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1.  Bright and fast multi-colored voltage reporters via electrochromic FRET 
Nature communications  2014;5:4625.
Genetically encoded fluorescent reporters of membrane potential promise to reveal aspects of neural function not detectable by other means. We present a palette of multi-colored brightly fluorescent genetically encoded voltage indicators with sensitivities from 8 – 13% ΔF/F per 100 mV, and half-maximal response times from 4 – 7 ms. A fluorescent protein is fused to an Archaerhodopsin-derived voltage sensor. Voltage-induced shifts in the absorption spectrum of the rhodopsin lead to voltage-dependent nonradiative quenching of the appended fluorescent protein. Through a library screen, we identify linkers and fluorescent protein combinations which report neuronal action potentials in cultured rat hippocampal neurons with a single-trial signal-to-noise ratio from 7 to 9 in a 1 kHz imaging bandwidth at modest illumination intensity. The freedom to choose a voltage indicator from an array of colors facilitates multicolor voltage imaging, as well as combination with other optical reporters and optogenetic actuators.
doi:10.1038/ncomms5625
PMCID: PMC4134104  PMID: 25118186
2.  All-optical electrophysiology in mammalian neurons using engineered microbial rhodopsins 
Nature methods  2014;11(8):825-833.
All-optical electrophysiology—spatially resolved simultaneous optical perturbation and measurement of membrane voltage—would open new vistas in neuroscience research. We evolved two archaerhodopsin-based voltage indicators, QuasAr1 and 2, which show improved brightness and voltage sensitivity, microsecond response times, and produce no photocurrent. We engineered a novel channelrhodopsin actuator, CheRiff, which shows improved light sensitivity and kinetics, and spectral orthogonality to the QuasArs. A co-expression vector, Optopatch, enabled crosstalk-free genetically targeted all-optical electrophysiology. In cultured neurons, we combined Optopatch with patterned optical excitation to probe back-propagating action potentials in dendritic spines, synaptic transmission, sub-cellular microsecond-timescale details of action potential propagation, and simultaneous firing of many neurons in a network. Optopatch measurements revealed homeostatic tuning of intrinsic excitability in human stem cell-derived neurons. In brain slice, Optopatch induced and reported action potentials and subthreshold events, with high signal-to-noise ratios. The Optopatch platform enables high-throughput, spatially resolved electrophysiology without use of conventional electrodes.
doi:10.1038/nmeth.3000
PMCID: PMC4117813  PMID: 24952910
3.  Prediction of Nanoparticle Prodrug Metabolism by Pharmacokinetic Modeling of Biliary Excretion 
Pharmacokinetic modeling and simulation is a powerful tool for the prediction of drug concentrations in the absence of analytical techniques that allow for direct quantification. The present study applied this modeling approach to determine active drug release from a nanoparticle prodrug formulation. A comparative pharmacokinetic study of a nanoscale micellar docetaxel (DTX) prodrug, Procet 8, and commercial DTX formulation, Taxotere, was conducted in bile duct cannulated rats. The nanoscale (~40 nm) size of the Procet 8 formulation resulted in confinement within the plasma space and high prodrug plasma concentrations. Ex vivo prodrug hydrolysis during plasma sample preparation resulted in unacceptable error that precluded direct measurement of DTX concentrations. Pharmacokinetic modeling of Taxotere and Procet 8 plasma concentrations, and their associated biliary metabolites, allowed for prediction of the DTX concentration profile and DTX bioavailability, and thereby evaluation of Procet 8 metabolism.
Procet 8 plasma decay and in vitro plasma hydrolytic rates were identical, suggesting systemic clearance of the prodrug was primarily metabolic. The Procet 8 and Taxotere plasma profiles, and associated docetaxel hydroxy-tert-butyl carbamate (HDTX) metabolite biliary excretion, were best fit by a two compartment model, with both linear and non-linear DTX clearance, and first order Procet 8 hydrolysis. The model estimated HDTX clearance rate agreed with in vitro literature values, supporting the predictability of the proposed model. Model simulation at the 10 mg DTX equivalent/kg dose level predicted DTX formation rate-limited kinetics and a peak plasma DTX concentration of 39 ng/mL at 4h for Procet 8, in comparison to 2826 ng/mL for Taxotere. As a result of nonlinear DTX clearance, the DTX AUCinf for the Procet 8 formulation was predicted to be 2.6 times lower than Taxotere (775 vs. 2017 h x ng/mL, respectively), resulting in an absolute bioavailability estimate of 38%. As DTX clearance in man is considered linear, this low bioavailability is likely species-dependent. These data support the use of pharmacokinetic modeling and simulation in cases of complex formulations, where analytical methods for direct measurement of free (released) drug concentrations are unavailable. Uses of such models may include interpretation of preclinical toxicology studies, selection of first in man dosing regimens, and PK/PD model development.
doi:10.1016/j.jconrel.2013.04.025
PMCID: PMC3788091  PMID: 23664969
biliary clearance; pharmacokinetic modeling and simulation; nanomicellar prodrug
4.  Kinetics of Sulforaphane in Mice after Consumption of Sulforaphane-Enriched Broccoli Sprout Preparation 
Molecular nutrition & food research  2013;57(12):10.1002/mnfr.201300210.
Scope
Sulforaphane is a natural isothiocyanate in broccoli sprouts with cancer chemopreventive activity. This study is aimed to to use different methods to develop broccoli sprout preparations to compare their ability to deliver sulforaphane to the mice and to evaluate the kinetics and biodistribution of sulforaphane.
Methods and Results
The sulforaphane-enriched sprout preparation generated by two-step procedure (quick-steaming followed by myrosinase treatment) contained the highest level of sulforaphane, which was 11 and 5 times higher than the freeze-dried fresh broccoli sprouts and the quick-steamed, freeze-dried broccoli sprouts, respectively. After oral administration of 2.5 mg/g body weight of the broccoli sprout preparations, sulforaphane was quickly absorbed and distributed throughout the tissues. The sulforaphane-rich preparation resulted in the highest exposure, with peak plasma sulforaphane concentration of 337 ng/ml, which is 6.0 times and 2.6 times higher compared to the other two preparations. A whole body physiologically-based pharmacokinetic model (developed with ADAPT 5 software) suggests that distribution of sulforaphane is perfusion-limited in all organs.
Conclusion
This study provides a broccoli sprout preparation that can serve as a good source of sulforaphane, and the model can be utilized to guide the dose design for the use of broccoli sprout preparation in chemoprevention.
doi:10.1002/mnfr.201300210
PMCID: PMC3855579  PMID: 23929742
Broccoli Sprout; Cancer Chemoprevention; Kinetics; Mouse; Sulforaphane
5.  Noninvasive Fluorescence Resonance Energy Transfer Imaging of in vivo Premature Drug Release from Polymeric Nanoparticles 
Molecular pharmaceutics  2013;10(11):4185-4194.
Understanding in vivo drug release kinetics is critical for the development of nanoparticle-based delivery systems. In this study, we developed a fluorescence resonance energy transfer (FRET) imaging approach to noninvasively monitor in vitro and in vivo cargo release from polymeric nanoparticles. The FRET donor dye (DiO or DiD) and acceptor dye (DiI or DiR) were individually encapsulated into poly(ethylene oxide)-b-polystyrene (PEO-PS) nanoparticles. When DiO (donor) nanoparticles and DiI (acceptor) nanoparticles were co-incubated with cancer cells for 2 h, increased FRET signals were observed from cell membranes, suggesting rapid release of DiO and DiI to cell membranes. Similarly, increased FRET ratios were detected in nude mice after intravenous co-administration of DiD (donor) nanoparticles and DiR (acceptor) nanoparticles. In contrast, another group of nude mice i.v. administrated with DiD/DiR co-loaded nanoparticles showed decreased FRET ratios. Based on the difference in FRET ratios between the two groups, in vivo DiD/DiR release half-life from PEO-PS nanoparticles was determined to be 9.2 min. In addition, it was observed that the presence of cell membranes facilitated burst release of lipophilic cargos while incorporation of oleic acid-coated iron oxide into PEO-PS nanoparticles slowed the release of DiD/DiR to cell membranes. The developed in vitro and in vivo FRET imaging techniques can be used to screening stable nano-formulations for lipophilic drug delivery.
doi:10.1021/mp4002393
PMCID: PMC3946412  PMID: 24033270
burst release; fluorescence resonance energy transfer; imaging; polymeric nanoparticle
6.  Development of a Standardized and Safe Airborne Antibacterial Assay, and Its Evaluation on Antibacterial Biomimetic Model Surfaces 
PLoS ONE  2014;9(10):e111357.
Bacterial infection of biomaterials is a major concern in medicine, and different kinds of antimicrobial biomaterial have been developed to deal with this problem. To test the antimicrobial performance of these biomaterials, the airborne bacterial assay is used, which involves the formation of biohazardous bacterial aerosols. We here describe a new experimental set-up which allows safe handling of such pathogenic aerosols, and standardizes critical parameters of this otherwise intractable and strongly user-dependent assay. With this new method, reproducible, thorough antimicrobial data (number of colony forming units and live-dead-stain) was obtained. Poly(oxonorbornene)-based Synthetic Mimics of Antimicrobial Peptides (SMAMPs) were used as antimicrobial test samples. The assay was able to differentiate even between subtle sample differences, such as different sample thicknesses. With this new set-up, the airborne bacterial assay was thus established as a useful, reliable, and realistic experimental method to simulate the contamination of biomaterials with bacteria, for example in an intraoperative setting.
doi:10.1371/journal.pone.0111357
PMCID: PMC4216082  PMID: 25360525
7.  Highly Pathogenic Avian Influenza A(H5N1) Mutants Transmissible by Air Are Susceptible to Human and Animal Neutralizing Antibodies 
The Journal of Infectious Diseases  2013;208(8):1315-1319.
A laboratory-generated reassortant H5 hemagglutinin (HA)/influenza A(H1N1) strain containing 4 mutations in influenza A(H5N1) HA has become transmissible by air among mammals. Here, we constructed 15 influenza A(H5N1) pseudoviruses containing a single mutation or a combination of mutations and showed that the pseudoviruses were susceptible to neutralizing antibodies from patients with influenza A(H5N1) infection and from mice immunized with a vaccine containing the conserved HA1 sequence of influenza A(H5N1). These results indicate that antibodies in patients currently infected by influenza A(H5N1) and antibodies induced by vaccines containing conserved sequences in HA1 of wild-type influenza A(H5N1) are highly effective in cross-neutralizing future influenza A(H5N1) mutants with airborne transmissibility, suggesting that human influenza pandemics caused by these influenza A(H5N1) variants can be prevented.
doi:10.1093/infdis/jit323
PMCID: PMC3778968  PMID: 23868877
Patient serum specimens; Neutralizing antibodies; H5N1 influenza virus; Air-transmissibility
8.  Association Between the XRCC6 Promoter rs2267437 Polymorphism and Cancer Risk: Evidence Based on the Current Literature 
Background: Increasing evidence suggests that the DNA repair gene XRCC6 (Ku70) may be critically involved in the aetiology of the human carcinogenesis. Many studies have investigated the association between the rs2267437 polymorphism and cancer susceptibility. However, the results of these studies have been controversial. This meta-analysis was conducted to quantitatively summarize the evidence for a relationship between the rs2267437 polymorphism and cancer risk. Methods: Electronic databases, including PUBMED and EMBASE, were searched for publications that met the inclusion criteria. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to evaluate the strength of the association between the XRCC6 promoter rs2267437 polymorphism and cancer risk in a fixed-effects model (the Mantel-Haenszel method) or a random-effects model (the DerSimonian and Laird method), as appropriate. Results: A total of 13 case–control studies, involving 3675 cases and 4247 controls, investigating the XRCC6 rs2267437 polymorphism and cancer susceptibility were identified for the meta-analysis. The pooled analysis showed that there is a significant relationship between the XRCC6 rs2267437 polymorphism and cancer susceptibility (GG vs. CC: OR=1.28, 95% CI=1.03–1.60). Subgroup analyses based on the cancer type, ethnicity, and source of the controls were also performed, and these results indicated that the XRCC6 promoter rs2267437 polymorphism was associated with cancer risk in breast cancer studies (GG vs. CC: OR=1.79, 95% CI=1.25–2.56; GG vs. CG+CC: OR=1.40, 95% CI=1.01–1.95), in Asian populations (GG vs. CC: OR=1.33, 95% CI=1.01–1.74) and in population-based studies (GG vs. CC: OR=1.57, 95% CI=1.12–2.22; CG vs. CC: OR=1.35, 95% CI=1.11–1.64; GG+CG vs. CC: OR=1.37, 95% CI=1.14–1.65). Conclusion: This meta-analysis suggests that the XRCC6 rs2267437 polymorphism may affect breast cancer susceptibility and increase the risk of cancer in Asian populations and in the general population. It is critical that further large-scale and well-designed studies be conducted to confirm the association between the rs2267437 genotype and cancer risk.
doi:10.1089/gtmb.2013.0083
PMCID: PMC3732414  PMID: 23745766
9.  A Potent Small-Molecule Inhibitor of the MDM2-p53 Interaction (MI-888) Achieved Complete and Durable Tumor Regression in Mice 
Journal of medicinal chemistry  2013;56(13):10.1021/jm4005708.
We previously reported the discovery of a class of spirooxindoles as potent and selective small-molecule inhibitors of the MDM2-p53 interaction (MDM2 inhibitors). We report herein our efforts to improve their pharmacokinetic properties and in vivo antitumor activity. Our efforts led to the identification of 9 (MI-888) as a potent MDM2 inhibitor (Ki = 0.44 nM) with a superior pharmacokinetic profile and enhanced in vivo efficacy. Compound 9 is capable of achieving rapid, complete, and durable tumor regression in two types of xenograft models of human cancer with oral administration and represents the most potent and efficacious MDM2 inhibitor reported to date.
doi:10.1021/jm4005708
PMCID: PMC3880646  PMID: 23786219
10.  Polymeric Curcumin Nanoparticle Pharmacokinetics and Metabolism in Bile Duct Cannulated Rats 
Molecular pharmaceutics  2013;10(5):1977-1987.
The objective of this study was to compare the pharmacokinetics and metabolism of polymeric nanoparticle encapsulated (nanocurcumin), and solvent solubilized curcumin formulations in Sprague Dawley (SD) rats. Nanocurcumin is currently under development for cancer therapy. Since free, unencapsulated curcumin is rapidly metabolized and excreted in rats, upon i.v. administration of nanocurcumin only nanoparticle encapsulated curcumin can be detected in plasma samples. Hence, the second objective of this study was to utilize the metabolic instability of curcumin to assess in vivo drug release from nanocurcumin. Nanocurcumin and solvent solubilized curcumin were administered at 10 mg curcumin/kg by jugular vein to bile duct-cannulated male SD rats (n = 5). Nanocurcumin increased the plasma Cmax of curcumin 1749 fold relative to the solvent solubilized curcumin. Nanocurcumin also increased the relative abundance of curcumin and glucuronides in bile, but did not dramatically alter urine and tissue metabolite profiles. The observed increase in biliary and urinary excretion of both curcumin and metabolites for the nanocurcumin formulation suggested rapid, “burst” release of curcumin. Although the burst release observed in this study is a limitation for targeted tumor delivery, nanocurcumin still exhibits major advantages over solvent solubilized curcumin, as the nanoformulation does not result in the lung accumulation observed for the solvent solubilized curcumin and increases overall systemic curcumin exposure. Additionally, the remaining encapsulated curcumin fraction following burst release is available for tumor delivery via the enhanced permeation and retention effect commonly observed for nanoparticle formulations.
doi:10.1021/mp4000019
PMCID: PMC3683459  PMID: 23534919
curcumin; nanoformulation; metabolite profile; biliary excretion; urinary excretion
11.  Proteomic Mapping of Mitochondria in Living Cells via Spatially-Restricted Enzymatic Tagging 
Science (New York, N.Y.)  2013;339(6125):1328-1331.
Microscopy and mass spectrometry (MS) are complementary techniques: the former provides spatiotemporal information in living cells, but only for a handful of recombinant proteins, while the latter can detect thousands of endogenous proteins simultaneously, but only in lysed samples. Here we introduce technology that combines these strengths by offering spatially- and temporally-resolved proteomic maps of endogenous proteins within living cells. The method relies on a genetically-targetable peroxidase enzyme that biotinylates nearby proteins, which are subsequently purified and identified by MS. We used this approach to identify 495 proteins within the human mitochondrial matrix, including 31 not previously linked to mitochondria. The labeling was exceptionally specific and distinguished between inner membrane proteins facing the matrix versus the intermembrane space (IMS). Several proteins previously thought to reside in the IMS or outer membrane, including protoporphyrinogen oxidase, were reassigned to the matrix. The specificity of live-cell peroxidase-mediated proteomic mapping combined with its ease of use offers biologists a powerful tool for understanding the molecular composition of living cells.
doi:10.1126/science.1230593
PMCID: PMC3916822  PMID: 23371551
12.  Correction: HIV-1 Fusion Is Blocked through Binding of GB Virus C E2D Peptides to the HIV-1 gp41 Disulfide Loop 
PLoS ONE  2014;9(1):10.1371/annotation/b46459e1-73ff-4b75-8f24-264cbcf4a5a9.
doi:10.1371/annotation/b46459e1-73ff-4b75-8f24-264cbcf4a5a9
PMCID: PMC3891527
13.  Nature-Inspired Antimicrobial Polymers – Assessment of Their Potential for Biomedical Applications 
PLoS ONE  2013;8(9):e73812.
We explored the potential of poly(oxonorbornene)-based synthetic mimics of antimicrobial peptides (SMAMPs), a promising new class of antimicrobial polymers with cell-selectivity and low resistance development potential, for clinical applications. We evaluated their antimicrobial activity against a panel of seven clinical and regulatory relevant bacteria strains, and tested their toxicity with two different kinds of primary human cells. For the antimicrobial activity, we performed the minimum inhibitory concentration (MIC) assay and determined the minimum bactericidal concentration (MBC) according to the NCCLS guidelines. The results revealed specific problems that may occur when testing the antimicrobial activity of amphiphilic cationic polymers, and confirmed the working hypothesis that the more hydrophilic SMAMP polymers in our portfolio were ‘doubly selective’, i.e. they are not only selective for bacteria over mammalian cells, but also for Gram-positive over Gram-negative bacteria. The data also showed that we could improve the broad-band activity of one SMAMP, and in combination with the results from the cell toxicity experiments, identified this polymer as a promising candidate for further in-vitro and in-vivo testing. Transmission electron studies revealed that the cellular envelopes of both E. coli and S. aureus were severely damaged due to SMAMP action on the bacterial membrane, which strengthened the argument that SMAMPs closely resemble antimicrobial peptides. To test cell toxicity, we used the traditional hemolysis assay with human red blood cells, and the novel xCelligence assay with primary human fibroblasts. The data reported here is the first example in which a hemolysis assay is benchmarked against the xCelligence assay. It revealed that the same trends were obtained using these complementary methods. This establishes the xCelligence assay with primary human cells as a useful tool for SMAMP characterization.
doi:10.1371/journal.pone.0073812
PMCID: PMC3767731  PMID: 24040079
14.  IDH1/IDH2 Mutations Define the Prognosis and Molecular Profiles of Patients with Gliomas: A Meta-Analysis 
PLoS ONE  2013;8(7):e68782.
Background
Isocitrate dehydrogenase isoforms 1 and 2 (IDH1 and IDH2) mutations have received considerable attention since the discovery of their relation with human gliomas. The predictive value of IDH1 and IDH2 mutations in gliomas remains controversial. Here, we present the results of a meta-analysis of the associations between IDH mutations and both progression-free survival (PFS) and overall survival (OS) in gliomas. The interrelationship between the IDH mutations and MGMT promoter hypermethylation, EGFR amplification, codeletion of chromosomes 1p/19q and TP53 gene mutation were also revealed.
Methodology and Principal Findings
An electronic literature search of public databases (PubMed, Embase databases) was performed. In total, 10 articles, including 12 studies in English, with 2,190 total cases were included in the meta-analysis. The IDH mutations were frequent in WHO grade II and III glioma (59.5%) and secondary glioblastomas (63.4%) and were less frequent in primary glioblastomas (7.13%). Our study provides evidence that IDH mutations are tightly associated with MGMT promoter hypermethylation (P<0.001), 1p/19q codeletion (P<0.001) and TP53 gene mutation (P<0.001) but are mutually exclusive with EGFR amplification (P<0.001). This meta-analysis showed that the combined hazard ratio (HR) estimate for overall survival and progression-free survival in patients with IDH mutations was 0.33 (95% CI: 0.25–0.42) and 0.38 (95% CI: 0.21–0.68), compared with glioma patients whose tumours harboured the wild-type IDH. Subgroup analyses based on tumour grade also revealed that the presence of IDH mutations was associated with a better outcome.
Conclusion
Our study suggests that IDH mutations, which are closely linked to the genomic profile of gliomas, are potential prognostic biomarkers for gliomas.
doi:10.1371/journal.pone.0068782
PMCID: PMC3718803  PMID: 23894344
15.  Proteomic dissection of cell type-specific H2AX-interacting protein complex associated with hepatocellular carcinoma 
Journal of proteome research  2010;9(3):1402-1415.
The replacement histone variant H2AX senses DNA double-strand breaks (DSBs) and recruits characteristic sets of proteins at its phosphorylated (γ-H2AX) foci for concurrent DNA repair. We reasoned that the H2AX interaction network, or interactome formed in the tumor-associated DNA DSB environment such as in hepatocellular carcinoma (HCC) cells, where pre-neoplastic lesions frequently occur, is indicative of HCC pathogenic status. By using an in vivo dual-tagging quantitative proteomic method, we identified 102 H2AX-specific interacting partners in HCC cells that stably expressed FLAG-tagged H2AX at close to the endogenous level. Using bioinformatics tools for data-dependent network analysis, we further found binary relationships among these interactors in defined pathway modules, implicating H2AX in a multi-functional role of coordinating a variety of biological pathways involved in DNA damage recognition and DNA repair, apoptosis, nucleic acid metabolism, Ca2+-binding signaling, cell cycle, etc. Furthermore our observations suggest that these pathways interconnect through key pathway components or H2AX interactors. The physiological accuracy of our quantitative proteomic approach in determining H2AX-specific interactors was evaluated by both co-immunoprecipitation/ immunoblotting and confocal co-localization experiments performed on HCC cells. Due to their involvement in diverse functions, the H2AX interactors involved in different pathway modules, such as Poly(ADP-ribose) polymerase1, 14-3-3ζ, coflin1, and peflin1, were examined for their relative H2AX binding affinities in paired hepatocytes and HCC cells. Treatment with the DSB-inducing agent bleomycin enhanced binding of these proteins to H2AX, suggesting an active role of H2AX in coordinating the functional pathways of each protein in DNA damage recognition and repair.
doi:10.1021/pr900932y
PMCID: PMC3670604  PMID: 20000738
H2AX; DSBs; DNA repair; protein-protein interactions; in vivo dual-tagging quantitative proteomic method; hepatocellular carcinoma pathogenesis
16.  Genetic polymorphisms of DNA double-strand break repair pathway genes and glioma susceptibility 
BMC Cancer  2013;13:234.
Background
Genetic variations in DNA double-strand break repair genes can influence the ability of a cell to repair damaged DNA and alter an individual’s susceptibility to cancer. We studied whether polymorphisms in DNA double-strand break repair genes are associated with an increased risk of glioma development.
Methods
We genotyped 10 potentially functional single nucleotide polymorphisms (SNPs) in 7 DNA double-strand break repair pathway genes (XRCC3, BRCA2, RAG1, XRCC5, LIG4, XRCC4 and ATM) in a case–control study including 384 glioma patients and 384 cancer-free controls in a Chinese Han population. Genotypes were determined using the OpenArray platform.
Results
In the single-locus analysis there was a significant association between gliomas and the LIG4 rs1805388 (Ex2 +54C>T, Thr9Ile) TT genotype (adjusted OR, 3.27; 95% CI, 1.87-5.71), as well as the TC genotype (adjusted OR, 1.62; 95% CI, 1.20-2.18). We also found that the homozygous variant genotype (GG) of XRCC4 rs1805377 (IVS7-1A>G, splice-site) was associated with a significantly increased risk of gliomas (OR, 1.77; 95% CI, 1.12-2.80). Interestingly, we detected a significant additive and multiplicative interaction effect between the LIG4 rs1805388 and XRCC4 rs1805377 polymorphisms with an increasing risk of gliomas. When we stratified our analysis by smoking status, LIG4 rs1805388 was associated with an increased glioma risk among smokers.
Conclusions
These results indicate for the first time that LIG4 rs1805388 and XRCC4 rs1805377, alone or in combination, are associated with a risk of gliomas.
doi:10.1186/1471-2407-13-234
PMCID: PMC3655843  PMID: 23663450
DNA double-strand breaks (DSBs); Single nucleotide polymorphisms (SNPs); Glioma; Susceptibility
17.  IDOL Stimulates Clathrin-Independent Endocytosis and Multivesicular Body-Mediated Lysosomal Degradation of the Low-Density Lipoprotein Receptor 
Molecular and Cellular Biology  2013;33(8):1503-1514.
The low-density lipoprotein receptor (LDLR) is a critical determinant of plasma cholesterol levels that internalizes lipoprotein cargo via clathrin-mediated endocytosis. Here, we show that the E3 ubiquitin ligase IDOL stimulates a previously unrecognized, clathrin-independent pathway for LDLR internalization. Real-time single-particle tracking and electron microscopy reveal that IDOL is recruited to the plasma membrane by LDLR, promotes LDLR internalization in the absence of clathrin or caveolae, and facilitates LDLR degradation by shuttling it into the multivesicular body (MVB) protein-sorting pathway. The IDOL-dependent degradation pathway is distinct from that mediated by PCSK9 as only IDOL employs ESCRT (endosomal-sorting complex required for transport) complexes to recognize and traffic LDLR to lysosomes. Small interfering RNA (siRNA)-mediated knockdown of ESCRT-0 (HGS) or ESCRT-I (TSG101) components prevents IDOL-mediated LDLR degradation. We further show that USP8 acts downstream of IDOL to deubiquitinate LDLR and that USP8 is required for LDLR entry into the MVB pathway. These results provide key mechanistic insights into an evolutionarily conserved pathway for the control of lipoprotein receptor expression and cellular lipid uptake.
doi:10.1128/MCB.01716-12
PMCID: PMC3624246  PMID: 23382078
18.  Applications of Human Pharmacokinetic Prediction in First-in-Human Dose Estimation 
The AAPS Journal  2012;14(2):262-281.
Quantitative estimations of first-in-human (FIH) doses are critical for phase I clinical trials in drug development. Human pharmacokinetic (PK) prediction methods have been developed to project the human clearance (CL) and bioavailability with reasonable accuracy, which facilitates estimation of a safe yet efficacious FIH dose. However, the FIH dose estimation is still very challenging and complex. The aim of this article is to review the common approaches for FIH dose estimation with an emphasis on PK-guided estimation. We discuss 5 methods for FIH dose estimation, 17 approaches for the prediction of human CL, 6 methods for the prediction of bioavailability, and 3 tools for the prediction of PK profiles. This review may serve as a practical protocol for PK- or pharmacokinetic/pharmacodynamic-guided estimation of the FIH dose.
doi:10.1208/s12248-012-9332-y
PMCID: PMC3326168  PMID: 22407287
allometric scaling; FIH dose; in vitro–in vivo correlations; pharmacokinetics; prediction
19.  HIV-1 Fusion Is Blocked through Binding of GB Virus C E2D Peptides to the HIV-1 gp41 Disulfide Loop 
PLoS ONE  2013;8(1):e54452.
A strategy for antiviral drug discovery is the elucidation and imitation of viral interference mechanisms. HIV-1 patients benefit from a coinfection with GB Virus C (GBV-C), since HIV-positive individuals with long-term GBV-C viraemia show better survival rates than HIV-1 patients without persisting GBV-C. A direct influence of GBV-C on HIV-1 replication has been shown in coinfection experiments. GBV-C is a human non-pathogenic member of the flaviviridae family that can replicate in T and B cells. Therefore, GBV-C shares partly the same ecological niche with HIV-1. In earlier work we have demonstrated that recombinant glycoprotein E2 of GBV-C and peptides derived from the E2 N-terminus interfere with HIV entry. In this study we investigated the underlying mechanism. Performing a virus-cell fusion assay and temperature-arrested HIV-infection kinetics, we provide evidence that the HIV-inhibitory E2 peptides interfere with late HIV-1 entry steps after the engagement of gp120 with CD4 receptor and coreceptor. Binding and competition experiments revealed that the N-terminal E2 peptides bind to the disulfide loop region of HIV-1 transmembrane protein gp41. In conjunction with computational analyses, we identified sequence similarities between the N-termini of GBV-C E2 and the HIV-1 glycoprotein gp120. This similarity appears to enable the GBV-C E2 N-terminus to interact with the HIV-1 gp41 disulfide loop, a crucial domain involved in the gp120-gp41 interface. Furthermore, the results of the present study provide initial proof of concept that peptides targeted to the gp41 disulfide loop are able to inhibit HIV fusion and should inspire the development of this new class of HIV-1 entry inhibitors.
doi:10.1371/journal.pone.0054452
PMCID: PMC3551756  PMID: 23349893
20.  Genetic oxidative stress variants and glioma risk in a Chinese population: a hospital-based case–control study 
BMC Cancer  2012;12:617.
Background
The oxidative stress mechanism is of particular interest in the pathogenesis of glioma, given the high rate of oxygen metabolism in the brain. Potential links between polymorphisms of antioxidant genes and glioma risk are currently unknown. We therefore investigated the association between polymorphisms in antioxidant genes and glioma risk.
Methods
We examined 16 single nucleotide polymorphisms (SNPs) of 9 antioxidant genes (GPX1, CAT, PON1, NQO1, SOD2/MnSOD, SOD3, and NOS1*2*3) in 384 glioma and 384 control cases in a Chinese hospital-based case–control study. Genotypes were determined using the OpenArray platform, which employs the chip-based Taq-Man genotyping technology. The adjusted odds ratio (OR) and 95% confidence interval (CI) were estimated using unconditional logistic regression.
Results
Using single-locus analysis, we identified four SNPs (SOD2 V16A, SOD3 T58A, GPX1 -46 C/T, and NOS1 3’-UTR) that were significantly associated with the risk of glioma development. To assess the cumulative effects, we performed a combined unfavourable genotype analysis. Compared with the reference group that exhibited no unfavourable genotypes, the medium- and high-risk groups exhibited a 1.86-fold (95% CI, 1.30-2.67) and a 4.86-fold (95% CI, 1.33-17.71) increased risk of glioma, respectively (P-value for the trend < 0.001).
Conclusions
These data suggest that genetic variations in oxidative stress genes might contribute to the aetiology of glioma.
doi:10.1186/1471-2407-12-617
PMCID: PMC3546059  PMID: 23259684
Oxidative stress; Single nucleotide polymorphism; Glioma; SOD2; SOD3; GPX1; NOS1
21.  Association of the Maternal MTHFR C677T Polymorphism with Susceptibility to Neural Tube Defects in Offsprings: Evidence from 25 Case-Control Studies 
PLoS ONE  2012;7(10):e41689.
Background
Methylenetetrahydrofolate reductase (MTHFR) is a critical enzyme in folate metabolism and is involved in DNA methylation, DNA synthesis, and DNA repair. In addition, it is a possible risk factor in neural tube defects (NTDs). The association of the C677T polymorphism in the MTHFR gene and NTD susceptibility has been widely demonstrated, but the results remain inconclusive. In this study, we performed a meta-analysis with 2429 cases and 3570 controls to investigate the effect of the MTHFR C677T polymorphism on NTDs.
Methods
An electronic search of PubMed and Embase database for papers on the MTHFR C677T polymorphism and NTD risk was performed. All data were analysed with STATA (version 11). Odds ratios (ORs) with 95% confidence intervals (CIs) were estimated to assess the association. Sensitivity analysis, test of heterogeneity, cumulative meta-analysis, and assessment of bias were performed in our meta-analysis.
Results
A significant association between the MTHFR C677T polymorphism and NTD susceptibility was revealed in our meta-analysis ( TT versus CC: OR  = 2.022, 95% CI: 1.508, 2.712; CT+TT versus CC: OR  = 1.303, 95% CI: 1.089, 1.558; TT versus CC+CT: OR  = 1.716, 95% CI: 1.448, 2.033; 2TT+CT versus 2CC+CT: OR  = 1.330, 95% CI: 1.160, 1.525). Moreover, an increased NTD risk was found after stratification of the MTHFR C677T variant data by ethnicity and source of controls.
Conclusion
The results suggested the maternal MTHFR C677T polymorphism is a genetic risk factor for NTDs. Further functional studies to investigate folate-related gene polymorphisms, periconceptional multivitamin supplements, complex interactions, and the development of NTDs are warranted.
doi:10.1371/journal.pone.0041689
PMCID: PMC3463537  PMID: 23056169
22.  The contribution of the ABCG2 C421A polymorphism to cancer susceptibility: a meta-analysis of the current literature 
BMC Cancer  2012;12:383.
Background
ABCG2, also known as BCRP, is a half ATP-binding cassette (ABC) transporter that localizes to plasma membranes. Recently, a number of studies have investigated the relationship between the C421A polymorphism in ABCG2 and cancer risk in multiple populations and various types of cancers; however, this relationship remains unclear. Therefore, we performed a meta-analysis to further explore this association.
Methods
The meta-analysis incorporated 10 studies involving a total of 3593 cases and 5875 controls. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated based on the date extracted from the studies to evaluate the strength of association. We also analyzed the heterogeneity and sensitivity of each report and the publication bias of the studies.
Results
Overall, our results showed that there appeared to be a significant association between the ABCG2 C421A polymorphism and decreased cancer susceptibility (heterozygote-AC versus CC: OR = 0.759, 95%CI = 0.620-0.930; dominant effects model-AA/AC versus CC: OR = 0.771, 95%CI = 0.634-0.938; additive effects model-A allele versus C allele: OR = 0.809, 95%CI = 0.687-0.952). Similarly, decreased cancer risk was also found after stratification of the SNP data by cancer type, ethnicity and source of controls in heterozygote model, dominant effects model and additive effects model.
Conclusions
We found that the ABCG2 C421A polymorphism is a protective factor for developing cancer. The same relationship was found when the studies were stratified by cancer type, ethnicity and source of controls.
doi:10.1186/1471-2407-12-383
PMCID: PMC3488524  PMID: 22937733
23.  Mutations of Gln64 in the HIV-1 gp41 N-Terminal Heptad Repeat Render Viruses Resistant to Peptide HIV Fusion Inhibitors Targeting the gp41 Pocket 
Journal of Virology  2012;86(1):589-593.
To prove that the peptidic HIV-1 fusion inhibitors containing the pocket-binding domain (PBD) mainly target the hydrophobic pocket in the gp41 N-terminal heptad repeat (NHR), we constructed pseudoviruses by replacement of Q64 in the gp41 pocket region with Ala (Q64A) or Leu (Q64L). These viruses were highly resistant to C34 and CP32M containing the PBD, while they were susceptible to T20 (enfuvirtide) lacking the PBD but containing the GIV-motif-binding domain (GBD) and lipid-binding domain (LBD). They were also sensitive to C52L, which contains the PBD, GBD, and LBD. Those mutations may disrupt the hydrophilic interaction between Q64 in the NHR and N113 in the peptides containing the PBD. This report provides insights into the mechanisms of drug resistance, with implications for the design of novel HIV fusion and entry inhibitors.
doi:10.1128/JVI.05066-11
PMCID: PMC3255876  PMID: 22013063
24.  Hsa-mir-499 rs3746444 polymorphism and cancer risk: a meta-analysis 
Journal of Biomedical Research  2012;26(4):253-259.
MicroRNAs (miRNAs) are gene regulators involved in numerous diseases including cancer, heart disease, neurological disorders, vascular abnormalities and autoimmune conditions. Although hsa-mir-499 rs3746444 polymorphism was shown to contribute to the susceptibility of multiple genes to cancer, the data have yielded conflicting results. Therefore, this meta-analysis was performed to provide a comprehensive assessment of potential association between hsa-mir-499 rs3746444 polymorphism and cancer risk. In this meta-analysis, a total of 9 articles regarding 10 eligible case-control studies in English (including 6134 cases and 7141 controls) were analyzed. No significant association between hsa-mir-499 rs3746444 polymorphism and overall cancer risk was demonstrated. However, an increased risk was observed in the subgroup of breast cancer patients (G allele vs A allele: OR = 1.10, 95% CI = 1.00-1.20; Pheterogeneity = 0.114; I2 = 53.9%) and population-based studies (G allele vs A allele: OR = 1.12, 95% CI = 1.00-1.25; Pheterogeneity = 0.062; I2 = 64.0%). The findings suggested an association between hsa-mir-499 rs3746444 polymorphism and increased risk to breast cancer.
doi:10.7555/JBR.26.20110122
PMCID: PMC3596741  PMID: 23554757
cancer; meta-analysis; hsa-mir-499 rs3746444; polymorphism; susceptibility; miRNAs; pre-miRNA
25.  Examination of the Pharmacokinetics of Active Ingredients of Ginger in Humans 
The AAPS Journal  2011;13(3):417-426.
Ginger extracts have been studied in various clinical trials for different indications. However, the pharmacokinetics of the ginger active constituents in human biological matrices is not well investigated. This study aims to develop a LC-MS/MS method for simultaneous measurement of 6-, 8-, and 10-gingerols and 6-shogaol and study their pharmacokinetics in human plasma and colon tissues. A sensitive LC-MS/MS method was established and validated with a low limit of quantification of 2–5 ng/mL. The intra- and inter-day accuracy ranged from −7.3% to 10.4% and from −9.4% to 9.8%, respectively. The intra- and inter-day precision ranged from 0.9% to 10.9% and from 2.0% to 12.4%, respectively. The glucuronide and sulfate metabolites of 6-, 8-, and 10-gingerols and 6-shogaol in plasma and colon tissues were quantified after hydrolysis with β-glucuronidase and sulfatase. After oral dosing of 2.0 g ginger extracts in human, free 10-gingerol and 6-shogaol were detected in plasma with peak concentrations (9.5 ± 2.2 and 13.6 ± 6.9 ng/mL, respectively) at 1 h after oral administration, but no free 6-gingerol and 8-gingerol were detected in plasma from 0.25 to 24 h. The peak concentrations of glucuronide metabolites of 6-, 8-, and 10-gingerols and 6-shogaol were 0.47 ± 0.31, 0.17 ± 0.14, 0.37 ± 0.19, and 0.73 ± 0.54 μg/mL at 1 h, respectively. The peak concentrations of the sulfate metabolites of 6-, 8-, and 10-gingerols and 6-shogaol were 0.28 ± 0.15, 0.027 ± 0.018, 0.018 ± 0.006, and 0.047 ± 0.035 μg/mL at 1 h, respectively. Very low concentrations (2–3 ng/mL) of 10-gingerol glucuronide and sulfate were found in colon tissues. Pharmacokinetic analysis showed that half-lives of these four analytes and their metabolites were 1–3 h in human plasma. No accumulation was observed for 6-, 8-, and 10-gingerols and 6-shogaol and their metabolites in both plasma and colon tissues after multiple daily dosing.
doi:10.1208/s12248-011-9286-5
PMCID: PMC3160151  PMID: 21638149
6-Gingerol; 8-Gingerol; 10-Gingerol and 6-shogaol; LC-MS/MS; glucuronide; sulfate; pharmacokinetics

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