Feature screening for survival trait with application to TCGA high-dimensional genomic data.

Background: In high-dimensional survival genomic data, identifying cancer-related genes is a challenging and important subject in the field of bioinformatics. In recent years, many feature screening approaches for survival outcomes with high-dimensional survival genomic data have been developed; however, few studies have systematically compared these methods. The primary purpose of this article is to conduct a series of simulation studies for systematic comparison; the second purpose of this article is to use these feature screening methods to further establish a more accurate prediction model for patient survival based on the survival genomic datasets of The Cancer Genome Atlas (TCGA). Results: Simulation studies prove that network-adjusted feature screening measurement performs well and outperforms existing popular univariate independent feature screening methods. In the application of real data, we show that the proposed network-adjusted feature screening approach leads to more accurate survival prediction than alternative methods that do not account for gene-gene dependency information. We also use TCGA clinical survival genetic data to identify biomarkers associated with clinical survival outcomes in patients with various cancers including esophageal, pancreatic, head and neck squamous cell, lung, and breast invasive carcinomas. Conclusions: These applications reveal advantages of the new proposed network-adjusted feature selection method over alternative methods that do not consider gene-gene dependency information. We also identify cancer-related genes that are almost detected in the literature. As a result, the network-based screening method is reliable and credible.

Molecular Mechanism for Selective Cytotoxicity towards Cancer Cells of Diselenide-Containing Paclitaxel Nanoparticles.

Diselenide-containing paclitaxel nanoparticles (SePTX NPs) indicated selectivity of cytotoxicity between cancerous and normal cells in our previous work. Herein, the mechanism is revealed by molecular biology in detail. Cancer cells and normal cells were treated with the SePTX NPs and cell proliferation was measured using 3-(4, 5-dimethyl-2-thiazolyl)-2, 5-diphenyl-2-H-tetrazolium bromide (MTT) assay and cell morphology. Measurement of reactive oxygen species (ROS) levels and biochemical parameters were employed to monitor oxidative stress of the cells. JC-1 assay was used to detect the mitochondrial dysfunction of the cells. Terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL) analysis was used to detect apoptosis of the cells. Immunofluorescence analysis and western blotting were employed to monitor changes in signaling pathway-related proteins. Compared with PTX, SePTX NPs has a good selectivity to cancer cells and can obviously induce the proliferation damage of cancer cells, but has no significant toxicity to normal cells, indicating that SePTX NPs has a specific killing effect on cancer cells. The results of mechanism research show that SePTX NPs can successfully inhibit the depolymerization of microtubules and induce cell cycle arrest, which is related to the upregulation of p53 and CyclinB1. Simultaneously, SePTX NPs can successfully induce oxidative stress, cause mitochondrial dysfunction, resulting in mitochondrial pathway-mediated apoptosis, which is related to the upregulation of autophagy-related protein LC3-II. On the other hand, lewis lung cancer C57BL/6 mice were used to evaluate the anti-tumor effects of SePTX NPs in vivo. Our data show that SePTX NPs exhibited high inhibiting efficiency against the growth of tumors and were able to reduce the side effects. Collectively, these data indicate that the high antitumor effect and selective cytotoxicities of SePTX NPs is promising in future cancer therapy.

Effect and mechanism of psoralidin on promoting osteogenesis and inhibiting adipogenesis.

BACKGROUND: Psoralidin (PL), a prenylated coumestrol, is isolated from Psoralea corylifolia L. (Fabaceae), which is frequently used for treatment of osteoporosis. PURPOSE: This study was designed to investigate the dual effects and potential mechanism of PL on promoting osteogenesis and inhibiting adipogenesis. METHODS: Bone marrow mesenchymal stem cells (BMSCs) were used to investigate the effect of PL on stimulating osteogenesis and inhibiting adipogenesis, while preosteoblast MC3T3-E1 cells and preadipocyte 3T3-L1 cells were employed to explore the potential mechanisms. Estradiol (E2) and ICI 182,780 (ICI) were used as the specific agonist and antagonist of classical estrogen receptors (ER), respectively, to interfere with classical ER signaling. Meanwhile, G-1 and G-15 were introduced as the selective agonist and antagonist of G protein coupled receptor 30 (GRP30, a membrane ER) to further clarify if membrane ER involved in PL mediating osteogenesis and adipogenesis RESULTS: PL not only promoted mineralization, but also inhibited adipocytes formation of BMSCs. In terms of osteogenesis, PL enhanced calcium nodule formation, alkaline phosphatase activity and osteocalcin levels in MC3T3-E1 cells. As for adipogenesis, PL decreased adipocyte formation in 3T3-L1 cells through down-regulating several mRNA expressions and protein synthesis of adipogenesis related factors. ICI completely blocked the effect of PL in promoting osteogenesis, but only partially suppressed its effect in inhibition of adipogenesis, while G-15 partially suppressed the effect of PL on promoting mineralization and inhibiting oil drop formation. Furthermore, during suppression of adipocyte differentiation, PL regulated protein kinase B / glycogen synthase kinase 3ß / ß-catenin signaling pathway. CONCLUSION: PL promoted osteogenesis via mediating classical ER pathway, and inhibited adipocytes formation by regulating combined classical and membrane ER pathways. PL might be a potential candidate for the treatment of postmenopausal osteoporosis by modulating the competitive relationship between osteogenesis and adipogenesis of bone marrow mesenchymal stem cells.

Modulation of Ca²âº signals by epigallocatechin-3-gallate(EGCG) in cultured rat hippocampal neurons.

Green tea has been receiving considerable attention as a possible neuroprotective agent against neurodegenerative disease. Epigallocatechin-3-gallate (EGCG) is the major compound of green tea. Calcium signaling has profound effects on almost all aspects of neuronal function. Using digital calcium imaging and patch-clamp technique, we determined the effects of EGCG on Ca(2+) signals in hippocampal neurons. The results indicated that EGCG caused a dose-dependent increase in intracellular Ca(2+) ([Ca(2+)](i)). This [Ca(2+)](i) increase was blocked by depleting intracellular Ca(2+) stores with the endoplasmic reticulum Ca(2+) pump inhibitor thapsigargin and cyclopiazonic acid. Furthermore, EGCG-stimulated increase in [Ca(2+)](i) was abolished following treatment with a PLC inhibitor. However, EGCG inhibited high-voltage activated Ca(2+) currents (I(HVA)) and NMDA-induced inward currents (I(NMDA)). These data suggest that EGCG triggers a cascade of events: it activates phospholipase C (PLC), mobilizes intracellular Ca(2+) stores, raises the cytosolic Ca(2+) levels, and inhibits the VGCC and NMDA receptors-mediated Ca(2+) influx through a process that remains to be determined.

Theaflavin ameliorates cerebral ischemia-reperfusion injury in rats through its anti-inflammatory effect and modulation of STAT-1.

Theaflavin, a major constituent of black tea, possesses biological functions such as the antioxidative, antiviral, and anti-inflammatory ones. The purpose of this study was to verify whether theaflavin reduces focal cerebral ischemia injury in a rat model of middle cerebral artery occlusion (MCAO). Male Sprague-Dawley rats were anesthetized and subjected to 2 hours of MCAO followed 24 hours reperfusion. Theaflavin administration (5, 10, and 20 mg/kg, i.v.) ameliorated infarct and edema volume. Theaflavin inhibited leukocyte infiltration and expression of ICAM-1, COX-2, and iNOS in injured brain. Phosphorylation of STAT-1, a protein which mediates intracellular signaling to the nucleus, was enhanced 2-fold over that of sham group and was inhibited by theaflavin. Our study demonstrated that theaflavin significantly protected neurons from cerebral ischemia-reperfusion injury by limiting leukocyte infiltration and expression of ICAM-1, and suppressing upregulation of inflammatory-related prooxidative enzymes (iNOS and COX-2) in ischemic brain via, at least in part, reducing the phosphorylation of STAT-1.