, thus, acted as a I prodrug. The intact drug remaining was assayed by high-pressure liquid chromatography (HPLC), and the reversibility of the bisulfite-I addition product above pH 6 was demonstrated by UV spectrophotometry and HPLC. The potential utility of the bisulfite-I addition product as a I prodrug in parenteral and possible oral dosage forms is discussed.

Kinetics and mechanisms of degradation of the antileukemic agent 5-azacytidine in aqueous solutions.

The hydrolytic degradation of 5-azacytidine was studied spectrophotometrically as a function of pH, temperature, and buffer concentration. Loss of drug followed apparent first-order kinetics in the pH region below 3. At pH less than 1,5-azacytosine and 5-azauracil were detected; at higher pH values, drug was lost to products which were essentially nonchromophoric if examined in acidic solutions. The apparent first-order rate constants associated with formation of 5-azacytosine and 5-azauracil from 5-azacytidine are reported. Above pH 2.6, first-order plots for drug degradation are biphasic. Apparent first-order rate constants and coefficients for the biexponential equation are given as a function of pH and buffer concentration. A reaction mechanism consistent with the data is discussed together with problems associated with defining the stability of the drug in aqueous solutions. At 50 degrees, the drug exhibited maximum stability at pH 6.5 in dilute phosphate buffer. Similar solutions were stored at 30 degrees to estimate their useful shelflife. Within 80 min, 6 times 10(-4) M solutions of 5-azacytidine decreased to 90% of original potency based on assumptions related to the proposed mechanisms.