Genetic markers associated with abstinence length in alcohol-dependent subjects treated with acamprosate.

Acamprosate supports abstinence in some alcohol-dependent subjects, yet predictors of response are unknown. To identify response biomarkers, we investigated associations of abstinence length with polymorphisms in candidate genes in glycine and glutamate neurotransmission pathways and genes previously implicated in acamprosate response. Association analyses were conducted in the discovery sample of 225 alcohol-dependent subjects treated with acamprosate for 3 months in community-based treatment programs in the United States. Data from 110 alcohol-dependent males treated with acamprosate in the study PREDICT were used for replication of the top association findings. Statistical models were adjusted for relevant covariates, including recruitment site and baseline clinical variables associated with response. In the discovery sample, shorter abstinence was associated with increased intensity of alcohol craving and lower number of days between the last drink and initiation of acamprosate treatment. After adjustment for covariates, length of abstinence was associated with the GRIN2B rs2058878 (P=4.6 × 10(-5)). In the replication sample, shorter abstinence was associated with increased craving, increased depressive mood score and higher alcohol consumption. Association of abstinence length with GRIN2B rs2058878 was marginally significant (P=0.0675); as in the discovery sample, the minor A allele was associated with longer abstinence. Furthermore, rs2300272, which is in strong linkage disequilibrium with rs2058878, was also associated with abstinence length (P=0.049). This is the first report of a replicated association of genetic markers with the length of abstinence in acamprosate-treated alcoholics. Investigation of the underlying mechanisms of this association and its usefulness for individualized treatment selection should follow.

The mitotic kinase Aurora--a promotes distant metastases by inducing epithelial-to-mesenchymal transition in ERα(+) breast cancer cells.

In this study, we demonstrate that constitutive activation of Raf-1 oncogenic signaling induces stabilization and accumulation of Aurora-A mitotic kinase that ultimately drives the transition from an epithelial to a highly invasive mesenchymal phenotype in estrogen receptor α-positive (ERα(+)) breast cancer cells. The transition from an epithelial- to a mesenchymal-like phenotype was characterized by reduced expression of ERα, HER-2/Neu overexpression and loss of CD24 surface receptor (CD24(-/low)). Importantly, expression of key epithelial-to-mesenchymal transition (EMT) markers and upregulation of the stemness gene SOX2 was linked to acquisition of stem cell-like properties such as the ability to form mammospheres in vitro and tumor self-renewal in vivo. Moreover, aberrant Aurora-A kinase activity induced phosphorylation and nuclear translocation of SMAD5, indicating a novel interplay between Aurora-A and SMAD5 signaling pathways in the development of EMT, stemness and ultimately tumor progression. Importantly, pharmacological and molecular inhibition of Aurora-A kinase activity restored a CD24(+) epithelial phenotype that was coupled to ERα expression, downregulation of HER-2/Neu, inhibition of EMT and impaired self-renewal ability, resulting in the suppression of distant metastases. Taken together, our findings show for the first time the causal role of Aurora-A kinase in the activation of EMT pathway responsible for the development of distant metastases in ERα(+) breast cancer cells. Moreover, this study has important translational implications because it highlights the mitotic kinase Aurora-A as a novel promising therapeutic target to selectively eliminate highly invasive cancer cells and improve the disease-free and overall survival of ERα(+) breast cancer patients resistant to conventional endocrine therapy.

Safety and efficacy of CYT387, a JAK1 and JAK2 inhibitor, in myelofibrosis.

JAK-STAT is a rational drug target in myelofibrosis (MF) given its association with JAK2/MPL mutations and aberrant inflammatory cytokine expression. We conducted a Phase 1/2 trial of CYT387, a potent JAK1/2 inhibitor, in patients with high- or intermediate-risk primary or post-polycythemia vera/essential thrombocythemia MF. Pre-planned safety and efficacy analysis has been completed for the initial 60 patients. In the dose-escalation phase (n=21), the maximum-tolerated dose was 300 mg/day based on reversible grade 3 headache and asymptomatic hyperlipasemia. Twenty-one and 18 additional patients were accrued at two biologically effective doses, 300 mg/day and 150 mg/day, respectively. Anemia and spleen responses, per International Working Group criteria, were 59% and 48%, respectively. Among 33 patients who were red cell-transfused in the month prior to study entry, 70% achieved a minimum 12-week period without transfusions (range 4.7->18.3 months). Most patients experienced constitutional symptoms improvement. Grade 3/4 adverse reactions included thrombocytopenia (32%), hyperlipasemia (5%), elevated liver transaminases (3%) and headache (3%). New-onset treatment-related peripheral neuropathy was observed in 22% of patients (sensory symptoms, grade 1). CYT387 is well tolerated and produces significant anemia, spleen and symptom responses in MF patients. Plasma cytokine and gene expression studies suggested a broad anticytokine drug effect.

Normal ageing is associated with an increase in Th2 cells, MCP-1 (CCL1) and RANTES (CCL5), with differences in sCD40L and PDGF-AA between sexes.

We have observed T helper type 2 (Th2) polarization of systemic immunity in patients with metastatic malignant melanoma. We hypothesized that similar changes in systemic immunity occur with ageing and may be permissive for the development of melanoma. We analysed the peripheral blood of 389 healthy blood donors. All subjects were profiled for peripheral blood T cell and B cell subsets, and 58 of these subjects were profiled for antigen-specific cytotoxic T cell subsets [cytomegalovirus (CMV), influenza and melanoma antigen recognized by T cells 1 (MART-1)]. Ninety-five separate healthy subjects underwent profiling of 42 plasma cytokines. Ageing was associated positively with CD4(+) CD294(+) Th2 cells, and associated negatively with CD3(+) T cells, cytotoxic T cells and T helper cells. Ageing was also associated negatively with CMV-, influenza- and MART-1-specific naive and CD8(+) T cells. There were significant increases in plasma monocyte chemotactic protein 1 (MCP-1) (CCL1) and regulated upon activation normal T cell expressed and secreted (RANTES) (CCL5) with age. We observed differences in cytokine profiles between males and females; specifically, women had higher levels of sCD40L and PDGF-AA. In summary, we demonstrated in healthy blood donors that ageing was associated with an increase in cellular Th2 bias and a decline in total numbers of T cells. Additionally, there was an increase in MCP-1 and RANTES with ageing. Women had higher levels of sCD40L and PDGF-AA than men.

The VIZIER project: preparedness against pathogenic RNA viruses.

Life-threatening RNA viruses emerge regularly, and often in an unpredictable manner. Yet, the very few drugs available against known RNA viruses have sometimes required decades of research for development. Can we generate preparedness for outbreaks of the, as yet, unknown viruses? The VIZIER (VIral enZymes InvolvEd in Replication) (http://www.vizier-europe.org/) project has been set-up to develop the scientific foundations for countering this challenge to society. VIZIER studies the most conserved viral enzymes (that of the replication machinery, or replicases) that constitute attractive targets for drug-design. The aim of VIZIER is to determine as many replicase crystal structures as possible from a carefully selected list of viruses in order to comprehensively cover the diversity of the RNA virus universe, and generate critical knowledge that could be efficiently utilized to jump-start research on any emerging RNA virus. VIZIER is a multidisciplinary project involving (i) bioinformatics to define functional domains, (ii) viral genomics to increase the number of characterized viral genomes and prepare defined targets, (iii) proteomics to express, purify, and characterize targets, (iv) structural biology to solve their crystal structures, and (v) pre-lead discovery to propose active scaffolds of antiviral molecules.

[Methods for improving the quality of prediction in the process of automatic annotating A4].

Modifications of the previously described adaptive algorithm of automatic annotating A4 have been considered, which make it possible to improve the quality of prediction. First, the direct use of the so-called basis statistics eta refines the quality of prediction compared with the previously proposed statistics gamma. Second, the quality is improved if not all similar sequences found but only part of them are used. This decreases the noising of the data, which in turn improves the quality of prognosis.

Adaptive algorithm of automated annotation.

MOTIVATION: It is common knowledge that the avalanche of data arriving from the sequencing projects cannot be annotated either experimentally or manually by experts. The need for a reliable and convenient tool for automated sequence annotation is broadly recognized. RESULTS: Here, we describe the Adaptive Algorithm of Automated Annotation (A(4)) based on a statistical approach to this problem. The mathematical model relates a set of homologous sequences and descriptions of their functional properties, and calculates the probabilities of transferring a sequence description onto its homologue. The proposed model is adaptive, its parameters (distribution characteristics, transference probabilities, thresholds, etc.) are dynamic, i.e. are generated individually for the sequences and various functional properties (words of the description). The proposed technique significantly outperforms the widely used test for frequency threshold, which is a special case of our model realized for the simplest set of parameters. The prediction technique has been realized as a computer program and tested on a random sequence sampling from SWISS-PROT. AVAILABILITY: The automated annotation program based on the proposed algorithm is available through the Web browser at http://www.genebee.msu.su/services/annot/basic.html.

Molecular and functional evidence for early divergence of an endothelin-like system during metazoan evolution: analysis of the Cnidarian, hydra.

A novel putative endothelin-converting enzyme (ECE) has been cloned from hydra, a freshwater invertebrate that belongs to the second oldest phylum of the animal kingdom. As an integral component of the endothelin system, vertebrate ECE functions in the activation of endothelin (ET) peptides. Vertebrate ETs are (1) the most potent vasoconstrictors known in mammals; and (2) function as essential signaling ligands during development of tissues derived from neural crest cells. To date, only a limited number of immunocytochemical studies have suggested the presence of endothelin-like peptides in invertebrates. Based on structural and functional analyses, we present evidence for a functional endothelin-like system in hydra that is involved in both muscle contraction and developmental processes. These findings indicate the broad use of endothelin systems in metazoans and also indicate that this type of signaling system arose early in evolution even before divergence of protostomes and deuterostomes.

Hydra metalloproteinase 1: a secreted astacin metalloproteinase whose apical axis expression is differentially regulated during head regeneration.

The newly emerging astacin metalloproteinase family comprises multiple members with diverse functions. Most recently, the development-related functions have been attributed to both (1) proteolytic cleavage and subsequent release of active TGF-beta-like growth factors from latent inhibitory complexes and (2) modification of extracellular matrix (ECM) assembly and composition. We previously identified and purified hydra metalloproteinase 1 (HMP-1), a developmentally important astacin proteinase that functions in head regeneration and transdifferentiation of tentacle battery cells (L. Yan et al., 1995, Development 121, 1591-1602). In the present study, further cloning revealed that HMP-1 is produced as a secreted zymogen with a conserved hydrophobic signal sequence and a putative propeptide. The processed HMP-1 is composed of a characteristic astacin proteinase domain and a unique Cys-rich C-terminus. With this simple domain structure, HMP-1 represents an ancestral astacin proteinase. Consistent with its role in head regeneration, HMP-1 mRNA is expressed at highest levels by endodermal cells at the apical pole of the body column just inferior to the base of tentacles, the region of active cell differentiation or transdifferentiation. A modified immunocytochemical procedure demonstrated that HMP-1 protein can be localized not only to ECM of tentacles as we previously reported, but also to endodermal cells of the body column in a pattern similar to its mRNA distribution. The localization of HMP-1 protein in tentacles was confirmed using an enzymatic approach. A translocation of HMP-1 protein from cells in the body column to the extracellular milieu in tentacles further suggests that HMP-1 is a secreted protein. HMP-1 expression undergoes extensive regulation at the transcriptional level both temporally and spatially during head regeneration. The involvement of HMP-1 in this morphogenetic process is further supported by the blockage of head regeneration with localized antisense treatment. Taken together, these results suggest that HMP-1 is a secreted astacin metalloproteinase that has an important role in regulating hydra head morphogenesis potentially through its differential expression along the body axis.

A novel hydra matrix metalloproteinase (HMMP) functions in extracellular matrix degradation, morphogenesis and the maintenance of differentiated cells in the foot process.

As a member of Cnidaria, the body wall of hydra is structurally reduced to an epithelial bilayer with an intervening extracellular matrix (ECM). Biochemical and cloning studies have shown that the molecular composition of hydra ECM is similar to that seen in vertebrates and functional studies have demonstrated that cell-ECM interactions are important to developmental processes in hydra. Because vertebrate matrix metalloproteinases (MMPs) have been shown to have an important role in cell-ECM interactions, the current study was designed to determine whether hydra has homologues of these proteinases and, if so, what function these enzymes have in morphogenesis and cell differentiation in this simple metazoan. Utilizing a PCR approach, a single hydra matrix metalloproteinase, named HMMP was identified and cloned. The structure of HMMP was similar to that of vertebrate MMPs with an overall identity of about 35%. Detailed structural analysis indicated some unique features in (1) the cysteine-switch region of the prodomain, (2) the hinge region preceding the hemopexin domain, and (3) the hemopexin domain. Using a bacterial system, HMMP protein was expressed and folded to obtain an active enzyme. Substrate analysis studies indicated that recombinant HMMP could digest a number of hydra ECM components such as hydra laminin. Using a fluorogenic MMP substrate assay, it was determined that HMMP was inhibited by peptidyl hydroxamate MMP inhibitors, GM6001 and matlistatin, and by human recombinant TIMP-1. Whole-mount in situ studies indicated that HMMP mRNA was expressed in the endoderm along the entire longitudinal axis of hydra, but at relatively high levels at regions where cell-transdifferentiation occurred (apical and basal poles). Functional studies using GM6001 and TIMP-1 indicated that these MMP inhibitors could reversibly block foot regeneration. Blockage of foot regeneration was also observed using antisense thio-oligo nucleotides to HMMP introduced into the endoderm of the basal pole using a localized electroporation technique. Studies with adult intact hydra found that GM6001 could also cause the reversible de-differentiation or inhibition of transdifferentiation of basal disk cells of the foot process. Basal disk cells are adjacent to those endoderm cells of the foot process that express high levels of HMMP mRNA. In summary, these studies indicate that hydra has at least one MMP that is functionally tied to morphogenesis and cell transdifferentiation in this simple metazoan.

[GeneBee-NET: An Internet based server for biopolymer structure analysis]. / GeneBee-NET: Baziruiushchiisia v seti Internet server po analizu struktur biopolimerov.

A network server providing biopolymer structure databank retrieval as well as some other biocomputing procedures for Internet users is described. Its basic procedures consist in looking for sequence and 3D homologies (similarities). Found homologies are used for constructing multiple alignment, for predicting RNA and protein secondary structures as well as for constructing phylogenetic trees. Alongside traditional methods of sequence homology retrieval, a "matrix-free" (correlation) method is proposed. A similar procedure is used to locate protein 3D similarities. For novel procedures algorithm ideas and their possible applications are discussed. The service ideology is based on the interaction of server and client programs. The client program (GeneBee for IBM PC) can be used to form queries to the server as well as to manipulate a treatment result. In the absence of the client program the interaction with the server can be in the text mode. The E-mail and WWW addresses for the server are as follows: SERVE/INDY.GENEBEE.MSU.SU and WWW.GENEBEE.MSU.SU.

Construction of the full local similarity map for two biopolymers.

A novel algorithm for construction of complete maps of local similarity for two biopolymer sequences is described. The algorithm is much faster than the related Altschul-Erickson procedure, it is implemented as the Dot-Helix module within the GeneBee package. Performance of the algorithm is exemplified with the analysis of the polyproteins of two poliovirus type 3 strains and its effectivity is compared to the Staden method. Possible applications of the algorithm are briefly discussed.

A novel method of multiple alignment of biopolymer sequences.

A novel algorithm for multiple alignment of biological sequences is suggested. At the first step the DotHelix procedure is employed for construction of motifs, i.e. continuous fragments of local similarity of various "thickness" and strength, and then these motifs are concatenated into chains consistent with the order of letters in the sequences. The algorithm is implemented in the MA-Tools program of the GeneBee package. An example illustrating the effectivity of the algorithm is presented.

[An analysis of the centriole orientation in tissue culture cells]. / Analiz orientatsii tsentriolei v kletkakh kul'tury tkani.

A mathematical description of random orientation of centrioles with respect to the plane has been suggested for two modes of experimental procedure: a) all the centrioles in a given volume are taken into account; b) all the centrioles crossing an ultrathin section are accounted. In the former case the function of distribution does not depend on the length of the centrioles. Histograms of the distribution of centriolar length projections on the plane of the section have been obtained. These histograms are compared with those obtained for centrioles in mitotic pig kidney embryo cells (PE-cells). Tables of credible occurrence intervals for "nearly perpendicular" (the angle is tipped to the substrate plane by over 74 degrees) and for "nearly parallel" (the angle is tipped to the substrate plane by less than 12 degrees) centrioles in different samplings are adduced.

[Estimation of the randomness of the overlapping of cellular structures]. / Otsenka sluchainosti perekryvaniia kletochnykh struktur.

Methods for estimation of randomness of mutual overlaps of cells, their parts, and intracellular structures are developed. Two methods are proposed: a "method of areas" based on the estimation of the area of overlaps of randomly located figures, and a "method of contours" based on the evaluation of the number of intersections of linear structures located randomly. Examples are given as applied to cells and cellular nuclei, in particular during contact inhibition of cellular movement.

[Quantitative characteristics of the transfer of the hematopoietic microenvironment]. / Kolichestvennye kharakteristiki perenosa gemopoéticheskogo mikrookruzheniia.

Heterotopic transplantation of marrow fragments results in the formation of new bone marrow organs. The amount of hemopoietic cells populating these organs is connected nonlinearly with the volume of the grafted tissue or with the number of transplanted marrow cells. Statistical analysis points out that the number of the populating cells depends on the radius of the initial bone marrow transplant. Thus, the previous data on the radiosensitivity of the microenvironmental transfering stromal cells and on their concentration obtained by measuring the size of the heterotopic bone marrow organs have turned out incorrect.

[Analysis of the activity of fibers in an entire nerve trunk and a study of impulse frequency in sympathetic preganglionic fibers]. / Analiz aktivnosti volokon v obshchem nervnom stvole i issledovanie chastot impul'satsii v simpaticheskikh preganglionarnykh volokon.

The firing rate in type "B" preganglionic sympathetic fibers during strong pressor reactions varied in different fibers from 0 to 80/sec. With an increase of the pressor reaction, the maximum of the density of frequency distribution shifts from 30--40 to 50--60/sec, previously "silent" fibers becoming involved.