EigenGWAS: An online visualizing and interactive application for detecting genomic signatures of natural selection.

Detecting genetic regions under selection in structured populations is of great importance in ecology, evolutionary biology and breeding programmes. We recently proposed EigenGWAS, an unsupervised genomic scanning approach that is similar to F ST but does not require grouping information of the population, for detection of genomic regions under selection. The original EigenGWAS is designed for the random mating population, and here we extend its use to inbred populations. We also show in theory and simulation that eigenvalues, the previous corrector for genetic drift in EigenGWAS, are overcorrected for genetic drift, and the genomic inflation factor is a better option for this adjustment. Applying the updated algorithm, we introduce the new EigenGWAS online platform with highly efficient core implementation. Our online computational tool accepts plink data in a standard binary format that can be easily converted from the original sequencing data, provides the users with graphical results via the R-Shiny user-friendly interface. We applied the proposed method and tool to various data sets, and biologically interpretable results as well as caveats that may lead to an unsatisfactory outcome are given. The EigenGWAS online platform is available at www.eigengwas.com, and can be localized and scaled up via R (recommended) or docker.

No Association Between Calcium Channel Blockers and Survival in Patients with Cancer: A Systematic Review and Meta-analysis.

BACKGROUND: Any association between calcium channel blockers (CCBs) and survival in cancer patients remains unclear and the results of related studies are conflicting. The objective of the study was to investigate the association between calcium channel blocker (CCB) use and survival in cancer patients. MATERIALS AND METHODS: We searched PubMed, EMBASE, Web of Science and Cochrane Library for studies published before January 2016 with terms related to CCBs and survival in cancer patients. The information was reviewed and extracted by two evaluators independently. Data from publications were extracted and used to calculate hazard ratios (HRs) for overall survival (OS). Statistical analysis was performed by using Review Manager 5.3. RESULTS: There were 11 studies included in our meta-analysis. Analysis of all showed that CCBs use was not associated with survival in cancer patients (HR=1.07; 95% CI: 0.91-1.25; P=0.42). No association between CCB use and overall survival in cancer patients existed, whether in Asian (HR=1.18, 95% CI: 0.72-1.93; P=0.52) or Caucasian populations (HR=1.03, 95% CI: 0.89-1.20; P=0.66). CONCLUSIONS: There is no evidence that CCB use is associated with a better or worse survival in cancer patients.

Conjugation of Uridine with Oleanolic Acid Derivatives as Potential Antitumor Agents.

According to fused two bioactive moieties together by bonds covalently and available as a new single hybrid entity known as pharmacophore hybridization, a total of 10 targeted uridine-oleanolic acid hybrids were synthesized. Most of these hybrids showed excellent proliferation inhibition against tested Hep-G2, A549, BGC-823, MCF-7, and PC-3 tumor cell lines (IC50 < 8 µm), even with some IC50 values under 0.1 µm. The detection of cytotoxicity selectivity revealed that hybrids 5 and 18 exhibited low cytotoxicity toward normal human liver cell HL-7702. Further studies revealed that selected hybrid 5 could induce apoptosis in Hep-G2 cells through the investigation of acridine orange/ethidium bromide, Hoechst 33258 fluorescence stainings, and annexin V/propidium iodide assay. It was also found that hybrid 5 could induce mitochondrial membrane potential disruption, arrest Hep-G2 cell line at G1 phase, and activate effector caspase-3/9 to trigger cell apoptosis.

Amiloride sensitizes human pancreatic cancer cells to erlotinib in vitro through inhibition of the PI3K/AKT signaling pathway.

AIM: Blockade of EGFR by EGFR tyrosine kinase inhibitors such as erlotinib is insufficient for effective treatment of human pancreatic cancer due to independent activation of the Akt pathway, while amiloride, a potassium-sparing diuretic, has been found as a potential Akt inhibitor. The aim of this study was to investigate the anticancer effects of combined amiloride with erlotinib against human pancreatic cancer cells in vitro. METHODS: Cell proliferation, colony formation, cell cycle and apoptosis were analyzed in 4 human pancreatic cancer cell lines Bxpc-3, PANC-1, Aspc-1 and CFPAC-1 treated with erlotinib or amiloride alone, or in their combination. The synergistic analysis for the effects of combinations of amiloride and erlotinib was performed using Chou-Talalay's combination index isobolographic method. RESULTS: Amiloride (10, 30, and 100 µmol/L) concentration-dependently potentiated erlotinib-induced inhibition of cell proliferation and colony formation in the 4 pancreatic cancer cell lines. Isobolographic analysis confirmed that combinations of amiloride and erlotinib produced synergistic cytotoxic effects. Amiloride significantly potentiated erlotinib-induced G0/G1 cell-cycle arrest and apoptosis in Bxpc-3 and PANC-1 cells. Amiloride inhibited EGF-stimulated phorsphorylation of AKT, and significantly enhanced erlotinib-induced downregulation of phorsphorylation of EGFR, AKT, PI3K P85 and GSK 3ß in Bxpc-3 and PANC-1 cells. CONCLUSION: Amiloride sensitizes human pancreatic cancer cells to erlotinib in vitro through inhibition of the PI3K/AKT signaling pathway. Treatment of pancreatic cancer patients with combination of erlotinib and amiloride merits further investigation.

Preclinical assessment of the distribution, metabolism, and excretion of S-propargyl-cysteine, a novel H2S donor, in Sprague-Dawley rats.

AIM: To study the distribution, metabolism and excretion of S-propargyl-cysteine (SPRC), a novel hydrogen sulfide (H2S) donor, after oral administration in rats. METHODS: Adult Sprague-Dawley rats were used. The tissue distribution of [(35)S] SPRC-derived radioactivity was measured using a liquid scintillation counter. The plasma protein binding of SPRC was examined using 96-well equilibrium dialysis. The excretion of SPRC in urine, bile and feces was analyzed using the LC-MS/MS method. The major metabolites in rat biomatrices were identified using MRM information-dependent, acquisition-enhanced product ion (MRM-IDA-EPI) scans on API 4000QTrap system. RESULTS: After oral administration of [(35)S]-SPRC at a dose of 75 mg/kg, [(35)S] SPRC-derived radioactivity displayed broad biological distribution in various tissues of rats, including its target organs (heart and brain) with the highest in kidney. On the other hand, the binding of SPRC to human, rat and dog plasma protein was low. Only 2.18% ± 0.61% and 0.77% ± 0.61% of the total SPRC administered was excreted unchanged in the bile and urine. However, neither intact SPRC nor its metabolites were detected in rat feces. The major metabolic pathway in vivo (rat bile, urine, and plasma) was N-acetylation. CONCLUSION: The preliminary results suggest that SPRC possesses acceptable pharmacokinetic properties in rats.

Pharmacokinetic characterization of ginsenoside Rh2, an anticancer nutrient from ginseng, in rats and dogs.

The pharmacokinetic characteristics of ginsenoside Rh2, an anticancer nutrient, were analyzed in dogs and rats, including plasma kinetics, bioavailability, tissue distribution, plasma protein binding and excretion. The bioavailability of Rh2 is about 5% in rats and 16% in dogs. Multiple-dosing (7 days, 1 mg/kg bid) did not affect the pharmacokinetics in dogs. After oral dosing, Rh2 distributed mainly to the liver and gastrointestinal tissues in rats. In rats, the circulating fraction of Rh2 bound to plasma proteins was around 70%. The systemic clearance, however, was low -- around 2 and 20 ml/min/kg in dogs and rats, respectively. Only 1% of dosed Rh2 were recovered in excreta of rats as the intact form after oral administration, while 30% was excreted unchanged in bile after i.v. dosing. We subsequently investigated the membrane permeability of Rh2 across Caco-2 cell monolayers, stability and elimination profiles in the gastrointestinal environment. Low membrane permeability (P(app)(AP-BL): 1.91 x 10(-8)cm/s), efflux transport (efflux ratio: 9.8), pre-systemic elimination (degradation in acidic condition; metabolism in intestine tissue and contents), as well as low solubility largely accounted for the low bioavailability of Rh2. Regarding the low solubility of Rh2, micronization of the dose almost doubled the rate of absorption in dogs. Preliminary metabolite profiling confirmed the presence of the deglycosidating product protopanaxadiol in rat feces. A possible metabolite in rat bile and a potential sulfate-conjugate in rat urine were also detected.