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Airway hyperresponsiveness (AHR) is a major clinical problem in allergic asthma mainly caused by the hypercontractility of airway smooth muscles (ASM). S100A8 is an important member of the S100 calcium-binding protein family with a potential to regulate cell contractility. Here, we analyze the potential of S100A8 to regulate allergen-induced AHR and ASM contraction. Treatment with recombinant S100A8 (rS100A8) diminished airway hyperresponsiveness in OVA-sensitized rats. ASM contraction assays showed that rS100A8 reduced hypercontractility in both isolated tracheal rings and primary ASM cells treated by acetylcholine. rS100A8 markedly rescued the phosphorylation level of myosin light chain induced by acetylcholine in ASM cells. These results show that rS100A8 plays a protective role in regulating AHR in asthma by inhibiting ASM contraction. These results support S100A8 as a novel therapeutic target to control ASM contraction in asthma. [ABSTRACT FROM AUTHOR]

S100A8 is an important member of the S100 protein family, which is involved in intracellular and extracellular regulatory activities. We previously reported that the S100A8 protein was differentially expressed in the asthmatic respiratory tracts. To understand the potential role of S100A8 in asthma, we investigated the effect of recombinant S100A8 protein on the platelet-derived growth factor (PDGF)-induced migration of airway smooth muscle cells (ASMCs) and the underlying molecular mechanism by using multiple methods, such as impedance-based xCELLigence migration assay, transwell migration assays and wound-healing assays. We found that exogenous S100A8 protein significantly inhibited PDGF-induced ASMC migration. Furthermore, the migration inhibition effect of S100A8 was blocked by neutralizing antibody against the receptor for advanced glycation end-products (RAGE), a potential receptor for the S100A8 protein. These findings provide direct evidence that exogenous S100A8 protein inhibits the PDGF-induced migration of ASMCs through the membrane receptor RAGE. Our study highlights a novel role of S100A8 as a potential means of counteracting airway remodeling in chronic airway diseases. [ABSTRACT FROM AUTHOR]

Abstract: Cytotoxicity and DNA double strand breaks (DSBs) were studied in HeLa cells treated with sulforaphane (SFN), a well-known chemo-preventive agent. Cell survival was impaired by SFN in a concentration and treatment time-dependent manner. Both constant field gel electrophoresis (CFGE) and γ-H2AX assay unambiguously indicated formation of DSBs by SFN, reflecting the cell survival data. These DSBs were predominantly processed by homologous recombination repair (HRR), judging from the SFN concentration-dependent manner of Rad51 foci formation. On the other hand, the phosphorylation of DNA-PKcs, a key non-homologous end joining (NHEJ) protein, was not observed by SFN treatment, suggesting that NHEJ may not be involved in DSBs induced by this chemical. G2/M arrest by SFN, a typical response for cells exposed to ionizing radiation was also observed. Our new data indicate the clear induction of DSBs by SFN and a useful anti-tumor aspect of SFN through the induction of DNA DSBs. [Copyright &y& Elsevier]

Abstract: Methionine aminopeptidase and N-terminal acetyltransferase are two enzymes that contribute most to the N-terminal acetylation, which has long been recognized as a frequent and important kind of co-translational modifications [R.A. Bradshaw, W.W. Brickey, K.W. Walker, N-terminal processing: the methionine aminopeptidase and N alpha-acetyl transferase families, Trends Biochem. Sci. 23 (1998) 263–267]. The combined action of these two enzymes leads to two types of N-terminal acetylated proteins that are with/without the initiator methionine after the N-terminal acetylation. To accurately predict these two types of N-terminal acetylation, a new method based on feature selection has been developed. 1047 N-terminal acetylated and non-acetylated decapeptides retrieved from Swiss-Prot database (http://cn.expasy.org) are encoded into feature vectors by amino acid properties collected in Amino Acid Index database (http://www.genome.jp/aaindex). The Maximum Relevance Minimum Redundancy method (mRMR) combining with Incremental Feature Selection (IFS) and Feature Forward Selection (FFS) is then applied to extract informative features. Nearest Neighbor Algorithm (NNA) is used to build prediction models. Tested by Jackknife Cross-Validation, the correct rate of predictors reach 91.34% and 75.49% for each type, which are both better than that of 84.41% and 62.99% acquired by using motif methods [S. Huang, R.C. Elliott, P.S. Liu, R.K. Koduri, J.L. Weickmann, J.H. Lee, L.C. Blair, P. Ghosh-Dastidar, R.A. Bradshaw, K.M. Bryan, et al., Specificity of cotranslational amino-terminal processing of proteins in yeast, Biochemistry 26 (1987) 8242–8246; R. Yamada, R.A. Bradshaw, Rat liver polysome N alpha-acetyltransferase: substrate specificity, Biochemistry 30 (1991) 1017–1021]. Furthermore, the analysis of the informative features indicates that at least six downstream residues might have effect on the rules that guide the N-terminal acetylation, besides the penultimate residue. The software is available upon request. [Copyright &y& Elsevier]

Abstract: Insulin-like growth factor I receptor (IGF-IR) is a transmembrane receptor tyrosine kinase whose activation strongly promotes cell growth and survival. We previously reported that IGF-IR activity confers intrinsic radioresistance in mouse embryo fibroblasts in vitro. However, it is still unclear whether tumor cells overexpressing IGF-IR exhibit radioresistance in vivo. For this purpose, we established HeLa cells that overexpress IGF-IR (HeLa-R), subcutaneously transplanted these cells into nude mice, and examined radioresponse in the resulting solid tumors. HeLa-R cells exhibited typical in vitro phenotypes generally observed in IGF-IR-overexpressing cells, as well as significant intrinsic radioresistance in vitro compared with parent cells. As expected, the transplanted HeLa-R tumors grew at a remarkably higher rate than parent tumors. Histological analysis revealed that HeLa-R tumors expressed more VEGF and had a higher density of tumor vessels. Unexpectedly, a marked growth delay was observed in HeLa-R tumors following 10Gy of X-irradiation. Immunostaining of HeLa-R tumors for the hypoxia marker pimonidazole revealed a significantly lower level of hypoxic cells. Moreover, clamp hypoxia significantly increased radioresistance in HeLa-R tumors. Tumor microenvironments in vivo generated by the IGF-IR expression thus could be a major factor in determining the tumor radioresponse in vivo. [Copyright &y& Elsevier]

Abstract: In order to investigate the mechanism of radio-sensitization by an Hsp90 inhibitor 17-allylamino-17-demethoxygeldanamycin (17-AAG), we studied repair of DNA double strand breaks (DSBs) in irradiated human cells pre-treated with 17-AAG. DSBs are thought to be the critical target for radiation-induced cell death. Two human tumor cell lines DU145 and SQ-5 which showed clear radio-sensitization by 17-AAG revealed a significant inhibition of DSB repair, while normal human cells which did not show radio-sensitization by the drug indicated no change in the DSB repair kinetics with 17-AAG. We further demonstrated that BRCA2 was a novel client protein for Hsp90, and 17-AAG caused the degradation of BRCA2 and in turn altered the behavior of Rad51, a critical protein for homologous recombination (HR) pathway of DSB repair. Our data demonstrate for the first time that 17-AAG inhibits the HR repair process and could provide a new therapeutic strategy to selectively result in higher tumor cell killing. [Copyright &y& Elsevier]

Abstract: Transcription factor binds to sequence specific sites in regulatory region to control nearby gene’s expression. It is termed as the major regulator of transcription. However, identifying DNA binding preference of transcription factors systematically is still a challenge. By using the nearest neighbor algorithm, a novel computational approach was developed to predict transcription factor DNA binding preference based on the gene ontology [M. Ashburner, C.A. Ball, J.A. Blake, D. Botstein, H. Butler, J.M. Cherry, A.P. Davis, K. Dolinski, S.S. Dwight, J.T. Eppig, M.A. Harris, D.P. Hill, L. Issel-Tarver, A. Kasarskis, S. Lewis, J.C. Matese, J.E. Richardson, M. Ringwald, G.M. Rubin, G. Sherlock, Gene Ontology: tool for the unification of biology, Nat. Genet. 25 (2000) 25–29.] and 0/1 encoding system of nucleotide. The overall success rate of Jackknife cross-validation test for our predictor reaches 76.6%, which indicates the DNA binding preference is closely correlated with its biological functions and computational method developed in this contribution could be a powerful tool to investigate transcription factor DNA binding preference, especially for those novel transcription factors with little prior knowledge on its DNA binding preference. [Copyright &y& Elsevier]

Abstract: To understand the transcriptional regulatory mechanism, it is indispensable to identify transcription factors (TF) from the whole genome and to classify transcription factors into different classes. New computational approaches have been developed to identify TFs/non-TFs, and furthermore to classify TFs into four different classes, based on the protein functional domain composition [K.C. Chou, Y.D. Cai, Using functional domain composition and support vector machines for prediction of protein subcellular location, J. Biol. Chem. 277 (2002) 45765–45769]. We trained and tested our method on a non-redundancy dataset consisting of 74 transcription factors collected from TRANSFAC v7.0 [V. Matys, O.V. Kel-Margoulis, E. Fricke, I. Liebich, S. Land, A. Barre-Dirrie, I. Reuter, D. Chekmenev, M. Krull, K. Hornischer, N. Voss, P. Stegmaier, B. Lewicki-Potapov, H. Saxel, A.E. Kel, E. Wingender, TRANSFAC(R) and its module TRANSCompel(R): transcriptional gene regulation in eukaryotes, Nucleic Acids Res. 34 (2006) D108–D110] and 1558 non-transcription factors from UniProtKB/Swiss-Prot Release 49.3 of 21-Mar-2006. The overall success rates of jackknife cross-validation tests reached 98.4% for TF/non-TF identification and 97.2% for classifications of TF classes: basic domains, zinc-coordinating DNA-binding domains, helix-turn-helix, and β-scaffold factors. [Copyright &y& Elsevier]

Abstract: Regulating most physiological processes by controlling the activation, synthesis, and turnover of proteins, proteases play pivotal regulatory roles in conception, birth, digestion, growth, maturation, ageing, and death of all organisms. Different types of proteases have different functions and biological processes. Therefore, it is important for both basic research and drug discovery to consider the following two problems. (1) Given the sequence of a protein, can we identify whether it is a protease or non-protease? (2) If it is, what protease type does it belong to? Although the two problems can be solved by various experimental means, it is both time-consuming and costly to do so. The avalanche of protein sequences generated in the post-genetic era has challenged us to develop an automated method for making a fast and reliable identification. By hybridizing the functional domain composition and pseudo-amino acid composition, we have introduced a new method called “FunD-PseAA predictor” that is operated in a hybridization space. To avoid redundancy and bias, demonstrations were performed on a dataset where none of the proteins has ⩾25% sequence identity to any other. The overall success rate thus obtained by the jackknife cross-validation test in identifying protease and non-protease was 92.95%, and that in identifying the protease type was 94.75% among the following six types: (1) aspartic, (2) cysteine, (3) glutamic, (4) metallo, (5) serine, and (6) threonine. Demonstration was also made on an independent dataset, and the corresponding overall success rates were 98.36% and 97.11%, respectively, suggesting the FunD-PseAA predictor is very powerful and may become a useful tool in bioinformatics and proteomics. [Copyright &y& Elsevier]

Abstract: Pigment epithelium-derived factor (PEDF) is acknowledged to be a non-inhibitory member of the serine protease inhibitor (serpin) superfamily, with antiangiogenesis, and neuroprotective and immunoregulatory function, mainly in the tissues of nervous system. Here, A PEDF gene homolog, Paralichthys olivaceus PEDF (PoPEDF), was isolated from flounder embryonic cells (FEC) treated with UV-inactivated Grass carp hemorrhage virus (GCHV) and subsequently identified as a differentially expressed gene. The full length of PoPEDF cDNA is 1803bp with an open reading frame of 1212bp encoding a 403-amino-acid protein. This deduced protein contains an N-terminal signal peptide, a glycosylation site, a consensus serpin motif, and a 34-mer and a 44-mer fragment, all of which are very conserved in the PEDF family. PoPEDF gene exhibits a conserved exon–intron arrangement with 8 exons and 7 introns. This conserved evolutionary relationship was further confirmed by a phylogenetic analysis, where fish PEDFs and mammalian members formed a well-supported clade. Constitutive expression of PoPEDF was widely detected in many tissues. In response to UV-inactivated GCHV or poly(I:C), PEDF mRNA was upregulated in FEC cells with time. This is the first report on the transcriptional induction of PEDF in virally infected cells. [Copyright &y& Elsevier]

Abstract: A novel classifier, the so-called “LogitBoost” classifier, was introduced to predict the structural class of a protein domain according to its amino acid sequence. LogitBoost is featured by introducing a log-likelihood loss function to reduce the sensitivity to noise and outliers, as well as by performing classification via combining many weak classifiers together to build up a very strong and robust classifier. It was demonstrated thru jackknife cross-validation tests that LogitBoost outperformed other classifiers including “support vector machine,” a very powerful classifier widely used in biological literatures. It is anticipated that LogitBoost can also become a useful vehicle in classifying other attributes of proteins according to their sequences, such as subcellular localization and enzyme family class, among many others. [Copyright &y& Elsevier]

Enzyme function is much less conserved than anticipated, i.e., the requirement for sequence similarity that implies similarity in enzymatic function is much higher than the requirement that implies similarity in protein structure. This is because the function of an enzyme is an extremely complicated problem that may involve very subtle structural details as well as many other physical chemistry factors. Accordingly, if simply based on the sequence similarity approach, it would hardly get a decent success rate in predicting enzyme sub-class even for a dataset consisting of samples with ⩾50% sequence identity. To cope with such a situation, the GO-PseAA predictor was adopted to identify the sub-class for each of the six main enzyme families. It has been observed that, even for the much more stringent datasets in which none of the enzymes has ⩾25% sequence identity to any others, the overall success rates are 73–95%, suggesting that the GO-PseAA predictor can catch the core features of the statistical samples concerned and may become a useful high throughput tool in proteomics and bioinformatics. [Copyright &y& Elsevier]

According to the recent experiments, proteins in budding yeast can be distinctly classified into 22 subcellular locations. Of these proteins, some bear the multi-locational feature, i.e., occur in more than one location. However, so far all the existing methods in predicting protein subcellular location were developed to deal with only the mono-locational case where a query protein is assumed to belong to one, and only one, subcellular location. To stimulate the development of subcellular location prediction, an augmentation procedure is formulated that will enable the existing methods to tackle the multi-locational problem as well. It has been observed thru a jackknife cross-validation test that the success rate obtained by the augmented GO-FnD-PseAA algorithm [BBRC 320 (2004) 1236] is overwhelmingly higher than those by the other augmented methods. It is anticipated that the augmented GO-FunD-PseAA predictor will become a very useful tool in predicting protein subcellular localization for both basic research and practical application. [Copyright &y& Elsevier]

The localization of a protein in a cell is closely correlated with its biological function. With the explosion of protein sequences entering into DataBanks, it is highly desired to develop an automated method that can fast identify their subcellular location. This will expedite the annotation process, providing timely useful information for both basic research and industrial application. In view of this, a powerful predictor has been developed by hybridizing the gene ontology approach [Nat. Genet. 25 (2000) 25], functional domain composition approach [J. Biol. Chem. 277 (2002) 45765], and the pseudo-amino acid composition approach [Proteins Struct. Funct. Genet. 43 (2001) 246; Erratum: ibid. 44 (2001) 60]. As a showcase, the recently constructed dataset [Bioinformatics 19 (2003) 1656] was used for demonstration. The dataset contains 7589 proteins classified into 12 subcellular locations: chloroplast, cytoplasmic, cytoskeleton, endoplasmic reticulum, extracellular, Golgi apparatus, lysosomal, mitochondrial, nuclear, peroxisomal, plasma membrane, and vacuolar. The overall success rate of prediction obtained by the jackknife cross-validation was 92%. This is so far the highest success rate performed on this dataset by following an objective and rigorous cross-validation procedure. [Copyright &y& Elsevier]

Based on the recent development in the gene ontology and functional domain databases, a new hybridization approach is developed for predicting protein subcellular location by combining the gene product, functional domain, and quasi-sequence-order effects. As a showcase, the same prokaryotic and eukaryotic datasets, which were studied by many previous investigators, are used for demonstration. The overall success rate by the jackknife test for the prokaryotic set is 94.7% and that for the eukaryotic set 92.9%. These are so far the highest success rates achieved for the two datasets by following a rigorous cross-validation test procedure, suggesting that such a hybrid approach may become a very useful high-throughput tool in the area of bioinformatics, proteomics, as well as molecular cell biology. The very high success rates also reflect the fact that the subcellular localization of a protein is closely correlated with: (1) the biological objective to which the gene or gene product contributes, (2) the biochemical activity of a gene product, and (3) the place in the cell where a gene product is active. [Copyright &y& Elsevier]

Available evidence suggests that insulin-like growth factor I receptor (IGF-IR) expression leads to increased cellular radioresistance. The most direct explanation of these findings predicts that IGF-IR is the source of survival signals in resistant cells. Mutational analysis revealed that protein truncated at amino acid 1245 in the C-terminus retained the ability of IGF-IR to confer radioresistance whereas point mutations at both Tyr-1250 and Tyr-1251 abrogated this effect using IGF-IR-deficient mouse embryo fibroblasts (R−) as a recipient. In cells expressing the latter mutant receptors, both phosphatidylinositol-3′ kinase (PI3-K) and mitogen-activated protein kinase (MAPK) signaling pathways remained intact, and addition of exogenous IGF-I could not change the radiosensitivity of these cells. Further analysis indicated that the abrogation of radioresistance required the presence of His-1293 and Lys-1294. These results suggest a novel regulatory role of the C-terminus of IGF-IR in mediating cellular radioresistance that may be independent of survival signals transmitted through this receptor. [Copyright &y& Elsevier]

In this paper, based on the approach by combining the “functional domain composition” [K.C. Chou, Y. D. Cai, J. Biol. Chem. 277 (2002) 45765] and the pseudo-amino acid composition [K.C. Chou, Proteins Struct. Funct. Genet. 43 (2001) 246; Correction Proteins Struct. Funct. Genet. 2044 (2001) 2060], the Nearest Neighbour Algorithm (NNA) was developed for predicting the protein subcellular location. Very high success rates were observed, suggesting that such a hybrid approach may become a useful high-throughput tool in the area of bioinformatics and proteomics. [Copyright &y& Elsevier]

Bacterial and synthetic DNAs, containing CpG dinucleotides in specific sequence contexts, activate the vertebrate immune system. Unlike phosphorothioate (PS) CpG DNAs, phosphodiester (PO) CpG DNAs require either palindromic sequences and/or poly(dG) sequences at the 3′-end for activity. Here, we report `PO-immunomers'' having two PO-CpG DNA molecules joined through their 3′-ends. These PO-imunomers permitted us, for the first time, to assess immunostimulatory properties of PO-CpG DNAs in vitro and in vivo without the need for palindromic and/or poly(dG) sequences. In medium containing 10% fetal bovine serum, PO-immunomers were more resistant than PO-CpG DNAs to nucleases. Compared to PS-CpG DNA in BALB/c and C3H/HeJ mice spleen cell culture assays, PO-immunomers showed increased IL-12 secretion and minimal amounts of IL-6 secretion. PO-immunomers activated NF-κB and induced cytokine secretion in J774 cell cultures. In addition, PO-immunomers showed antitumor activity in nude mice bearing human breast (MCF-7) and prostate (DU145) cancer xenografts. [Copyright &y& Elsevier]

Nijmegen breakage syndrome (NBS) is an autosomal recessive disorder sharing a pleiotropic phenotype with ataxia-telangiectasia (A-T), including increased radiosensitivity and cancer disposition. Insulin-like growth factor I receptor (IGF-IR) expression is reportedly decreased in A-T cells, which is thought to contribute to its increased radiosensitivity. In this study, we investigated whether the same mechanism underlies the radiosensitivity of NBS cells. GM7166VA7 cells lacking NBS1 protein displayed a phenotype of increased radiosensitivity, while the introduction of NBS1 cDNA conferred radioresistance comparable to normal cells. IGF-IR expression levels were essentially the same among normal, NBS, and NBS1-complemented NBS cells. There was no significant difference between NBS and NBS1-complemented cells in activation of major downstream pathways of IGF-IR upon IGF-I stimulation, including phosphatidylinositol-3′ kinase (PI3-K) and mitogen-activated protein kinase (MAPK). Collectively, IGF-IR-related events are unlikely to be disrupted in NBS cells, and therefore, defects in IGF-IR signaling do not explain the increased radiosensitivity of NBS cells. [Copyright &y& Elsevier]

Abstract: Cell membranes are crucial to the life of a cell. Although the basic structure of biological membrane is provided by the lipid bilayer, most of the specific functions are carried out by membrane proteins. Knowledge of membrane protein type often offers important clues toward determining the function of an uncharacterized protein. Therefore, predicting the type of a membrane protein from its primary sequence, or even just identifying whether the uncharacterized protein belongs to a membrane protein or not, is an important and challenging problem in bioinformatics and proteomics. To deal with these problems, the GO-PseAA predictor is introduced that is operated in a hybridization space by combining the gene ontology and pseudo amino acid composition. Meanwhile, to test the prediction quality, a dataset was constructed that contains 6476 non-membrane proteins and 5122 membrane proteins classified into five different types. To avoid redundancy and bias, none of the proteins included has ⩾40% sequence identity to any other. It has been observed that the overall success rate by the jackknife cross-validation test in identifying non-membrane proteins and membrane proteins was 94.76%, and that in identifying the five membrane protein types was 95.84%. The high success rates suggest that the GO-PseAA predictor can catch the core feature of the statistical samples concerned and may become an automated high throughput toll in molecular and cell biology. [Copyright &y& Elsevier]

The functional domain composition is introduced to predict the structural class of a protein or domain according to the following classification: all-α, all-β, α/β, α+β, μ (multi-domain), σ (small protein), and ρ (peptide). The advantage by doing so is that both the sequence-order-related features and the function-related features are naturally incorporated in the predictor. As a demonstration, the jackknife cross-validation test was performed on a dataset that consists of proteins and domains with only less than 20% sequence identity to each other in order to get rid of any homologous bias. The overall success rate thus obtained was 98%. In contrast to this, the corresponding rates obtained by the simple geometry approaches based on the amino acid composition were only 36–39%. This indicates that using the functional domain composition to represent the sample of a protein for statistical prediction is very promising, and that the functional type of a domain is closely correlated with its structural class. [Copyright &y& Elsevier]

Chronic hepatitis is a major cause of liver cancer, so earlier treatment of hepatitis might be reducing liver cancer incidence. Hepatitis can be induced in mice by treatment with Concanavalin A (Con A); the resulting liver injury causes significant CD4 + T cell activation and infiltration. In these T cells, Roquin, a ring-type E3 ubiquitin ligase, is activated. To investigate the role of Roquin, we examined Con A-induced liver injury and T cell infiltration in transgenic (Tg) mice overexpressing Roquin specifically in T cells. In Roquin Tg mice, Con A treatment caused greater increases in both the levels of liver injury enzymes and liver tissue apoptosis, as revealed by TUNEL and H&E staining, than wild type (WT) mice. Further, Roquin Tg mice respond to Con A treatment with greater increases in the T cell population, particularly Th17 cells, though Treg cell counts are lower. Roquin overexpression also enhances increases in pro-inflammatory cytokines, including IFN-γ, TNF-α and IL-6, upon liver injury. Furthermore, Roquin regulates the immune response and apoptosis in Con A induced hepatitis via STATs, Bax and Bcl2. These findings suggest that over-expression of Roquin exacerbates T-cell mediated hepatitis. [ABSTRACT FROM AUTHOR]

Abstract: The circling (cir/cir) mouse is one of the murine models for human non-syndromic deafness DFNB6. The mice have abnormal circling behavior, suggesting a balanced disorder and profound deafness. The causative gene was transmembrane inner ear (tmie) gene of which the mutation is a 40-kb genomic deletion including tmie gene itself. In this study, tmie-overexpression trasngenic mice were established. Individuals with germline transmission have been mated with circling homozygous mutant mice (cir/cir) in order to produce the transgenic mutant mice (cir/cir-tg) as a gene therapy. After the genotyping, phenotypic analyses were performed so that the insertion of the new gene might compensate for the diseases such as hearing loss, circling behavior, or swimming inability. Some individuals exhibited complete recovery in their behavior and hearing but the others did not show any amelioration in behavior or hearing. Individual mice had very different levels of tmie transgene expression in the cochlea. These results clearly indicate that tmie protein plays an important role when the appropriate expression level of tmie was expressed in the inner ear. The protein levels were variable in each individual and these are thought to induce the differences in disease amelioration levels. [Copyright &y& Elsevier]

We demonstrate a new design for immunomodulatory CpG DNA containing two sequences each with as few as five or six-nucleotides joined together via 3′–3′ linkers. These do not require the –PuPu(Py)CGPyPy– hexameric motif generally found essential for CpG DNA immune stimulation. These novel, short-immunomers show potent immunostimulatory activity manifested by IL-12 and IL-6 secretion in murine spleen cell and PBMC cultures and splenomegaly in vivo. Short-immunomers show strong activation of NF-κB and stress-activated signaling pathways and induce cytokines in J774 cell cultures. The same sequences also induce cytokines in healthy human PBMC cultures whereas conventional CpG DNA requires different optimal sequences for murine and human immune cells. Additionally, short-immunomers inhibit IL-5 secretion and induce IFN-γ secretion in conalbumin-sensitized mouse spleen cell cultures, suggesting reversal of established Th2 responses to Th1 type responses. Short-immunomer also inhibits growth of MCF-7 human tumor xenograft in nude mice. This is the first report of activity with such short DNA sequences and also of sequences lacking hexameric motifs proposed in earlier studies. [Copyright &y& Elsevier]

Highlights: [•] The expression of Jazf1 in the liver suppressed lipid accumulation. [•] Jazf1 significantly increases transcription of fatty acid synthase. [•] Jazf1 plays a critical role in the regulation of energy and lipid homeostasis. [•] Jazf1 associates the development of metabolic disorder. [•] Jazf1 may provide a new therapeutic target in the management of metabolic disorder. [ABSTRACT FROM AUTHOR]

Abstract: The T-cell receptor (TCR) engages with an antigen and initiates a signaling cascade that leads to the activation of transcription factors. Roquin, a protein encoded by the RC3H1 gene and characterized as an immune regulator, was recently identified as a novel RING-type ubiquitin ligase family member, but the mechanisms by which Roquin regulates T-cell responses are unclear. We used the EL-4 murine lymphoma cell line to elucidate the role of Roquin in vitro. Roquin-overexpressing EL-4 cells became hyper-responsive after anti-CD3/CD28 stimulation in vitro and were a major source of the cytokines IL-2 and TNF-α. Upon activation, these cells showed particularly enhanced production of IL-2 and TNF-α. To clarify the important role played by Roquin in T-cell responses ex vivo, we generated T-cell-specific Roquin transgenic (Tg) mice. Roquin-Tg CD4+ T-cells showed enhanced production of IL-2 and TNF-α in response to TCR stimulation with anti-CD28 co-stimulation. Further studies are necessary to investigate the role of Roquin in the regulation of primary T-cell activation, survival, and differentiation. [Copyright &y& Elsevier]

Abstract: S100A9 is a member of the S100 family of proteins that contain two EF-hand calcium-binding motifs. We previously reported that S100A9 was differentially expressed during the early airway response phase of asthma and can be regulated by acupuncture. To understand the possible role of S100A9 in asthma, the effects of the S100A9 were investigated in a rat model of asthma and in isolated tracheal spirals. The pulmonary function and isometric tension were measured after the administration of purified recombinant S100A9. The results of in vivo experiments showed that S100A9 (0.1μg/kg) significantly decreased the pulmonary resistance and increased the dynamic compliance. The in vitro experimental results showed that S100A9 (100, 200, 400, or 800ng/ml, final concentrations) significantly reduced the isometric tension of isolated tracheal spirals. These results suggest that S100A9 elicits dose-dependent anti-asthmatic effects and may provide further insight into the treatment of asthma. [ABSTRACT FROM AUTHOR]

Abstract: Single-stranded RNAs act as ligands of Toll-like receptors (TLRs) 7 and 8 and induce immune responses. In the present study, we have designed and synthesized phosphorothioate oligoribonucleotides (ORNs) with self-complementary sequences that form duplex structures with either 3′- or 5′-overhanging sequences. We studied the new ORNs for their duplex formation, nuclease stability, and ability to induce immune-stimulatory activate through TLR7 and TLR8 in TLR-transfected cell lines, human PBMCs, human pDCs, and in vivo in mice. Thermal melting and gel electrophoresis studies showed that all ORNs formed secondary structures and that the thermal stability of the duplex is depended on the length and GC composition of the duplex. Nuclease stability of ORNs increased with increasing thermal stability of the duplex formed. All ORN showed TLR8 activity in HEK293 cells, and induced cytokine and chemokine production in human PBMC cultures. In addition to TLR8 activity, two ORNs containing a ‘CUGAAUU’ motif in the duplex-forming region induced immune stimulation through TLR7 in HEK293 cells, human PBMC and pDC cultures, and in vivo in mice. These results suggest that secondary structures in ORN provide nuclease stability and lead to stimulation of immune responses through TLR8 as well as TLR7 depending on the presence of specific nucleotide motifs. [Copyright &y& Elsevier]

Abstract: Microcephaly is a malformation associated with in utero exposed atomic bomb survivors and can be induced in mice by fetal exposure to ionizing radiation (IR). The pathogenesis of IR-induced microcephaly, however, has not been fully understood. Our analyses of high-coverage expression profiling (HiCEP) demonstrated that the abnormal spindle-like microcephaly associated gene (ASPM) was down-regulated in irradiated human diploid fibroblasts. ASPM was recently reported as the causative gene for MCPH-5, the most common type of congenital microcephaly in humans. Here, we show that the expression of the Aspm gene was significantly reduced by IR in various human and murine cells. Additionally, Aspm was found downregulated in the irradiated fetal mouse brain, particularly in the ventricular zones. A similar suppression was observed in the irradiated neurosphere cultures. This is the first report suggesting that the suppression of Aspm by IR could be the initial molecular target leading to the future microcephaly formation. [Copyright &y& Elsevier]

Abstract: Hypoxia-inducible factor-1 (HIF-1) represents an important tumor-selective therapeutic target for solid tumors. In search of novel small molecule HIF-1 inhibitors, 5400 natural product-rich extracts from plants, marine organisms, and microbes were examined for HIF-1 inhibitory activities using a cell-based reporter assay. Bioassay-guided fractionation and isolation, followed by structure elucidation, yielded three potent natural product-derived HIF-1 inhibitors and two structurally related inactive compounds. In a T47D cell-based reporter assay, manassantin B1, manassantin A, and 4-O-methylsaucerneol inhibited hypoxia-induced HIF-1 activation with IC50 values of 3, 3, and 20nM, respectively. All three compounds are relatively hypoxia-specific inhibitors of HIF-1 activation, in comparison to other stimuli. The hypoxic induction of HIF-1 target genes CDKN1A, VEGF, and GLUT-1 were also inhibited. These compounds inhibit HIF-1 by blocking hypoxia-induced nuclear HIF-1α protein accumulation without affecting HIF-1α mRNA levels. In addition, preliminary structure–activity studies suggest specific structural requirements for this class of HIF-1 inhibitors. [Copyright &y& Elsevier]

We recently showed that 5′-terminal secondary structures in CpG DNA affect activity significantly more than those at the 3′-end [Biochem. Biophys. Res. Commun. 306 (2003) 948]. The need for an accessible 5′-end of CpG DNA for activity suggested that the receptor reads the DNA sequence from this end. In continuation of these studies, we have designed immunomodulatory oligonucleotides (IMOs), consisting of a nine-mer stimulatory domain, containing a CpG motif and a hairpin-loop structure at the 3′-end, referred to as self-stabilized CpG DNAs. We studied the ability of self-stabilized CpG DNAs to stimulate human B-cell proliferation and interferon-α (IFN-α) secretion in plasmacytoid dendritic cell (pDC) culture assays. Self-stabilized CpG DNAs activated human B cells and induced plasmacytoid dendritic cells to secrete high levels of IFN-α. While both stimulatory and secondary structures in CpG DNAs were required for pDC activation, CpG motifs were sufficient to activate B cells. Interestingly, CpG motifs were not required for activity in the hairpin duplex region. Further modifications of the hairpin duplex region with a mixture of oligodeoxynucleotides and oligo-2′-O-methylribonucleotides in a heteroduplex formation permitted activation of both human B cells and pDCs. [Copyright &y& Elsevier]

Oligodeoxynucleotides containing CpG dinucleotides in specific sequence contexts activate the vertebrate immune system. Our previous studies showed that the 5′-end of a CpG oligonucleotide should be accessible for receptor recognition and subsequent immune stimulation. Activity is abrogated if this end is blocked by joining two CpG oligos through 5′–5′ linkage. It was not known whether a similar effect would arise from secondary structures at either end of a CpG oligo, such as hairpin loops or terminal dimers. In the present study we found that 5′-terminal secondary structures affect activity significantly more than those at the 3′-end. The need for an open 5′-end suggests that the receptor responsible for immune stimulation reads the DNA sequence from this end. These results may also provide insights to place CpG motifs appropriately in DNA vaccines to induce additional Th1 type responses. [Copyright &y& Elsevier]

Acute promyelocytic leukemia (APL) is characterized by a specific chromosome translocation t(15;17), which results in the fusion of the promyelocytic leukemia gene (PML) and retinoic acid receptor α gene (RARα). APL can be effectively treated with the cell differentiation inducer all-trans retinoic acid (ATRA). NB4 cells, an acute promyelocytic leukemia cell line, have the t(15;17) translocation and differentiate in response to ATRA, whereas HL-60 cells lack this chromosomal translocation, even after differentiation by ATRA. To identify changes in the gene expression patterns of promyelocytic leukemia cells during differentiation, we compared the gene expression profiles in NB4 and HL-60 cells with and without ATRA treatment using a cDNA microarray containing 10,000 human genes. NB4 and HL-60 cells were treated with ATRA (10−6 M) and total RNA was extracted at various time points (3, 8, 12, 24, and 48 h). Cell differentiation was evaluated for cell morphology changes and CD11b expression. PML/RARα degradation was studied by indirect immunofluoresence with polyclonal PML antibodies. Typical morphologic and immunophenotypic changes after ATRA treatment were observed both in NB4 and HL-60 cells. The cDNA microarray identified 119 genes that were up-regulated and 17 genes that were down-regulated in NB4 cells, while 35 genes were up-regulated and 36 genes were down-regulated in HL60 cells. Interestingly, we did not find any common gene expression profiles regulated by ATRA in NB4 and HL-60 cells, even though the granulocytic differentiation induced by ATRA was observed in both cell lines. These findings suggest that the molecular mechanisms and genes involved in ATRA-induced differentiation of APL cells may be different and cell type specific. Further studies will be needed to define the important molecular pathways involved in granulocytic differentiation by ATRA in APL cells. [Copyright &y& Elsevier]