Seed-weighted random walk ranking for cancer biomarker prioritisation: a case study in leukaemia.

A central focus of clinical proteomics for cancer is to identify protein biomarkers with diagnostic and therapeutic application potential. Network-based analyses have been used in computational disease-related gene prioritisation for several years. The Random Walk Ranking (RWR) algorithm has been successfully applied to prioritising disease-related gene candidates by exploiting global network topology in a Protein-Protein Interaction (PPI) network. Increasing the specificity and sensitivity ofbiomarkers may require consideration of similar or closely-related disease phenotypes and molecular pathological mechanisms shared across different disease phenotypes. In this paper, we propose a method called Seed-Weighted Random Walk Ranking (SW-RWR) for prioritizing cancer biomarker candidates. This method uses the information of cancer phenotype association to assign to each gene a disease-specific, weighted value to guide the RWR algorithm in a global human PPI network. In a case study of prioritizing leukaemia biomarkers, SW-RWR outperformed a typical local network-based analysis in coverage and also showed better accuracy and sensitivity than the original RWR method (global network-based analysis). Our results suggest that the tight correlation among different cancer phenotypes could play an important role in cancer biomarker discovery.

Eyes absent tyrosine phosphatase activity is not required for Drosophila development or survival.

Eyes absent (Eya) is an evolutionarily conserved transcriptional coactivator and protein phosphatase that regulates multiple developmental processes throughout the metazoans. Drosophila eya is necessary for survival as well as for the formation of the adult eye. Eya contains a tyrosine phosphatase domain, and mutations altering presumptive active-site residues lead to strongly reduced activities in ectopic eye induction, in vivo genetic rescue using the Gal4-UAS system, and in vitro phosphatase assays. However, these mutations have not been analyzed during normal development with the correct levels, timing, and patterns of endogenous eya expression. To investigate whether the tyrosine phosphatase activity of Eya plays a role in Drosophila survival or normal eye formation, we generated three eya genomic rescue (eyaGR) constructs that alter key active-site residues and tested them in vivo. In striking contrast to previous studies, all eyaGR constructs fully restore eye formation as well as viability in an eya null mutant background. We conclude that the tyrosine phosphatase activity of Eya is not required for normal eye development or survival in Drosophila. Our study suggests the need for a re-evaluation of the mechanism of Eya action and underscores the importance of studying genes in their native context.

Evolution of prokaryotic homologues of the eukaryotic SEFIR protein domain.

SEF/IL17 receptor (SEFIR) domains are mainly found in IL17 receptors (IL17Rs) and their adaptor proteins CIKS (connection to IKK and SAPK/JNK), which exert a host defense role in numbers of infectious diseases and promote inflammatory pathology in autoimmunity. Exploring the evolutionary pathway of SEFIR domains will provide further insight into their functions. Here, we have identified 84 SEFIR domain-containing proteins from more than 1400 prokaryotic genomes. As most SEFIR domain-containing bacterial genomes possess a single SEFIR encoding gene and the SEFIR protein domain forms homodimeric complexes like the Toll/IL1 receptor (TIR) domain, the single bacterial SEFIR proteins may receive binding partners from other organisms. Through comparative and phylogenetic sequence analyses, we show that bacterial SEFIR domain is more similar to that of vertebrate CIKS than IL17R, and it possibly emerges via a lateral gene transfer (LGT) from animals. In addition, our secondary and three-dimensional structural predictions of SEFIR domains reveal that human and pathogenic bacterial SEFIR domains share similar structural and electrostatic features. Our findings provide important clues for further experimental researches on determining the functions of SEFIR proteins in pathogenic prokaryotes.

Evolution of the IL17 receptor family in chordates: a new subfamily IL17REL.

The human interleukin 17 receptor (IL17R) family plays a critical role in inflammatory responses and contributes to the pathology of many autoimmune diseases. So far, five members, IL17RA to IL17RE, have been identified. Recently, some IL17R genes have been identified in non-mammalian species, such as zebrafish IL17RD; however, there are no reports on the evolutionary history of this complex gene family through comparative phylogenetic approaches. Here, we concentrated on the IL17R evolution in chordates. There are two IL17Rs in the genome of the basal chordate amphioxus: IL17RA and IL17RD. After two rounds of whole genome duplications, these two IL17R genes expanded into five early vertebrate IL17R genes, IL17RA to IL17RE. IL17RA and IL17RD are found in most vertebrates, whereas the other three, IL17RB, ILR17RC, and IL17RE, underwent some loss in vertebrates during evolution. Our sequence and structure analyses reveal functional similarities and distinctions between the different IL17Rs. Based on similarity searches for IL17R-like proteins within chordate sequences, a group of IL17RE-like (IL17REL) proteins were identified from mammalians to lower vertebrates. In silico and expression analyses on the novel IL17RELs showed that this group of receptors is highly conserved across species, indicating that IL17REL may represent a unique subfamily of IL17Rs.

Dynamic evolution of CIKS (TRAF3IP2/Act1) in metazoans.

CIKS (TRAF3IP2/Act1) is important for inflammatory responses and autoimmunity control through its dual functions in CD40L/BAFF and IL17 signaling in mammalians. In this study, we performed comparative and evolutionary analyses of CIKSs from metazoans. Although nematode (Caenorabditis elegans) and sea urchin (Strongylocentrotus purpuratus) have IL17 and IL17 receptors, we found no CIKS in their genomes. The ancient CIKS-like (CIKSL) genes from the invertebrates lottia (Lottia gigantea) and amphioxus (Branchiostoma floridae) have an additional DEATH domain compared with other CIKSLs/CIKSs. Our data suggest that the ancient CIKSL evolved into early chordate CIKS possibly through gene tandem duplication and gene fission. Based on phylogenetic and synteny analyses, vertebrate CIKS genes are divided into two groups, one of which is orthologous to human CIKS and the other is paralogous. Expression analysis indicated that cephalochordata amphioxus IL17 together with CIKS might play an ancient and conserved role in host defense against bacterial infections. During the evolutionary process, the CIKS genes have obtained more and more functions through cooperation with other genes.

High-efficiency continuously tunable single-frequency doubly resonant optical parametric oscillator.

We report a high-efficiency continuously tunable single-frequency doubly resonant optical parametric oscillator (OPO) based on periodically poled KTiOPO4. Pumped by a frequency-doubled Nd:YLF laser at 526.5 nm, the OPO has a low threshold of 30 mW and can deliver up to 156 mW single-frequency output at 0.8 µm and 89 mW single-frequency output at 1.5 µm with 390 mW of pump power. Coarse and continuous frequency tuning are also demonstrated experimentally.

Comparative and phylogenetic analyses of three TIR domain-containing adaptors in metazoans: implications for evolution of TLR signaling pathways.

Toll-like receptor adaptor molecule 1/2 (TICAM-1/2) and Toll-interleukin 1 receptor (TIR) domain-containing adaptor protein (TIRAP) play key roles in the Toll-like receptor (TLR) signaling pathways, which respond to viral and bacterial infections. These genes have been identified and studied in several vertebrates. However, our understanding of their evolutionary history and their roles in immune responses is far from complete. In this study, comparative and evolutionary analyses were performed for TICAM-1, TICAM-2 and TIRAP within the range of 25 representative species. Our data show that the origin of the TICAM-like and TIRAP-like genes may coincide with the origin of chordates (amphioxus). Several putative TICAMs and TIRAPs were identified for different chordate species. Shark is the only non-mammalian species whose genome contains a TICAM-2 gene. Structural modeling and comparison of TIR domains of these adaptors support their potential functional motifs and residues. Together with analyses of other genes involved in the TLR signaling pathways, we speculate that TICAM-1, TICAM-2 and TIRAP might have co-evolved with the TLR3/22 antivirus signaling, the LPS-specific TLR4 signaling and the Gram-positive bacteria-induced TLR2 signaling pathways, respectively. Our results are valuable contributions to the understanding of TICAM/TIRAP evolutional functions and may provide targets for therapeutic intervention in TLR-mediated vertebrate diseases.

Increased proteolytic processing of full-length Gli2 transcription factor reduces the hedgehog pathway activity in vivo.

The proteolytic processing of Gli2 and Gli3 full-length transcription factors into repressors is a key step of the regulation in Hedgehog (Hh) signaling. The differential Gli2 and Gli3 processing is controlled by the processing determinant domain or PDD, but its significance is not clear. We generated a Gli2 mutant allele, Gli2(3PDD) , in which the Gli3PDD substitutes for the Gli2PDD. As expected, Gli2(3PDD) is processed more efficiently and at a different position as compared to Gli2, indicating that PDD also determines the extent and site of Gli2 and Gli3 processing in vivo. The increase in levels of the Gli2 repressor in Gli2(3PDD) mutant reduces the Hh pathway activity. Gli2(3PDD) processing is still regulated by Hh signaling. These results indicate that the proper balance between the Gli2 full-length activator and repressor is essential for Hh signaling.

Domain combination of the vertebrate-like TLR gene family: implications for their origin and evolution.

Domain shuffling, which is an important mechanism in the evolution of multi-domain proteins, has shaped the evolutionary development of the immune system in animals. Toll and Toll-like receptors (TLRs) are a class of proteins that play a key role in the innate and adaptive immune systems. Draft genome sequences provide the opportunity to compare the Toll/TLR gene repertoire among representative metazoans. In this study, we investigated the combination of Toll/interleukin-1 receptor (TIR) and leucine-rich repeat (LRR) domains of metazoan Toll/TLRs. Before Toll with both domains occurred in Cnidaria (sea anemone, Nematostella vectensis), through domain combinations, TIR-only and LRR-only proteins had already appeared in sponges (Amphimedon queenslandica). Although vertebrate-like TIR (V-TIR) domain already appeared in Cnidaria, the vertebrate-like TLR (V-TLR) with both domains appeared much later. The first combination between V-TIR domain and vertebrate-like LRR (V-LRR) domain for V-TLR may have occurred after the divergence of Cnidaria and bilateria. Then, another combination for V-TLR, a recombination of both domains, possibly occurred before or during the evolution of primitive vertebrates. Taken together, two rounds of domain combinations may thus have co-shaped the vertebrate TLRs.

Prolonged survival of human hepatocarcinoma cells in the liver of newborn C57BL/6 mice and resulting cellular xenorejection, especially the activation of hepatic natural killer T cells.

OBJECTIVE: To investigate the fate of human hepatocellular carcinoma (HCC) in the livers of newborn mice and the resulting cellular rejection. METHODS: Two HCC cell lines (HepG2 and HCCLM3) labeled with DMAHAS were orthotopically transplanted to newborn and adult mice with or without low-dose cyclosporin A (CsA) treatment (10 mg/kg). The fate of tumor xenografts was examined and the resulting cellular response was investigated. RESULTS: Tumor xenografts survived in newborn mice for > 4 weeks, with a delayed lymphocyte infiltration mediated by CD4+ T, CD8+ T and NK1.1+ cells. In contrast, the xenografts survived in adults < 8-10 days with an acute cellular rejection by CD8+T cells, NK1.1+ cells, macrophages or neutrophils. Orthotopic transplantation of human HCC xenografts elicited a strong cytotoxic response in newborn mice (p < 0.05), and selective T/NK1.1+ cell deletion in vitro suggested that such effector cells were mainly CD8+ T cells. Moreover, tumor xenografts induced a rapid activation of hepatic natural killer T (NKT) cells in both newborn and adult mice with enhanced secretion of IL-4 and IFN-gamma in serum and subsequent NKT-like cytotoxicity. The rapid activation of NKT cells could be efficiently suppressed by low-dose CsA treatment, possibly in a CD1d-independent manner. CONCLUSION: Our data suggest that the livers of newborn mice were more suitable for the survival of xenografts than those of adult mice. Cell-mediated tumor xenorejection in newborn mice was different from that in adults, and hepatic NKT cells may play an important role in early tumor xenorejection.

[Effects of osteogenic growth peptide to the proliferation and differentiation of bone marrow stromal cells].

OBJECTIVE: To investigate the effects of osteogenic growth peptide (OGP) to the proliferation and differentiation of cultured bone marrow stromal cells (BMSCs) of rats. METHODS: The SD rats (age 6 weeks) were sacrified, and the bone marrow stromal cells as the adherent stromal cell population were separated from the bone marrow culcure. The proliferation curves of bone marrow stromal cells which were conditioned cultured with four kind of different concentrations of osteogenic growth peptide were measured with the MTT method, and the osteogenesis markers including alkaline phosphatase and calcic deposition detected by histochemical staining. RESULTS: Osteogenic growth peptide at the concentration of 10(-10), 10(-11) mol/L promoted the proliferation of bone marrow stromal cells, while at the concentrations of 10(-8), 10(-9) mol/L suppressed the proliferation of bone marrow stromal cells. However,osteogenic growth peptide at the concentration of 10(-9), 10(-8) mol/L advanced the ratio of positive cells in alkaline phosphatase histochemical staining. CONCLUSION: Osteogenic growth peptide shows distinct effects on the proliferation and differentiation of bone marrow stromal cells depending on its concentration. Osteogenic growth peptide at the concentration of 10(-8), 10(-9) mol/L can promote bone marrow stromal cell differentiation to the osteogenic in vitro.

Alpha-fetoprotein-specific transfer factors downregulate alpha-fetoprotein expression and specifically induce apoptosis in Bel7402 alpha-fetoprotein-positive hepatocarcinoma cells.

AIM: To investigate the mechanisms of AFP-specific transfer factors (AFP-TF) in induced Bel7402 cells apoptosis. Further, we investigate the interaction between AFP-TF and AFP in the apoptosis. METHODS: Bel7402 and HepG2 AFP-positive hepatocarcinoma cell lines, SK-Hep-1 AFP-negative hepatocarcinoma cell line and Changliver normal liver cell line are used. Cell viability is evaluated by MTT assay and apoptosis is measured by Hoechst33342 staining and TUNEL assay. FACS is used to analyze the cell cycle. AFP expression is examined by RT-PCR, Western blotting and immunocytochemistry. The interaction between AFP-TF and AFP in the apoptosis is investigated by addition of AFP in cultures or AFP transfection in Bel7402 cells prior to AFP-TF treatment. Mitochondrial membrane potential (DeltaPsi(m)) and intracellular Ca2+ concentration are respectively measured by Rhodamine123 and Fluo-3 AM Ester. Western blotting detects the involvement of several apoptosis-related proteins. Finally, caspase-3 and Caspase-9 activity are respectively examined. RESULTS: AFP-TF can induce apoptosis in Bel7402 and HepG2 AFP-positive hepatocarcinoma cells, but not SK-Hep-1 and Changliver cells. AFP-mRNA level changes little in apoptotic Bel7402 cells; while AFP expression is downregulated and uniformly dispersed throughout the whole cell. Addition of exogenous AFP or overexpression of intracellular AFP can reduce such apoptotic effect. Besides, apoptotic Bel7402 cells show a disruption of DeltaPsi(m), an immediate elevation of Ca2+ concentration, a prominently decreased ratio of bcl-2 to bax, a release of cytochrome c from mitochondria to cytosol, and ultimately an activation of caspase-9 and caspase-3. CONCLUSION: AFP-TF induced Bel7402 cells apoptosis is mitochondrial-dependent and is mediated by the interaction of AFP-TF with intracellular AFP.

[Reconstruction of embryo using an improved nuclear transfer method].

Previous methods used for nuclear transplantation were further investigated to develop a method that was both easy to carryout and did not require any special apparatus, such as Piezoimpact or Spindle-View. Following the puncture of zona pellucida with two holes by injection pipette that contained donor nuclei or cells, the injection pipette was pulled back to the perivitelline space while the negative pressure was increased in the holding pipette until the polar body and karyoplasm were wiped off completely. Then a reconstructed embryo was completed by the direct injection of the donor nucleus or cell without pulling out the injection pipette. 200 oocytes were manipulated using this method and it cost about 40 seconds with nucleus injection and about 30 seconds with cell injection to complete a reconstructed embryo. The success rates were 62.6% and 86. 0%, respectively, and enucleation rate was about 73.3% validated by Hoechst 33342. Using this method, the nucleus was completely eliminated and another was injected using the microscope and micromanipulator. Moreover, the efficiency of nuclear transplantation and survival rate of reconstructed embryos were greatly improved. Furthermore, it is very easy to manipulate and popularize in practice.

Factors derived from mouse embryonic stem cells promote self-renewal of goat embryonic stem-like cells.

Goat embryonic stem (ES)-like cells could be isolated from primary materials-inner cell masses (ICMs) and remain undifferentiated for eight passages in a new culture system containing mouse ES cell conditioned medium (ESCCM) and on a feeder layer of mouse embryo fibroblasts (MEFs). However, when cultured in medium without mouse ESCCM, goat ES-like cells could not survive for more than three passages. In addition, no ES-like cells could be obtained when ICMs were cultured on goat embryo fibroblasts or the primary materials-whole goat blastocysts were cultured on MEFs. Goat ES-like cells isolated from ICMs had a normal karyotype and highly expressed alkaline phosphatase. Multiple differentiation potency of the ES-like cells was confirmed by differentiation into neural cells and fibroblast-like cells in vitro. These results suggest that mouse ES cells might secrete factors playing important roles in promoting goat ES-like cells' self-renewal, moreover, the feeder layers and primary materials could also influence the successful isolation of goat ES-like cells.

Efficient differentiation of embryonic stem cells into neurons in glial cell-conditioned medium under attaching conditions.

Embryonic stem (ES) cells can differentiate into neurons in vitro, which provides hope for the treatment of some neurodegenerative diseases through cell transplantation. However, it remains a challenge to efficiently induce ES cells to differentiate into neurons. Here, we show that murine ES cells can efficiently differentiate into neurons when cultured in glial cell-conditioned medium (GCM) under attaching conditions without the formation of embryoid bodies. In comparison with murine embryonic fibroblast-conditioned medium, we found that GCM has a positive effect on limiting the generation of non-neuronal cells, such as astrocytes. In addition, compared with suspension conditions, attaching conditions delay the differentiation process of ES cells.

Inhibitory role of transcription factor COUP-TFII in expression of hTERT in HeLa cells.

OBJECTIVE: To clone and identify the proteins involved in regulating the transcription of hTERT and study the role of genes in both hTERT transcription and telomerase activity. METHODS: The full cDNA of COUP-TFII was cloned from HeLa cDNA library by hTERT promoter-based yeast one-hybrid assay and then in-frame inserted into His-tag fusion expression vector pEK318. The His-tag COUP-TFII fusion proteins were purified by Ni-NTA chromatography. The interaction of COUP-TFII with hTERT promoter in vitro was identified by electrophoretic mobility shift assay and Footprint. The role of COUP-TFII in both hTERT transcription and telomerase activity were probed through Luciferase reporter assay, Northern blot, and TRAP-PCR ELISA. RESULTS: COUP-TFII could firmly bind to the downstream E-box and the other two binding sites in hTERT promoter. Luciferase reporter assay indicated COUP-TFII could suppress hTERT promoter activity and stable introduction of COUP-TFII into HeLa cells also decreased both endogenous hTERT transcription and telomerase activity. CONCLUSION: The human COUP-TFII can firmly bind to hTERT promoter, and inhibit telomerase activity through decreasing hTERT transcription. It will greatly facilitate understanding of telomerase regulation in normal and cancer cells.

The evidences of human orphan receptor COUP-TFII inhibiting telomerase activity through decreasing hTERT transcription.

Activation of hTERT, the human telomerase catalytic subunit, has been implicated as the critical event in triggering telomerase activity of cancer cells, but the details of regulation of hTERT need to be elucidated. By screening HeLa cDNA library with hTERT promoter-based yeast one-hybrid assay, one of positive clones, which potentially interacted with hTERT promoter, contained the full sequences of COUP-TFII cDNA. EMSA showed that the prepared His-tagged COUP-TFII could firmly bind to -201 to +35 fragment of hTERT promoter. The precise binding sites were confirmed by DNase I footprint analysis and proved to involve the E-box motif of hTERT promoter. Luciferase reporter assays indicated that COUP-TFII could suppress the transcription of hTERT promoter, and the inhibition to some extent could be reversed by co-transfection of c-myc. Stable introduction of COUP-TFII into HeLa cells decreased both endogenous hTERT expression and telomerase activity. The results suggested that the human COUP-TFII could specifically interact with hTERT promoter, in part via the E-box, and suppress the expression of hTERT.

Macrophage-associated erythropoiesis and lymphocytopoiesis in mouse fetal liver: ultrastructural and ISH analysis.

To elucidate the process of fetal liver hematopoiesis, the relationships between stroma and hematopoietic cells involved in maturation were investigated. Cultured mouse fetal liver explants were established for morphological analysis of the interactions between fetal liver stroma and hematopoietic cells ex vivo. Fetal liver stroma comprised epithelial cells and macrophages, which occupied most of the culture surface. Macrophages proliferated extensively in primary culture, but almost disappeared after 3 passages. Close morphological and functional relationships were established between macrophages and hemopoietic cells, whereas epithelial cells did not interact with blood cells. Scanning electron microscopy revealed that macrophages were in close contact with erythroblasts and formed a three-dimensional network. In each erythroblastic island, 2-3 lymphocytes were also in contact with the macrophages; erythroblasts, lymphocytes and macrophages formed close, firm associations through their cytoplasmic membranes. This cell orientation was confirmed by transmission electron microscopy of fetal liver in vivo. In situ hybridization revealed that the macrophages expressed jagged-1, an important ligand of the Notch signaling system in hematopoiesis.

Measurement of alkaline phosphatase isoenzymes in individual mouse bone marrow fibroblast cells based on capillary electrophoresis with on-capillary enzyme-catalyzed reaction and electrochemical detection.

A novel method for the determination of alkaline phosphatase (ALP) isoenzymes in individual fibroblast cells of mouse bone marrow was developed by combining capillary electrophoresis with an on-capillary enzyme-catalyzed reaction and electrochemical detection. In this method, a single an cell, followed by 5.0 x 10(-2) mol/L Na2B4O7- 3.0 x 10(-2) mol/L NaCl (pH 9.8) as cell lysis solution, was injected into the inlet of the separation capillary by electromigration. The cell was lysed by applying a voltage of 2 kV. The ALP isoenzymes in the cell were preseparated at 20 kV for 1 min, and then allowed to react for 30 min with disodium phenyl phosphate as enzyme substrate in the running buffer. ALP converted disodium phenyl phosphate into its product, phenol, at a relatively high reaction rate without consumption, with resultant amplification of the signal on prolonged reaction time, producing an adequate amount of product for final detection. A mass detection limit as low as 3.5 x 10(-21) mol/L (corresponding to 1.5 nU) was achieved. Finally, the two zones of products generated by ALP isoenzymes were detected at the outlet of the capillary by using the end-capillary amperometric detection at a carbon fiber microdisk bundle electrode with a constant potential.

Viral replication modulated by synthetic peptide derived from hepatitis B virus X protein.

AIM: A strategy for viral vaccine design is the use of conserved peptides to overcome the problem of sequence diversity. At present it is still unclear whether conserved peptide is safe as a candidate vaccine. We reported it here for the first time not only to highlight the biohazard issue and safety importance for viral peptide vaccine, but also to explore the effect of a fully conserved peptide on HBV replication within the carboxyl terminus of HBx. METHODS: We synthesized the fully conserved peptide (CP) with nine residues, FVLGGCRHK. HBV-producing 2.2.15 cells were treated with or without 3.5 microM CP for 36 hours. Quantitative detection of viral DNA was performed by real-time PCR. HBV antigens were determined by enzyme-linked immunoadsorbent assay (ELISA). Quantitative analyses of p53 and Bax proteins were based on immunofluorescence. Flow cytometry was performed to detect cell cycle and apoptosis. RESULTS: Both extracellular and intracellular copies of HBV DNA per ml were significantly increased after incubation with 3.5 microM of CP. HBsAg and HBeAg in the cultured medium of CP-treatment cells were as abundant as untreated control cells. CP influenced negatively the extracellular viral gene products, and 3.5 microM CP could significantly inhibit intracellular HBsAg expression. In response to CP, intracellular HBeAg displayed an opposite pattern to that of HBsAg, and 3.5 microM CP could efficiently increase the level of intracellular HBeAg. Flow cytometric analyses exhibited no significant changes on cell cycle, apoptosis, p53 and Bax proteins in 2.2.15 cells with or without CP. CONCLUSION: Together with the results generated from the synthetic peptide, we address that the conserved region, a domain of HBx, may be responsible for modulating HBV replication. As conserved peptides from infectious microbes are used as immunogens to elicit immune responses, their latent biological hazard for human beings should be evaluated.