Effects of the sesquiterpene lactone parthenolide on prostate tumor-initiating cells: An integrated molecular profiling approach.

Recent evidence suggests tumor-initating cells (TICs), also called cancer stem cells, are responsible for tumor initiation and progression; therefore, they represent an important cell population for development of future anti-cancer therapies. In this study, we show that the sesquiterpene lactone parthenolide (PTL) is cytotoxic to prostate TICs isolated from prostate cancer cell lines: DU145, PC3, VCAP, and LAPC4, as well as primary prostate TICs. Furthermore, PTL inhibited TIC-driven tumor formation in mouse xenografts.

A cell-based high-throughput screen to identify synergistic TRAIL sensitizers.

We have developed a high-throughput screen (HTS) to search for novel molecules that can synergize with TRAIL, thus promoting apoptosis of ACHN renal tumor cells in a combinatorial fashion. The HTS detects synthetic compounds and pure natural products that can pre-sensitize the cancer cells to TRAIL-mediated apoptosis, yet have limited toxicity on their own. We have taken into account the individual effects of the single agents, versus the combination, and have identified hits that are synergistic, synergistic-toxic, or additive when combined with TRAIL in promoting tumor cell death.

Cross-reactive HIV-1-neutralizing activity of serum IgG from a rabbit immunized with gp41 fused to IgG1 Fc: possible role of the prolonged half-life of the immunogen.

The elicitation of broadly cross-reactive HIV-1 neutralizing antibodies in humans remains a major challenge in developing a viable AIDS vaccine. We hypothesized that prolonged exposure to candidate vaccine immunogens could enhance the elicitation of such antibodies. In an attempt to develop HIV-1 vaccine immunogens with prolonged half-lives and increased stability, we constructed a fusion protein, gp41Fc, in which a truncated HIV-1 gp41(89.

Site-specific linking of biomolecules via glycan residues using glycosyltransferases.

The structural information on glycosyltransferases has revealed that the sugar-donor specificity of these enzymes can be broadened to include modified sugars with a chemical handle that can be utilized for conjugation chemistry. Substitution of Tyr289 to Leu in the catalytic pocket of bovine beta-1,4-galactosyltransferase generates a novel glycosyltransferase that can transfer not only Gal but also GalNAc or a C2-modified galactose that has a chemical handle, from the corresponding UDP-derivatives, to the non-reducing end GlcNAc residue of a glycoconjugate. Similarly, the wild-type polypeptide-N-acetyl-galactosaminyltransferase, which naturally transfers GalNAc from UDP-GalNAc, can also transfer C2-modified galactose with a chemical handle from its UDP-derivative to the Ser/Thr residue of a polypeptide acceptor substrate that is tagged as a fusion peptide to a non-glycoprotein.

Novel method for in vitro O-glycosylation of proteins: application for bioconjugation.

Here, we describe a new method for the bioconjugation of a nonglycoprotein with biomolecules. Using polypeptide-alpha- N-acetylgalactosaminyltransferase II (ppGalNAc-T2), we transfer a C2-modified galactose that has a chemical handle, such as ketone or azide, from its respective UDP-sugars to the Ser/Thr residue(s) of an acceptor polypeptide fused to the nonglycoprotein. The protein with the modified galactose is then coupled to a biomolecule that carries an orthogonal reactive group.

RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign.

We developed a database called RNAJunction that contains structure and sequence information for RNA structural elements such as helical junctions, internal loops, bulges and loop-loop interactions. Our database provides a user-friendly way of searching structural elements by PDB code, structural classification, sequence, keyword or inter-helix angles. In addition, the structural data was subjected to energy minimization.

Mouse Ripply2 is downstream of Wnt3a and is dynamically expressed during somitogenesis.

Somites are blocks of mesoderm that form when segment boundaries are periodically generated in the anterior presomitic mesoderm (PSM). Periodicity is thought to be driven by an oscillating Notch-centered segmentation clock, whereas boundaries are spatially positioned by the secreted signaling molecules Wnt3a and Fgf8. We identified the putative transcriptional corepressor Ripply2 as a differentially expressed gene in wild-type and Wnt3a(-/-) embryos.

Trinucleotide cassettes increase diversity of T7 phage-displayed peptide library.

Background: Amino acid sequence diversity is introduced into a phage-displayed peptide library by randomizing library oligonucleotide DNA. We recently evaluated the diversity of peptide libraries displayed on T7 lytic phage and M13 filamentous phage and showed that T7 phage can display a more diverse amino acid sequence repertoire due to differing processes of viral morphogenesis.

Methods: In this study, we evaluated and compared the diversity of a 12-mer T7 phage-displayed peptide library randomized using codon-corrected trinucleotide cassettes with a T7 and an M13 12-mer phage-displayed peptide library constructed using the degenerate codon randomization method.

Functional and genomic analyses of FOXP3-transduced Jurkat-T cells as regulatory T (Treg)-like cells.

FOXP3, a forkhead transcription factor is essential for the development and function of CD4(+)CD25(+) regulatory T cells (Tregs). In contrast to conversion of murine naive T cells to Tregs by transduction of Foxp3, it is controversial whether ectopic expression of FOXP3 in human CD4(+) T cells is sufficient for acquisition of suppressive activity. Here, we show that retroviral transduction of FOXP3 induces a Treg phenotype in human leukemic CD4(+) Jurkat-T cells, evidenced by increased expression of Treg-associated cell surface markers as well as inhibition of cytokine production.

Genome-wide association study of prostate cancer identifies a second risk locus at 8q24.

Recently, common variants on human chromosome 8q24 were found to be associated with prostate cancer risk. While conducting a genome-wide association study in the Cancer Genetic Markers of Susceptibility project with 550,000 SNPs in a nested case-control study (1,172 cases and 1,157 controls of European origin), we identified a new association at 8q24 with an independent effect on prostate cancer susceptibility. The most significant signal is 70 kb centromeric to the previously reported SNP, rs1447295, but shows little evidence of linkage disequilibrium with it.

Bridging the gap in RNA structure prediction.

The field of RNA structure prediction has experienced significant advances in the past several years, thanks to the availability of new experimental data and improved computational methodologies. These methods determine RNA secondary structures and pseudoknots from sequence alignments, thermodynamics-based dynamic programming algorithms, genetic algorithms and combined approaches. Computational RNA three-dimensional modeling uses this information in conjunction with manual manipulation, constraint satisfaction methods, molecular mechanics and molecular dynamics.

Direct identification of nonreducing GlcNAc residues on N-glycans of glycoproteins using a novel chemoenzymatic method.

The mutant beta1,4-galactosyltransferase (beta4Gal-T1), beta4Gal-T1-Y289L, in contrast to wild-type beta4Gal-T1, can transfer GalNAc from the sugar donor UDP-GalNAc to the acceptor, GlcNAc, with efficiency as good as that of galactose from UDP-Gal. Furthermore, the mutant can also transfer a modified sugar, C2 keto galactose, from its UDP derivative to O-GlcNAc modification on proteins that provided a functional handle for developing a highly sensitive chemoenzymatic method for detecting O-GlcNAc post-translational modification on proteins. We report herein that the modified sugar, C2 keto galactose, can be transferred to free GlcNAc residues on N-linked glycoproteins, such as ovalbumin or asialo-agalacto IgG1.

Compressing drug development timelines in oncology using phase '0' trials.

The optimal evaluation of molecularly targeted anticancer agents requires the integration of pharmacodynamic assays into early clinical investigations. Phase '0' trials conducted under the new Exploratory Investigational New Drug Guidance from the US Food and Drug Administration can provide a platform to establish the feasibility of assays for target modulation in human samples, evaluate biomarkers for drug effects and provide pharmacokinetic data. Phase 0 trials could facilitate rational drug selection, identify therapeutic failures early, and might compress timelines for anticancer drug development.

Utilization of achiral alkenyl amines for the preparation of high affinity Grb2 SH2 domain-binding macrocycles by ring-closing metathesis.

A family of previously reported ring-closing metathesis (RCM)-derived macrocycles that exhibit potent Grb2 SH2 domain-binding affinity is characterized by stereoselectively-introduced upper ring junctions that bear bicyclic aryl substituents. However, the synthetic complexity of these macrocycles presents a potential limit to their therapeutic application. Therefore, the current study was undertaken to simplify these macrocycles through the use of achiral 4-pentenylamides as ring-forming components.

Consensus features in amyloid fibrils: sheet-sheet recognition via a (polar or nonpolar) zipper structure.

Amyloid fibrils characterized as highly intractable thread-like species are associated with many neurodegenerative diseases. Although neither the mechanism of amyloid formation nor the origin of amyloid toxicity is currently completely understood, the detailed three-dimensional atomic structures of the yeast protein Sup35 and Abeta amyloid protein determined by recent experiments provide the first and important step towards the comprehension of the pathogenesis and aggregation mechanisms of amyloid diseases. By analyzing these two amyloid peptides which have available crystal structures and other amyloid sequences with proposed structures using computational simulations, we delineate three common features in amyloid organizations and amyloid structures.

Design and synthesis of phosphonodifluoromethyl phenylalanine (F2Pmp): a useful phosphotyrosyl mimetic.

Hydrolytically-stable phosphotyrosyl (pTyr) mimetics can be useful tools for the study of cellular signal transduction processes. Among pTyr mimetics reported to date, phosphono(diflouromethyl)phenylalanine (F(2)Pmp) has shown particular utility when dealing with protein-tyrosine phosphatases (PTPs). The current overview presents the development of F(2)Pmp and a summary of approaches toward its synthesis and use.

Vascular defects and liver damage by the acute inactivation of the VHL gene during mouse embryogenesis.

Inactivation of the von Hippel-Lindau (VHL) tumor suppressor gene leads to the development of central nervous system hemangioblastomas, pheochromocytomas and renal cell carcinomas. The biological role of the VHL gene during development is poorly understood because of early lethality of VHL-null embryos. To overcome early embryo lethality observed in the conventional knockout mouse, we introduced a tamoxifen-inducible Cre (CreER(TM)) transgene for the stage specific inactivation of the VHL gene.

Comparison of the human and worm p53 structures suggests a way for enhancing stability.

Maintaining the native conformation is essential for the proper function of tumor suppressor protein p53. However, p53 is a low-stability protein that can easily lose its function upon structural perturbations such as those resulting from missense mutations, leading to the development of cancer. Therefore, it is important to develop strategies to design stable p53 which still maintains its normal function.

Recombinant production of anti-HIV protein, griffithsin, by auto-induction in a fermentor culture.

Griffithsin (GRFT) is a novel anti-HIV protein isolated from the red alga Griffithia sp. The potent anti-viral activity of GRFT against both laboratory and primary isolates of HIV at picomolar concentrations makes this protein an attractive candidate microbicide to prevent sexual transmission of HIV. Here, we describe the recombinant production and purification of a biologically active hexa-histidine-tagged GRFT (His-GRFT) from Escherichia coli.

Carbohydrate array analysis of anti-Tn antibodies and lectins reveals unexpected specificities: implications for diagnostic and vaccine development.

The Tn antigen is a carbohydrate antigen expressed in most carcinomas, during embryogenesis, on pathogenic parasites, and on HIV. It has been evaluated extensively as a potential diagnostic marker and several Tn-based vaccines are in clinical trials. Based on discrepancies in the literature regarding Tn expression, we began to question whether antibodies and lectins used routinely to detect the Tn antigen were providing accurate information.

Isolation and characterization of griffithsin, a novel HIV-inactivating protein, from the red alga Griffithsia sp.

Griffithsin (GRFT), a novel anti-HIV protein, was isolated from an aqueous extract of the red alga Griffithsia sp. The 121-amino acid sequence of GRFT has been determined, and biologically active GRFT was subsequently produced by expression of a corresponding DNA sequence in Escherichia coli. Both native and recombinant GRFT displayed potent antiviral activity against laboratory strains and primary isolates of T- and M- tropic HIV-1 with EC50 values ranging from 0.

Co-operative functions between nuclear factors NFkappaB and CCAT/enhancer-binding protein-beta (C/EBP-beta) regulate the IL-6 promoter in autocrine human prostate cancer cells.

Background: IL-6 is a growth and survival factor for prostate cancer cells through autocrine pathways. Here, we have systematically examined the transcriptional regulation mechanisms of IL-6 in autocrine prostate cancer cells.

Methods: RT-PCR and immunohistochemical staining were used to determine IL-6 production in the cells.

Epigenetic Up-regulation of Gene Expression in KAS 6/1 Human Multiple Myeloma Cells.

Cytosine methylation, an epigenetic form of regulating gene transcription, has gained importance upon the discovery that genes involved in the carcinogenic process may be regulated by this mechanism and, moreover, that certain cancers respond to treatment with demethylation-promoting drugs. Typically, the use of DNA methyltransferase inhibitor drugs results in the up-regulation of important tumor suppressor genes, previously down-regulated by the existence of abnormal cytosine methylation within their promoters. Here, we show microarray and RT-PCR results indicating that many genes are down-regulated upon treatment of KAS 6/1 multiple myeloma cells with Zebularine, a demethylating agent.

Structure of monellin refined to 2.3 a resolution in the orthorhombic crystal form.

The structure of orthorhombic crystals of monellin, a sweet protein extracted from African serendipity berries, has been solved by molecular replacement and refined to 2.3 A resolution. The final R factor was 0.

An expanding appreciation of the role chemokine receptors play in cancer progression.

The contribution of small molecular weight chemoattractant cytokines (chemokines) and their receptors in the trafficking of tumor, immune and vascular cells pertaining to the development and progression of cancer has begun to be investigated. The current literature indicates that interactions between the immune network, angiogenic and cell survival cascades are important for the trafficking and progression of human cancer and that chemokines and chemokine receptors play a central role in these complex inter-related pathways. Several therapeutic approaches have been reviewed and suggest that the most promising arise from the development of combinations of chemokine receptor antagonists.