Prognosis and diagnosis of prostate cancer based on hypergraph regularization sparse least partial squares regression algorithm.

BACKGROUND: Prostate cancer (PCa) is a malignant tumor of the male reproductive system, and its incidence has increased significantly in recent years. This study aimed to further identify candidate biomarkers with prognostic and diagnostic significance by integrating gene expression and DNA methylation data from PCa patients through association analysis. MATERIAL AND METHODS: To this end, this paper proposes a sparse partial least squares regression algorithm based on hypergraph regularization (HR-SPLS) by integrating and clustering two kinds of data. Next, module 2, with the most significant weight, was selected for further analysis according to the weight of each module related to DNA methylation and mRNAs. Based on the DNA methylation sites in module 2, this paper uses multiple machine learning methods to construct a PCa diagnosis-related model of 10-DNA methylation sites. RESULTS: The results of Receiver Operating Characteristic (ROC) analysis showed that the DNA methylation-related diagnostic model we constructed could diagnose PCa patients with high accuracy. Subsequently, based on the mRNAs in module 2, we constructed a prognostic model for 7-mRNAs (MYH11, ACTG2, DDR2, CDC42EP3, MARCKSL1, LMOD1, and MYLK) using multivariate Cox regression analysis. The prognostic model could predict the disease free survival of PCa patients with moderate to high accuracy (area under the curve (AUC) =0.761). In addition, Gene Set EnrichmentAnalysis (GSEA) and immune analysis indicated that the prognosis of patients in the risk group might be related to immune cell infiltration. CONCLUSIONS: Our findings may provide new methods and insights for identifying disease-related biomarkers by integrating DNA methylation and gene expression data.

Cripto-1 expression in patients with clear cell renal cell carcinoma is associated with poor disease outcome.

BACKGROUND: Cripto-1 (CR-1) has been reported to be involved in the development of several human cancers. The potential role of CR-1 in clear cell renal cell carcinoma (ccRCC) is still not clear. METHODS: CR-1 expression was evaluated in ccRCC tissues by Real-time quantitative PCR, Western blot and immunohistochemistry. Serum levels of CR-1 were tested by enzyme-linked immunosorbent assay (ELISA). The clinical significance of CR-1 was analyzed. The effects of CR-1 on cell proliferation, migration, invasion and angiogenesis were investigated in ccRCC cell lines in vitro and in vivo, and markers of the epithelial -mesenchymal transition (EMT) were analyzed. The impact of CR-1 on Wnt/ß-catenin signaling pathway was also evaluated in vitro and in vivo. RESULTS: CR-1 expression was elevated in ccRCC tumor tissues and serum samples. CR-1 expression was correlated with aggressive tumor phenotype and poor survival. Ectopic expression of CR-1 significantly promoted cell proliferation, migration, invasion and angiogenesis whereas knockdown of CR-1 inhibited these activities both in vitro and in vivo. Moreover, we found that CR-1 induced EMT and activated Wnt/ß-catenin signaling pathway both in vitro and in vivo. CONCLUSIONS: These results suggest that CR-1 is likely to play important roles in ccRCC development and progression, and that CR-1 is a prognostic biomarker and a promising therapeutic target for ccRCC.

Caffeine treatment disturbs the angiogenesis of zebrafish embryos.

Caffeine is a widely consumed substance that occurs in numerous dietary sources, but teratogenic effects of caffeine intake during embryonic development are still not clear. In the present study, we used the zebrafish as a model to assess caffeine-induced toxicity on embryonic vascular development. A green fluorescent vascular endothelium transgenic line, Tg(fli1:egfp), was utilized for the sensitive detection of vascular development, including vasculo- and angiogenesis. Caffeine-treated embryos showed no defects in vasculogenesis, but revealed dose-dependent (250-350 ppm) developmental defects in intersegmental vessels, dorsal longitudinal anastomotic vessels, and subintestinal vein sprouting. Further, real-time polymerase chain reaction analysis of caffeine-treated embryos showed an upregulation of nrp1a along with a downregulation of sema3aa and sema3c. In conclusion, caffeine treatment induces defects of angiogenesis in zebrafish embryos.

Twist controls skeletal development and dorsoventral patterning by regulating runx2 in zebrafish.

BACKGROUND: Twist1a and twist1b are the principal components of twists that negatively regulate a number of cellular signaling events. Expression of runx2 and downstream targets is essential for skeletal development and ventral organizer formation and specification in early vertebrate embryos, but what controls ventral activity of maternal runx2 and how twists function in zebrafish embryogenesis still remain unclear. METHODOLOGY/PRINCIPAL FINDINGS: By studying the loss of twist induced by injection of morpholino-oligonucleotide in zebrafish, we found that twist1a and twist1b, but not twist2 or twist3, were required for proper skeletal development and dorsoventral patterning in early embryos. Overexpression of twist1a or twist1b following mRNA injection resulted in deteriorated skeletal development and formation of typical dorsalized embryos, whereas knockdown of twist1a and twist1b led to the formation of abnormal embryos with enhanced skeletal formation and typical ventralized patterning. Overexpression of twist1a or twist1b decreased the expression of runx2b, whereas twist1a and twist1b knockdown increased runx2b expression. We have further demonstrated that phenotypes induced by twist1a and twist1b knockdown were rescued by runx2b knockdown. CONCLUSIONS/SIGNIFICANCE: Together, these results suggest that twist1a and twist1b control skeletal development and dorsoventral patterning by regulating runx2b in zebrafish and provide potential targets for the treatment of diseases or syndromes associated with decreased skeletal development.

Oligomeric sensor kinase DcuS in the membrane of Escherichia coli and in proteoliposomes: chemical cross-linking and FRET spectroscopy.

DcuS is the membrane-integral sensor histidine kinase of the DcuSR two-component system in Escherichia coli that responds to extracellular C(4)-dicarboxylates. The oligomeric state of full-length DcuS was investigated in vitro and in living cells by chemical cross-linking and by fluorescence resonance energy transfer (FRET) spectroscopy. The FRET results were quantified by an improved method using background-free spectra of living cells for determining FRET efficiency (E) and donor fraction {f(D) = (donor)/[(donor) + (acceptor)]}. Functional fusions of cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP) variants of green fluorescent protein to DcuS were used for in vivo FRET measurements. Based on noninteracting membrane proteins and perfectly interacting proteins (a CFP-YFP fusion), the results of FRET of cells coexpressing DcuS-CFP and DcuS-YFP were quantitatively evaluated. In living cells and after reconstitution of purified recombinant DcuS in proteoliposomes, DcuS was found as a dimer or higher oligomer, independent of the presence of an effector. Chemical cross-linking with disuccinimidyl suberate showed tetrameric, in addition to dimeric, DcuS in proteoliposomes and in membranes of bacteria, whereas purified DcuS in nondenaturing detergent was mainly monomeric. The presence and amount of tetrameric DcuS in vivo and in proteoliposomes was not dependent on the concentration of DcuS. Only membrane-embedded DcuS (present in the oligomeric state) is active in (auto)phosphorylation. Overall, the FRET and cross-linking data demonstrate the presence in living cells, in bacterial membranes, and in proteoliposomes of full-length DcuS protein in an oligomeric state, including a tetramer.

Polar accumulation of the metabolic sensory histidine kinases DcuS and CitA in Escherichia coli.

Signal transduction in prokaryotes is frequently accomplished by two-component regulatory systems in which a histidine protein kinase is the sensory component. Many of these sensory kinases control metabolic processes that do not show an obvious requirement for inhomogeneous distribution within bacterial cells. Here, the sensory kinases DcuS and CitA, two histidine kinases of Escherichia coli, were investigated. Both are membrane-integral and involved in the regulation of carboxylate metabolism. The two-component sensors were fused with yellow fluorescent protein (YFP) and live images of immobilized cells were obtained by confocal laser fluorescence microscopy. The fluorescence of the fusion proteins was concentrated at the poles of the cells, indicating polar accumulation of the sensory kinases. For quantitative evaluation, line profiles of the imaged fluorescence intensities were generated; these revealed that the fluorescence intensity of the polar bright spots was 2.3-8.5 times higher than that of the cytoplasm. With respect to the cylindrical part of the membrane, the values were lower by about 40 %. The polar accumulation was comparable to that of methyl-accepting chemotaxis proteins (MCPs) and MCP-related proteins. The degree of DcuS-YFP localization was independent of the presence of MCP and the expression level of dcuS-yfp (or DcuS concentration). The presence of effector (fumarate or citrate, respectively) increased the polar accumulation by more than 20 %. Cell fractionation demonstrated that polar accumulation was not related to inclusion body formation. Therefore, sensory kinases DcuS and CitA, which regulate metabolic processes without obvious polar function, exhibit polar accumulation.

[Cytocompatibility of silk fibroin film with rabbit urinary bladder transitional epithelial cells in vitro].

OBJECTIVE: To obtain large quantities of well differentiated urinary bladder transitional epithelial cells for used as the seed cells in bladder tissue engineering, and evaluate the cytocompatibility of silk fibroin film with the transitional cells in vitro to assess the possibility of tissue-engineered urinary organ construction. METHODS: The urinary bladder transitional epithelial cells were isolated from the bladders of New Zealand rabbits and cultured in vitro as the seed cells, whose morphology was observed and the specific protein (cytokeratin) expression identified by immunofluorescence assay. The cells were seeded in 96-well plates at 1 x 10(>4)/ml and incubated with silk fibroin film leaching solution or culture medium (negative control). MTT assay was performed to determine the cell proliferation rates of the wells and evaluate the cytotoxicity and cytocompatibility of the silk fibroin film. RESULTS: The isolated urinary bladder transitional epithelial cells reached confluence after 9-10 days of culture, which showed positive staining for immunocytochemistry with monoclonal antibody against cytokeratin. The absorbance of the cells culture in the presence of silk fibroin film leaching solution averaged 0.424-/+0.020, 0.996-/+0.118 and 1.285-/+0.048 after at 24, 72 and 120 h of cell culture, and that of the negative control group at the time points was 0.419-/+0.030, 1.105-/+0.098 and 1.228-/+0.052, respectively, showing no significant difference between the two groups (P>0.05). CONCLUSION: Silk fibroin film has good cytocompatibility with rabbit urinary bladder transitional epithelial cells, and may serve as good scaffold material for urologic tissue engineering.