Rule-based modelling and simulation of biochemical systems with molecular finite automata

The authors propose a theoretical formalism, molecular finite automata (MFA), to describe individual proteins as rule-based computing machines. The MFA formalism provides a framework for modelling individual protein behaviours and systems-level dynamics via construction of programmable and executable machines. Models specified within this formalism explicitly represent the context-sensitive dynamics of individual proteins driven by external inputs and represent protein-protein interactions as synchronised machine reconfigurations. Both deterministic and stochastic simulations can be applied to quantitatively compute the dynamics of MFA models. They apply the MFA formalism to model and simulate a simple example of a signal-transduction system that involves an MAP kinase cascade and a scaffold protein.

Low agreement between the T-SPOT®.TB assay and the tuberculin skin test among college students in China

T-SPOT®.TB and the tuberculin skin test (TST) were used to screen for latent tuberculosis infection among 899 Chinese college students. The positivity rates for T-SPOT®.TB and TST were respectively 13.0% (95% confidence interval [CI] 10.4-15.9) and 24.9% (95%CI 21.5-28.6) among students with a bacille Calmette-Guérin (BCG) scar (agreement of both tests 72.3%; 95%CI 68.6-75.8; κ = 0.118), and respectively 17.3% (95%CI 11.7-24.2) and 23.7% (95%CI 17.3-31.2) among those without a BCG scar (agreement 73.1%; 95%CI 65.4-79.9; κ = 0.179). These results demonstrate low agreement between the TST and T-SPOT.TB in the Chinese population studied.

Abstract P2-09-32: Estrogen Receptor-Related Genes Are Important Predictors of Response to Neo-Adjuvant Chemotherapy in Breast Cancer

Background: Clinical data suggest a contribution of estrogen receptor (ER) to chemotherapy response. However, ER status alone is not perfectly predictive, and there is an urgent need for more reliable markers of chemotherapy responsiveness. In this study, we set out to find novel ER-related genes in predicting chemotherapy response by microarrays, hoping to provide more robust multi-variable prediction to chemotherapy. Material and Methods: One hundred and ten patients with stage II-III breast cancer were included, receiving preoperative four cycles of weekly PCb (paclitaxel plus carboplatin) regimen. Pretreatment gene expression profiling was performed with gene microarrays on core biopsy specimens. 55 training cases were used for marker discovery and to identify any ER-related genes that might be associated with response (“training cases”), and the other 55 patients were available as an independent validation set (“validation cases”) to test whether the ER-related genes do predict pCR in protein levels by immunohistochemistry (IHC). Results: In the training cases, the yield of total RNA was insufficient to assay in 16 patients and 8 chips failed in the quality check (QC) process. Therefore, gene expression profile from 31 samples were available for this study. The overall pCR rate in the 86 patients was 19.7% (n=17, 6 cases of pCR in training set and 11 pCR in validation set). In the training set, by Significance Analysis of Microarrays (SAM), 300 probes (231 genes) were identified as differentially expressed between pCR versus non-pCR when fold change > 2. There were 20 differentially expressed genes, setting fold change > 3. Among these 20 genes, TFF1, ESR1, GATA3, TFF3 were found as ER-related. In 55 independent validation cases, univariate analysis indicated that clinical variables and ER-related genes, including ER, PR, GATA3, TFF1 and TFF3 were all significantly associated with pCR (Pearson x2, P<0.001, P=0.013, P<0.001, P<0.001, P<0.001). Multivariate logistic regression model showed that ER (P=0.016) remained significantly associated with complete remission. In spearman analysis, these 5 ER-related genes were significantly correlated with each other (P<0.05). It was found that pCR rate was as high as 80% (4/5) when these 5 factors were all negative. In contrast, these 5 factors were all positive in 7 of 9 PD/SD patients.

Discussion: ER combined with ER-related genes expression status may provide important predictive value of response to neoadjuvant chemotherapy and allows to identify a subgroup of patients who might highly benefit from chemotherapy and who might be resistant to it.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P2-09-32.

Two-fold elevation of expression of FoxM1 transcription factor in mouse embryonic fibroblasts enhances cell cycle checkpoint activity by stimulating p21 and Chk1 transcription

OBJECTIVES

Forkhead Box M1 (FoxM1) transcription factor regulates expression of cell cycle effective genes and is stabilized by checkpoint kinase 2 (Chk2) to stimulate expression of DNA repair enzymes in response to DNA damage. This study intended to test whether FoxM1 is involved in cell cycle checkpoint pathways.

MATERIALS AND METHODS

Analysis of senescence and cell proliferation in FoxM1 transgenic (TG) mouse embryonic fibroblasts (MEFs) with 2-fold elevation of FoxM1, and overexpression or knockdown of FoxM1 in an inducible FoxM1 expression cell line, or FoxM1 siRNA. Chromatin immunoprecipitation (ChIP), electrophoretic mobility shift assays (EMSA), and cotransfection to determine FoxM1 transcription targets, as well as RNase protection assays and western blot analysis, were performed.

RESULTS

Two-fold elevation of FoxM1 in FoxM1-TG-MEFs resulted in low levels of cell proliferation and increase in permanent cell cycle arrest at early passages (from passage 6 to 9). These phenotypes correlated with increased phosphorylation of p53 on Ser15, elevated expression of cell cycle inhibitor p21 and Chk1 at passage 3. FoxM1 was stabilized in response to DNA damage in MEFs and FoxM1 overexpression induced p21. Knockdown of FoxM1 resulted in decrease in Chk1. ChIP, EMSA and cotransfection assays confirmed that FoxM1 stimulated promoters of p21 and Chk1.

CONCLUSIONS

Chk1 and p21 are direct transcription targets of FoxM1 and FoxM1 participates in transcriptional responses to stress in normal cells.

The pharmacokinetics of nitazoxanide active metabolite (tizoxanide) in goats and its protein binding ability in vitro

The pharmacokinetics of tizoxanide (T), the active metabolite of nitazoxanide (NTZ), and its protein binding ability in goat plasma and in the solutions of albumin and alpha-1-acid-glycoprotein were investigated. The plasma and protein binding samples were analyzed using a high-performance liquid chromatography (HPLC) assay with UV detection at 360 nm. The plasma concentration of T was detectable in goats up to 24 h. Plasma concentrations vs. time data of T after 200 mg/kg oral administration of NTZ in goats were adequately described by one-compartment open model with first order absorption. As to free T, the values of t(1/2Ka), t(1/2Ke), T(max), C(max), AUC, V/F((c)), and Cl((s)) were 2.51 +/- 0.41 h, 3.47 +/- 0.32 h, 4.90 +/- 0.13 h, 2.56 +/- 0.25 microg/mL, 27.40 +/- 1.54 (microg/mL) x h, 30.17 +/- 2.17 L/kg, and 7.34 +/- 1.21 L/(kg x h), respectively. After beta-glucuronidase hydrolysis to obtain total T, t(1/2ke), C(max), T(max), AUC increased, while the V/F((c)) and Cl((s)) decreased. Study of the protein binding ability showed that T with 4 microg/mL concentration in goat plasma and in the albumin solution achieved a protein binding percentage of more than 95%, while in the solution of alpha-1-acid-glycoprotein, the percentage was only about 49%. This result suggested that T might have much more potent binding ability with albumin than with alpha-1-acid-glycoprotein, resulting from its acidic property.

Population pharmacokinetic modeling of pantoprazole in pediatric patients from birth to 16 years

The population pharmacokinetics of pantoprazole was characterized in pediatric patients from birth to 16 years using NONMEM and evaluated via bootstrap and predictive check. Data were described using a 2-compartment model with a typical parameterized in terms of clearance (CL) (95% CI) of 1.93 L per hour (1.53, 2.61), given the reference covariates (female, full term, extensive/unknown CYP2C19 metabolizer status, non-African American, 10 kg weight, intravenous or tablet administration). Pantoprazole pharmacokinetic parameters appear to be similar in pediatric patients compared to adults when allometrically scaled. The effect of age on allometrically scaled CL was best described by a sigmoid Emax model with the age effect reaching an asymptote approximately equal to the adult CL by 1 year. CYP2C19 poor metabolizers exhibited reduced CL with the point estimate and 95% CI more than 70% lower than the typical value. Simulations from the final model indicated that the 1.2-mg/kg dose provides the best comparison to adults.

1,5-Anhydroglucitol attenuates cytokine release and protects mice with type 2 diabetes from inflammatory reactions

1,5-anhydroglucitol (1,5-AG) decreases in diabetic patients and is used as a marker of glycemic control. Type 2 diabetic patients are susceptibile to lipopolysaccharides (LPS), which stimulate macrophages to release large quantities of tumor necrosis factor (TNF)-alpha and interleukin (IL)-6. This study examines the effects of 1,5-AG on lung inflammation induced by LPS and consequent systemic inflammation to determine whether the decrease of 1,5-AG concentration induces susceptibility to LPS. Before the challenge with LPS (1 mg/kg in vivo and 500 ng/ml in vitro), we pretreated db/db mice and RAW264.7 cells with 1,5-AG at 38.5 mg/kg and 500 microg/ml, respectively. The levels of IL-6, TNF-alpha, macrophage chemoattractant protein (MCP)-1 and IL-1beta in the serum and in the cell supernatants were measured. We also measured macrophage recruitment and the expression of inducible nitric oxide synthase (iNOS) in pulmonary tissues. We found that 1,5-AG attenuated serum cytokine release and protected db/db mice from LPS-induced pulmonary inflammation. In addition, 1,5-AG suppressed cytokine release and iNOS expression by suppressing Akt/NF-kB activity in RAW264.7 cells. These results suggest that 1,5-AG may be a mediator in, as well as marker for diabetes, and 1,5-AG intake may confer tolerance to LPS in patients with type 2 diabetes.

Integrated HPLC-MS and (1)H-NMR spectroscopic studies on acyl migration reaction kinetics of model drug ester glucuronides

Acyl glucuronides (AGs) are common, chemically reactive metabolites of acidic xenobiotics. Concerns about the potential of this class of conjugate to cause toxicity in man require efficient methods for the determination of reactivity, and this is commonly done by measuring transacylation kinetics. High-performance liquid chromatography-mass spectrometry (HPLC-MS) and nuclear magnetic resonance (NMR) spectroscopy were applied to the kinetic analysis of AG isomerization and hydrolysis for the 1-beta-O-AGs of ibufenac, (R)- and (S)-ibuprofen, and an alpha,alpha-dimethylated ibuprofen analogue. Each AG was incubated in either aqueous buffer at pH 7.4 or human plasma at 37 degrees C. Aliquots of these samples, taken throughout the reaction time course, were analysed by HPLC-MS and (1)H-NMR spectroscopy and the results compared. For identification of the AGs incubated in pH 7.4 buffer and for analysis of kinetic rates, (1)H-NMR spectroscopy generally gave the most complete set of data, but for human plasma the use of (1)H-NMR spectroscopy was impractical and HPLC-MS was more suitable. HPLC-MS was more sensitive than (1)H-NMR spectroscopy, but the lack of suitable stable-isotope labelled internal standards, together with differences in response between glucuronides and aglycones, made quantification problematic. Using HPLC-MS a specific 1-beta-O-AG-related ion at m/z 193 (the glucuronate fragment) was noted enabling selective determination of these isomers. In buffer, transacylation reactions predominated, with relatively little hydrolysis to the free aglycone observed. In human plasma incubations the observed rates of reaction were much faster than for buffer, and hydrolysis to the free aglycone was the major route. These results illustrate the strengths and weaknesses of each analytical approach for this class of analyte.

Safety and tolerability of rivastigmine transdermal patch compared with rivastigmine capsules in patients switched from donepezil: data from three clinical trials

OBJECTIVES

To compare the safety and tolerability of switching patients with mild-to-moderate Alzheimer's disease from donepezil to either rivastigmine capsule or transdermal patch.

METHODS

Three studies investigated the switch from donepezil to rivastigmine; study US13 was a 26-week, single-arm, immediate-switch study; US18 was a 26-week, sequential cohort study (both studies evaluated rivastigmine capsules 3-12 mg/day); study US38 was a 25-week, randomised, parallel-group, open-label study which investigated switch (immediate or after 7 days' withdrawal) from donepezil to rivastigmine transdermal patch (4.6 mg/24 hr). Safety outcomes included adverse events (AEs), discontinuations caused by AEs and serious AEs (SAEs).

RESULTS

Patient groups receiving rivastigmine patch (n = 261) or capsules (n = 331) had mean +/- SD ages of 77.3 +/- 8.0 and 78.1 +/- 7.8 years, dementia durations of 3.9 +/- 2.6 and 3.6 +/- 2.2 years and Mini-Mental State Examination scores of 18.3 +/- 4.00 and 17.9 +/- 4.4 respectively. Overall, 184 (70.5%) and 276 (83.4%) patients experienced at least one AE, and 23 (8.8%) and 55 (16.6%) patients experienced an SAE with the rivastigmine patch and capsules respectively. Of the patients who experienced an AE, 10 (3.8%) and 109 (32.9%) experienced nausea, and 11 (4.2%) and 80 (24.1%) experienced vomiting with the rivastigmine patch and capsules respectively. Discontinuations because of AEs occurred in 64 (19.3%) patients receiving capsules and 38 (14.6%) patients in the transdermal patch group. The most common reasons for discontinuation with the transdermal patch were application site reaction and disease progression, and nausea and vomiting with the capsules.

CONCLUSIONS

The rivastigmine transdermal patch appears to have better tolerability than rivastigmine capsules, with fewer gastrointestinal AEs and discontinuations because of these AEs. Simple daily rotation of patch location will likely reduce the frequency of skin reactions. This post hoc analysis was carried out by Novartis Pharmaceuticals Corporation. Data for the analysis were collected from the US13 study (CENA713B US13), the US18 study (CENA713B US18) and the US38 study (CENA713D US38).