Metabolomics coupled with proteomics advancing drug discovery toward more agile development of targeted combination therapies

To enhance the therapeutic efficacy and reduce the adverse effects of traditional Chinese medicine, practitioners often prescribe combinations of plant species and/or minerals, called formulae. Unfortunately, the working mechanisms of most of these compounds are difficult to determine and thus remain unknown. In an attempt to address the benefits of formulae based on current biomedical approaches, we analyzed the components of Yinchenhao Tang, a classical formula that has been shown to be clinically effective for treating hepatic injury syndrome. The three principal components of Yinchenhao Tang are Artemisia annua L., Gardenia jasminoids Ellis, and Rheum Palmatum L., whose major active ingredients are 6,7-dimethylesculetin (D), geniposide (G), and rhein (R), respectively. To determine the mechanisms underlying the efficacy of this formula, we conducted a systematic analysis of the therapeutic effects of the DGR compound using immunohistochemistry, biochemistry, metabolomics, and proteomics. Here, we report that the DGR combination exerts a more robust therapeutic effect than any one or two of the three individual compounds by hitting multiple targets in a rat model of hepatic injury. Thus, DGR synergistically causes intensified dynamic changes in metabolic biomarkers, regulates molecular networks through target proteins, has a synergistic/additive effect, and activates both intrinsic and extrinsic pathways.

Metabolomic analysis of key regulatory metabolites in hepatitis C virus-infected tree shrews

Metabolomics is a powerful new technology that allows the assessment of global low-molecular-weight metabolites in a biological system and which shows great potential in biomarker discovery. Analysis of the key metabolites in body fluids has become an important part of improving the diagnosis, prognosis, and therapy of diseases. Hepatitis C virus (HCV) is a major leading cause of liver disease worldwide and a serious burden on public health. However, the lack of a small-animal model has hampered the analysis of HCV pathogenesis. We hypothesize that an animal model (Tupaia belangeri chinensis) of HCV would produce a unique characterization of metabolic phenotypes. Ultra-performance liquid-chromatography/electrospray ionization-SYNAPT-high-definition mass spectrometry (UPLC/ESI-SYNAPT-HDMS) coupled with pattern recognition methods and system analysis was carried out to obtain comprehensive metabolomics profiling and pathways of large biological data sets. Taurine, hypotaurine, ether lipid, glycerophospholipid, arachidonic acid, tryptophan, and primary bile acid metabolism pathways were acutely perturbed, and 38 differential metabolites were identified. More important, five metabolite markers were selected via the "significance analysis for microarrays" method as the most discriminant and interesting biomarkers that were effective for the diagnosis of HCV. Network construction has led to the integration of metabolites associated with the multiple perturbation pathways. Integrated network analysis of the key metabolites yields highly related signaling pathways associated with the differentially expressed proteins, which suggests that the creation of new treatment paradigms targeting and activating these networks in their entirety, rather than single proteins, might be necessary for controlling and treating HCV efficiently.

Quantitative determination of lattice fluoride effects on the solubility and crystallinity of carbonated apatites with incorporated fluoride

The purpose of this study was to evaluate quantitatively the effects of fluoride on the solubility and crystallinity of carbonated apatites (CAPs) after its incorporation into the crystal lattice using the metastable equilibrium solubility (MES) distribution method. Fluoride-incorporated CAPs (F-CAPs) of two different carbonate levels (3 and 5%) and fluoride contents from 0 to 20,000 µg/g were synthesized. X-ray diffraction experiments and Rietveld analysis were conducted to obtain crystallite microstrain and unit cell parameters. Acetate buffer MES solution media were prepared at two solution fluoride concentrations (0.2 and 2.0 mg/l) and at two pHs (5.0 and 5.7). The unit cell a-axis values of the F-CAPs were found to decrease as the fluoride content increased, consistent with the fluoride being incorporated into the crystal lattice. The fluoride concentrations in the MES solution media were high enough to provide a 'swamping' effect such that the fluoride released from the F-CAPs during dissolution was minimal in changing the solution fluoride concentration. Employing the MES distribution superposition method, it was shown that the surface complex possessing the fluorapatite (FAP) stoichiometry [Ca10(PO4)6F2] accounted for the MES distribution behavior of all experiments. In addition, the mean pIFAP [the value of -log(aCa(10)aPO4(6)aF(2)) calculated from the ionic activity product based on FAP stoichiometry of the MES dissolution media in which 50% of the F-CAPs had dissolved] correlated well with the crystallite microstrain parameters of the F-CAPs. The incorporated fluoride in the F-CAPs showed only modest effects on F-CAP crystallinity and solubility.

Pharmacokinetics of hesperetin and naringenin in the Zhi Zhu Wan, a traditional Chinese medicinal formulae, and its pharmacodynamics study

Zhi Zhu Wan (ZZW), a classical Chinese medical formulae consisted of Atractylodes Rhizome and Fructus Citrus Immaturus, has been commonly used for treatment of gastrointestinal diseases. Hesperetin and naringenin are the main components of ZZW, and both can alleviate intestinal tract disorders. In this work, plasma pharmacokinetics and pharmacodynamics characteristics of ZZW after oral administration were investigated using a rapid and sensitive ultra performance liquid chromatography-tandem mass spectrometry method with an electrospray ionization source in positive ion mode. Biosamples were prepared using methanolic precipitation, and the separation of hesperetin and naringenin was achieved on a Waters ACQUITY HSS BEH (2.1 mm × 5 mm, 1.7 µm) column by linear gradient elution, and the total run time was only 3 min. Data were analyzed and estimated using WinNonlin Professional version 5.1. With pharmacokinetic analysis, the estimated pharmacokinetic parameters (i.e. C(max), area under the concentration-time curve (AUC) and t(1/2)), were C(max)  = 776.06 ng/mL, AUC = 9473 ng/mL·h, t1/2 = 5.26 h for hesperetin and C(max)  = 2910.6 ng/mL, AUC = 40607.9 ng/mL·h, t1/2 = 4.69 h for naringenin, respectively. In the present study, we have also valuated and clarified the effect of ZZW on small intestinal movement. It was found that ZZW can accelerate intestinal motility in mice and may hold a promising treatment for intestinal diseases.

[Identification technique for in vivo ingredients of traditional Chinese medicines based on LC-MS analysis]

Serum pharmacochemistry of traditional Chinese medicine (TCM) is a direct and effective method for determining efficacious substance foundation of TCM. However, the complexity of chemical constituents of TCM and the interaction among ingredients in the in vitro process make the analysis on in vitro ingredients of TCM arduous. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) has become the cornerstone in detection and characterization of in vivo ingredients of TCM because of its sensitivity and ability to analyze complex mixtures. However, due to significant interference from endogenous species, detection and identification of the constituents of TCM in the biological matrices are often difficult. There is a crying need for introducing specialized ingredient identification techniques to avoid artificial omission of in vivo ingredients of TCM. On the basis of the analysis on transitional ingredients in rat blood, this essay introduces the application of such pattern recognition methods as mass defect filter, Metabolynx software and principal component analysis, partial least squared discriminant analysis and orthogonal partial least squared discriminant analysis in identifying in vivo ingredients of TCM.

[Analysis on isofraxidin contained in Acanthopanax senticosus extracts and its metabolites by UPLC-Q-TOF-MS and automatic data processing technique]

OBJECTIVE

To analyze isofraxidin and its metabolites in rat plasma, bile, urine and feces after the oral administration of A. senticosus extracts.

METHOD

After the oral administration of 325 mg x kg(-1) of A. senticosus extracts, rat blood samples were collected at 1, 1.5, 2, 4, 6 h and bile samples were collected during 0-12 h. The above samples were prepared by SPE. Their urine and feces samples were collected during 0-12 h and 12-24 h. These samples were analyzed by UPLC-Q-TOF-MS and processed using Metabolynx XS.

RESULT

M0 was detected in rat plasma, bile, urine and feces, isofraxidin glucuronide (M1) was detected in rat plasma and bile, which was first reported as the metabolite of isofraxidin.

CONCLUSION

Isofraxidin can be metabolized in the form of glucuronidation in vivo and evacuated in the form of isofraxidin.

SU-E-J-69: Development of an Ambiguity-Free Optical Tracking System for SBRT

PURPOSE

Commercial optical tracking system such as BrainLab ExacTrac© suffers from ambiguous markers which can cause significant delay in patient treatment. We developed an ambiguity-free optical tracking system for high precision SBRT.

METHODS

The optical tracking system consists of a pair of camera sensors, 4∼8 infra-red (IR) reflective markers affixed on patient skin and in-house developed software. We developed an effective algorithm to automatically eliminate ambiguous markers. A recursive backtracking algorithm was developed to build one-to-one correspondence between reference markers and optical markers. The algorithm was able to deal with missing, misplaced, or occluded markers by introducing 'dummy' markers. Isocenter displacements were calculated in six-degree of freedom through rigid-body registration between reference markers and optical markers. The system accuracy was evaluated with a pelvis phantom against cone beam CT (CBCT) and ExacTrac. The impact of number of markers on tracking accuracy was also evaluated. The performance of automatic ambiguity elimination was assessed with synthetic and clinic marker patterns.

RESULTS

Difference of isocenter displacement reported by our system and commercial systems (CBCT, ExacTrac) were within 0.5 mm/0.1o. Impact of number of markers on tracking accuracy in our phantom test was negligible with isocenter displacement varying within 0.2 mm/0.2o when number of markers varied from 4 to 8. The system successfully identified and eliminated ambiguous markers in both synthetic and clinic marker patterns.

CONCLUSIONS

An accurate optical tracking system free of ambiguous markers was developed for patient positioning and monitoring in high precision SBRT. The developed algorithms to eliminate ambiguous markers and to handle missing, misplaced or occluded markers were effective and efficient.

SU-D-BRCD-02: A Novel Cylindrical 3D Water Scanner for Beam Data Collection: I. Validation of the Automatic-Setup

PURPOSE

To determine the accuracy and reproducibility of the automatic- setup procedure of a 3D water scanner (3D SCANNER, Sun Nuclear Corp). The procedure automatically aligns the scanner's coordinate system to the Linac coordinate system. A unique off-center detector holder extends the scan range to 630 mm, eliminating the need for scanner shifts for large-field scans.

METHODS

The automatic-setup procedure provides means to automatically (1) level the tank; (2) zero the detector position to water surface; (3) align the scanner's coordinate system to the Linac system; and (4) correct motor hysteresis. After automatic-setup, (1) and (2) were evaluated visually by three physicists. Step (3) was tested by moving one of the jaws to the isocenter and scans were made along the jaw edge. Angular misalignment between the scanner and the Linac would Result in a noticeably tilted profile. Step (4) was tested by scanning with the chamber moving forward and then backward five times. The accuracy of the off-center detector holder was tested by comparing scans made using the regularand the off-center detector holders. All tests were repeated three times.

RESULTS

All tests of the water surface and horizontal chamber movementwere acceptable from the nine independent evaluations. Scans along the jawedge resulted in < 1% in profile tilt, corresponding to < 0.05 degree in angular misalignment. Same direction scans resulted in field edge differences < 0.05 mm, and < 0.2 mm when compared to scans in thereverse direction. There was no difference in accuracy when different scan speeds were used. Profiles obtained using the regular and the off-centerdetector holders were identical.

CONCLUSIONS

The automatic-setupprocedure resulted in accurate alignment of the 3D SCANNER to the Linac. These results were user-independent. It also provides the ability to scan large fields without the need to change tank setup. This work was partially supported by a research grant from Sun Nuclear Corp., Melbourne, FL.

NUR77 inhibits the expression of TIMP2 and increases the migration and invasion of HTR-8/SVneo cells induced by CYR61

OBJECTIVE

To investigate the function and mechanism of CYR61 on the migration and invasion of the trophoblast cell line, HTR-8/SVneo cells.

STUDY DESIGN

The mRNA and protein levels of NUR77 in the placentas of normal and preeclampsia (PE) women were evaluated using real-time PCR and Western blot, respectively. Paraffin-embedded tissues were processed for localization of NUR77 protein in placental villus by immunohistochemistry. HTR-8/SVneo cells were cultured in the presence of CYR61, Ad-NUR77 or a small interfering RNA for NUR77 (Ad-sinur77). The expression of NUR77 in the HTR-8/SVneo cells was detected and the effects of CYR61 on the migration and invasion of HTR-8/SVneo cells were assessed in wound-healing and transwell experiments, respectively. Gelatin zymography was used to measure the MMP2 release in HTR-8/SVneo cells.

RESULTS

NUR77 is significantly decreased in the placenta of women with PE compared with the levels during a normal pregnancy. CYR61 can significantly increase the expression of NUR77 in HTR-8/SVneo cells. CYR61, as well as NUR77, can promote HTR-8/SVneo cells migration and invasion, which can be blocked by Ad-sinur77. Both CYR61 and Ad-nur77 reduced the mRNA expression of TIMP2 in HTR-8/SVneo cells.

CONCLUSIONS

CYR61 may promote HTR-8/SVneo cells migration and invasion through the upregulation of NUR77, leading to the increase of MMP2 release and the downregulation of TIMP2 expression.

A prototype of an anchoring and extending intestinal micro-robot and an in vitro experiment

In order to minimize the invasiveness of intestinal disease diagnosis and surgery, we propose an anchoring and extending micro-robot. The gait of the micro-robot was designed according to the biomechanical features of the intestinal tract. The locomotion condition showed that the anchoring capability and extending ability should be balanced to enhance locomotion efficiency. The mechanical and control system was designed and fabricated under the requirements of the locomotive model. The assembled micro-robot was 90 mm in length and 13 mm in diameter. The micro-robot prototype was tested in in vitro experiments; its locomotion efficiency was approximately 100% in an ideal environment, but around 50% in a pig's small bowel (20 mm in diameter). The in vitro experiment results demonstrated that the gait is feasible for locomotion in the small bowel although the diameter of the small bowel is a limiting factor.