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Pathways database system.

During the next phase of the Human Genome Project, research will focus on functional studies of attributing functions to genes, their regulatory elements, and other DNA sequences. To facilitate the use of genomic information in such studies, a new modeling perspective is needed to examine and study genome sequences in the context of many kinds of biological information. Pathways are the logical format for modeling and presenting such information in a manner that is familiar to biological researchers. In this paper, we introduce an integrated system, called "Pathways Database System," with a set of software tools for modeling, storing, analyzing, visualizing, and querying biological pathways data at different levels of genetic, molecular, biochemical and organismal detail.

Computational Biology↗

Uncoupling of the base excision and nucleotide incision repair pathways reveals their respective biological roles.

The multifunctional DNA repair enzymes apurinic/apyrimidinic (AP) endonucleases cleave DNA at AP sites and 3'-blocking moieties generated by DNA glycosylases in the base excision repair pathway. Alternatively, in the nucleotide incision repair (NIR) pathway, the same AP endonucleases incise DNA 5' of a number of oxidatively damaged bases. At present, the physiological relevance of latter function remains unclear. Here, we report genetic dissection of AP endonuclease functions in base excision repair and NIR pathways. Three mutants of Escherichia coli endonuclease IV (Nfo), carrying amino acid substitutions H69A, H109A, and G149D have been isolated. All mutants were proficient in the AP endonuclease and 3'-repair diesterase activities but deficient in the NIR. Analysis of metal content reveals that all three mutant proteins have lost one of their intrinsic zinc atoms. Expression of the nfo mutants in a repair-deficient strain of E. coli complemented its hypersensitivity to alkylation but not to oxidative DNA damage. The differential drug sensitivity of the mutants suggests that the NIR pathway removes lethal DNA lesions generated by oxidizing agents. To address the physiological relevance of the NIR pathway in human cells, we used the fluorescence quenching mechanism of molecular beacons. We show that in living cells a major human AP endonuclease, Ape1, incises DNA containing alpha-anomeric 2'-deoxyadenosine, indicating that the intracellular environment supports NIR activity. Our data establish that NIR is a distinct and separable function of AP endonucleases essential for handling lethal oxidative DNA lesions.

Animals↗

Expression profiling of lipopolysaccharide target genes in RAW264.7 cells by oligonucleotide microarray analyses.

In inflammatory responses, induction of cytokines and other immune regulator genes in macrophages by pathogen-associated signal such as lipopolysaccharide (LPS) plays a crucial role. In this study, the gene expression profile changes by LPS treatment in the macrophage/monocyte lineage cell line RAW264.7 was investigated. A 60-mer oligonucleotide microarray of which probes target 32381 mouse genes was used. A reverse transcription-in vitro translation labeling protocol and a chemileuminescence detection system were employed. The mRNA expression levels in RAW264.7 cells treated for 6 h with LPS and the control vehicle were compared. 747 genes were up-regulated and 523 genes were down-regulated by more than 2 folds. 320 genes showing more than 4-fold change by LPS treatment were further classified for the biological process, molecular function, and signaling pathway. The biological process categories that showed high number of increased genes include the immunity and defense, the nucleic acid metabolism, the protein metabolism and modification, and the signal transduction process. The chemokine-cytokine signaling, interleukin signaling, Toll receptor signaling, and apoptosis signaling pathways involved high number of genes differentially expressed in response to LPS. These expression profile data provide more comprehensive information on LPS-target genes in RAW264.7 cells, which will be useful in comparing gene expression changes induced by extracts and compounds from anti-inflammatory medicinal herbs.

Animals↗

Targeting transcription factors in cell regulation.

The author compares transcription factors (TFs) with 13 other protein classes from the point of their ability to regulate various cellular processes. The comparison is performed using data from the ResNet 4.0 database containing molecular interactions extracted from scientific literature. The author introduces two quantitative characteristics for evaluating the ability of every protein to regulate a cell process. Using these measures, he evaluates the efficiency of TFs and other protein classes to regulate the biological process pathways. It was found that TFs, on average, are not the best class for regulating an individual cell process. They have lower regulatory specificity, (i.e., single TF tends to regulate many different biological processes). TFs also tend to be placed downstream in the biological process pathways, being a target of the regulatory relation more often than being a regulator. Possible implications of these findings for drug development are discussed.

Cell Physiological Phenomena↗

Biological role of HGF/MET pathway in renal cell carcinoma.

PURPOSE: Several lines of evidence show that hepatocyte growth factor (HGF) and its receptor MET play a significant role in the progression of various cancers including renal cell carcinoma (RCC). Our objectives were to evaluate the gene expression of HGF and MET in RCC, and to examine the effect of HGF on the biological activities of cultured RCC cells. MATERIALS AND METHODS: We examined the gene expression of HGF and MET in 27 primary RCC tumors by quantitative competitive RT-PCR. The effects of HGF on in vitro chemoinvasion assay and the expression of matrix metalloproteinase-9 (MMP-9), and the induction of Fas-induced apoptosis were studied by transfection of HGF cDNA to cultured RCC cells, Caki-1. RESULTS: HGF mRNA and MET mRNA were detected in all surgical specimens. The level of expressed HGF mRNA was proportional with the volume of tumor (r = 0.50, p = 0.015). Caki-1 cells overexpressing HGF cells showed enhanced in vitro invasiveness in the chemoinvasion assay and increased activity of 92 kDa type IV collagenase (MMP-9). The sensitivity to Fas-induced cell death was reduced in HGF transfectants, which was reversed by the presence of anti-HGF antibody. CONCLUSIONS: HGF enhanced the invasive properties of cultured RCC cells and inhibited Fas-induced apoptosis in vitro. Both HGF and MET mRNA were expressed in RCC tissues tested. Our results indicate that HGF/MET pathway may have a significant role in the progression of RCC.

Apoptosis↗

A correlated motif approach for finding short linear motifs from protein interaction networks.

BACKGROUND: An important class of interaction switches for biological circuits and disease pathways are short binding motifs. However, the biological experiments to find these binding motifs are often laborious and expensive. With the availability of protein interaction data, novel binding motifs can be discovered computationally: by applying standard motif extracting algorithms on protein sequence sets each interacting with either a common protein or a protein group with similar properties. The underlying assumption is that proteins with common interacting partners will share some common binding motifs. Although novel binding motifs have been discovered with such approach, it is not applicable if a protein interacts with very few other proteins or when prior knowledge of protein group is not available or erroneous. Experimental noise in input interaction data can further deteriorate the dismal performance of such approaches. RESULTS: We propose a novel approach of finding correlated short sequence motifs from protein-protein interaction data to effectively circumvent the above-mentioned limitations. Correlated motifs are those motifs that consistently co-occur only in pairs of interacting protein sequences, and could possibly interact with each other directly or indirectly to mediate interactions. We adopted the (l, d)-motif model and formulate finding the correlated motifs as an (l, d)-motif pair finding problem. We present both an exact algorithm, D-MOTIF, as well as its approximation algorithm, D-STAR to solve this problem. Evaluation on extensive simulated data showed that our approach not only eliminated the need for any prior protein grouping, but is also more robust in extracting motifs from noisy interaction data. Application on two biological datasets (SH3 interaction network and TGFbeta signaling network) demonstrates that the approach can extract correlated motifs that correspond to actual interacting subsequences. CONCLUSION: The correlated motif approach outlined in this paper is able to find correlated linear motifs from sparse and noisy interaction data. This, in turn, will expedite the discovery of novel linear binding motifs, and facilitate the studies of biological pathways mediated by them.

Algorithms↗

The mannan-binding lectin pathway of complement activation: biology and disease association.

Mannan-binding lectin (MBL) is a plasma protein found in association with several serine proteases (MASPs) forming the MBL complex. MBL recognises carbohydrate structures arranged in a particular geometry, such as those found on the surface of micro-organisms. When bound to e.g. bacteria the MBL complex will initiate the activation of the complement cascade. Mounting evidence supports the importance of the MBL pathway of complement activation in innate immunity. In this review, we focus on the structure and function of the proteins within the MBL pathway and address the properties of the pathway as an initiator of the host response against potential pathogenic micro-organisms.

Amino Acid Sequence↗

Comprehensive analysis of metabolomics and transcriptomics of radiation-induced rectal injury.

Radiation-induced rectal injury (RRI) significantly affects the quality of life in patients with locally advanced rectal cancer (LARC) undergoing neoadjuvant chemoradiotherapy (NCRT). Non-targeted liquid chromatography-mass spectrometry metabolomics analysis and transcriptomic analysis were conducted to explore RRI characteristics. Hematoxylin-eosin and Masson staining confirmed radiation-induced injury in rectal tissue within the radiotherapy target region. Orthogonal partial least squares discriminant analysis identified 823 differentially expressed metabolites (DEMs). Transcriptomic analysis revealed 400 differentially expressed genes (DEGs). Enrichment analysis revealed that DEMs and DEGs were primarily involved in metabolic, immune, and signal transduction pathways. Integrated analysis demonstrated significant enrichment of DEMs and DEGs in the arachidonic acid metabolism pathway. Pearson's correlation and canonical correlation analyses were used to assess the association between DEMs and DEGs within this pathway. In conclusion, this study identified key biological regulatory pathways involved in RRI through a multi-omics approach, offering potential targets for its diagnosis and treatment.

Humans↗

Control of transcription factor activity and osteoblast differentiation in mammalian cells using an evolved small-molecule-dependent intein.

Inteins are naturally occurring protein elements that catalyze their own excision from within a larger protein together with the ligation of the flanking "extein" sequences. Previously we reported the directed evolution of an intein-based molecular switch in which intein splicing in yeast cells was made dependent on the cell-permeable small molecule 4-hydroxytamoxifen (4-HT). Here we show that these evolved inteins are effective means of rendering protein function and biological signaling pathway activation dependent on 4-HT in mammalian cells. We have characterized the generality, speed, and dose dependence of ligand-induced protein splicing in murine NIH3T3 cells and in human HEK293 cells. Evolved inteins were used to control in mammalian cells the function of Gli1 and a truncated form of Gli3, two transcriptional mediators of the Hedgehog signaling pathway. Finally, we show that a complex biological process such as osteoblast differentiation can be made dependent on 4-HT using the evolved intein system. Our findings suggest that evolved small-molecule-dependent inteins may serve as a general means of achieving gene-specific, dose-dependent, post-translational, and small-molecule-induced control over protein activity in mammalian systems.

Animals↗

Biologic therapy of inflammatory bowel disease.

Advancing knowledge regarding the biology of chronic inflammation has led to the development of specific biologic therapies that mechanistically target individual inflammatory pathways. Many biologic therapies are being evaluated for the treatment of the chronic inflammatory bowel diseases, Crohn's disease and ulcerative colitis. Biologic compounds proven to be effective for Crohn's disease include monoclonal antibodies to tumor necrosis factor (infliximab and CDP571) and to the leukocyte adhesion molecule alpha4 integrin (natalizumab). Other biologic compounds for which there is insufficient evidence to judge efficacy for inflammatory bowel disease include: p55 tumor necrosis factor binding protein (onercept); interferon alpha; interferon beta-1a; anti-interferon gamma antibody; anti-interleukin 12 antibody; p65 anti-sense oligonucleotide (blocks NF-kappaB); granulocyte colony stimulating factor, and granulocyte macrophage colony stimulating factor; anti-interleukin 2 receptor antibody; epidermal growth factor; keratinocyte growth factor 2 (repifermin); human growth hormone; anti-CD4 antibody; and anti-alpha4beta7 antibody. Biologic therapies that have been proven ineffective for inflammatory bowel disease include: interleukin 10; interleukin 11; anti-sense intercellular adhesion molecule-1; and the tumor necrosis factor receptor fusion protein etanercept. Based on the early successes of infliximab, CDP571 and natalizumab, it seems certain that biologic therapy will play an important role in the future treatment of inflammatory bowel disease.

Biological Therapy↗

The possible biological importance of lipoxygenase pathway in aorta endothelial cells.

Cultured calf aortic endothelial cells metabolize exogenous 1-[14C] arachidonic acid via the lipoxygenase pathway to 12-hydroxyeicosatetraenoic acid and dihydroxyeicosatetraenoic acid(s). Disruption of the cells by freezing and thawing strongly increases the formation of lipoxygenase metabolites. Under these conditions mainly 15-hydroxy-eicosatetraenoic acid was formed in addition to 12-hydroxyeicosatetraenoic acid. From the calculation of the specific radioactivity of the lipoxygenase products formed it was concluded that not only the exogenous but also endogenous arachidonic acid released from intracellular sources such as phospholipids, triglycerides or cholesterol esters is oxygenated. The possible biological significance of the lipoxygenase metabolites is discussed.

Animals↗

Vascular permeability factor (VPF)/vascular endothelial growth factor (VEGF) peceptor-1 down-modulates VPF/VEGF receptor-2-mediated endothelial cell proliferation, but not migration, through phosphatidylinositol 3-kinase-dependent pathways.

Vascular permeability factor (VPF)/vascular endothelial growth factor (VEGF) achieves its multiple functions by activating two receptor tyrosine kinases, Flt-1 (VEGF receptor-1) and KDR (VEGF receptor-2), both of which are selectively expressed on primary vascular endothelium. To dissect the respective signaling pathways and biological functions mediated by these receptors in primary endothelial cells with these two receptors intact, we developed a chimeric receptor system in which the N terminus of the epidermal growth factor receptor was fused to the transmembrane domain and intracellular domain of KDR (EGDR) and Flt-1 (EGLT). We observed that KDR, but not Flt-1, was responsible for VPF/VEGF-induced human umbilical vein endothelial cell (HUVEC) proliferation and migration. Moreover, Flt-1 showed an inhibitory effect on KDR-mediated proliferation, but not migration. We also demonstrated that the inhibitory function of Flt-1 was mediated through the phosphatidylinositol 3-kinase (PI-3K)-dependent pathway because inhibitors of PI-3K as well as a dominant negative mutant of p85 (PI-3K subunit) reversed the inhibition, whereas a constitutively activated mutant of p110 introduced the inhibition to HUVEC-EGDR. We also observed that, in VPF/VEGF-stimulated HUVECs, the Flt-1/EGLT-mediated down-modulation of KDR/EGDR signaling was at or before intracellular Ca(2+) mobilization, but after KDR/EGDR phosphorylation. By mutational analysis, we further identified that the tyrosine 794 residue of Flt-1 was essential for its antiproliferative effect. Taken together, these studies contribute significantly to our understanding of the signaling pathways and biological functions triggered by KDR and Flt-1 and describe a unique mechanism in which PI-3K acts as a mediator of antiproliferation in primary vascular endothelium.

Base Sequence↗

Calculating the statistical significance of changes in pathway activity from gene expression data.

We present a statistical approach to scoring changes in activity of metabolic pathways from gene expression data. The method identifies the biologically relevant pathways with corresponding statistical significance. Based on gene expression data alone, only local structures of genetic networks can be recovered. Instead of inferring such a network, we propose a hypothesis-based approach. We use given knowledge about biological networks to improve sensitivity and interpretability of findings from microarray experiments. Recently introduced methods test if members of predefined gene sets are enriched in a list of top-ranked genes in a microarray study. We improve this approach by defining scores that depend on all members of the gene set and that also take pairwise co-regulation of these genes into account. We calculate the significance of co-regulation of gene sets with a nonparametric permutation test. On two data sets the method is validated and its biological relevance is discussed. It turns out that useful measures for co-regulation of genes in a pathway can be identified adaptively. We refine our method in two aspects specific to pathways. First, to overcome the ambiguity of enzyme-to-gene mappings for a fixed pathway, we introduce algorithms for selecting the best fitting gene for a specific enzyme in a specific condition. In selected cases, functional assignment of genes to pathways is feasible. Second, the sensitivity of detecting relevant pathways is improved by integrating information about pathway topology. The distance of two enzymes is measured by the number of reactions needed to connect them, and enzyme pairs with a smaller distance receive a higher weight in the score calculation.

Journal Article↗

Exposures to airborne particulate matter and adverse perinatal outcomes: a biologically plausible mechanistic framework for exploring potential effect modification by nutrition.

OBJECTIVES: The specific objectives are threefold: to describe the biologically plausible mechanistic pathways by which exposure to particulate matter (PM) may lead to the adverse perinatal outcomes of low birth weight (LBW), intrauterine growth retardation (IUGR), and preterm delivery (PTD); review the evidence showing that nutrition affects the biologic pathways; and explain the mechanisms by which nutrition may modify the impact of PM exposure on perinatal outcomes. METHODS: We propose an interdisciplinary conceptual framework that brings together maternal and infant nutrition, air pollution exposure assessment, and cardiopulmonary and perinatal epidemiology. Five possible albeit not exclusive biologic mechanisms have been put forth in the emerging environmental sciences literature and provide corollaries for the proposed framework. CONCLUSIONS: Protecting the environmental health of mothers and infants remains a top global priority. The existing literature indicates that the effects of PM on LBW, PTD, and IUGR may manifest through the cardiovascular mechanisms of oxidative stress, inflammation, coagulation, endothelial function, and hemodynamic responses. PM exposure studies relating mechanistic pathways to perinatal outcomes should consider the likelihood that biologic responses and adverse birth outcomes may be derived from both PM and non-PM sources (e.g., nutrition). In the concluding section, we present strategies for empirically testing the proposed model and developing future research efforts.

Air Pollutants↗

Antagonism of receptor-activated biological effects mediated by second messenger pathways.

It is generally held that many biologically active compounds produce their effects through a sequence of events that are initiated when the substances combine with selective receptors located on the cell surface membrane. Activation of these receptors produces a stimulus that is somehow transmitted intracellularly. The transduction between the stimulus and the response is now known to be mediated, in many systems, by an intracellular intermediary or second messenger. A model describing the relation of agonist concentration, receptor occupation, and biological response in such a system is herein extended to include antagonist binding at two target sites the cell-surface receptor and the receptor for the second messenger. It is demonstrated that the shift of an agonist's dose-response curve is characteristic of the site of antagonism and that analysis of this shift can reveal the existence of a second messenger pathway or, if this is known, the site of action of the antagonist.

Binding, Competitive↗

Structure and biology of tissue factor pathway inhibitor.

Human tissue factor pathway inhibitor (TFPI) is a modular protein comprised of three Kunitz type domains flanked by peptide segments that are less structured. The sequential order of the elements are: an N-terminal acidic region followed by the first Kunitz domain (K1), a linker region, a second Kunitz domain (K2), a second linker region, the third Kunitz domain (K3), and the C-terminal basic region. The K1 domain inhibits factor VIIa complexed to tissue factor (TF) while the K2 domain inhibits factor Xa. No direct protease inhibiting functions have been demonstrated for the K3 domain. Importantly, the Xa-TFPI complex is a much more potent inhibitor of the VIIa-TF than TFPI by itself. Furthermore, the C-terminal basic region of TFPI is required for rapid physiologic inhibition of coagulation and is needed for the inhibition of smooth muscle cell proliferation. Although a number of additional targets for attachment have been reported, the C-terminal basic region appears to play an important role in binding of TFPI to cell surfaces. A primary site of TFPI synthesis is endothelium and the endothelium-bound TFPI contributes to the antithrombotic potential of the vascular endothelium. Further, increased levels of plasma TFPI under septic conditions may represent endothelial dysfunction. We have proposed that the extravascular cells that synthesize TF also synthesize TFPI providing dual components necessary for the regulation of clotting in their microenvironment. Like the TF synthesis in these cells is augmented by serum, so is the case with the TFPI gene expression. TFPI gene knock out mice reveal embryonic lethality suggesting a possible role of this protein in early development. Since TF-induced coagulation is thought to play a significant role in many disease states, including disseminated intravascular clotting, sepsis, acute lung injury and cancer, recombinant TFPI may be a beneficial therapeutic agent in these disease states to attenuate pathologic clotting. The purpose of this review is to outline recent developments in the field related to the structural specificity and biology of TFPI.

Acute Disease↗

Organization and evolution of the avian forebrain.

Early 20th-century comparative anatomists regarded the avian telencephalon as largely consisting of a hypertrophied basal ganglia, with thalamotelencephalic circuitry thus being taken to be akin to thalamostriatal circuitry in mammals. Although this view has been disproved for more than 40 years, only with the recent replacement of the old telencephalic terminology that perpetuated this view by a new terminology reflecting more accurate understanding of avian brain organization has the modern view of avian forebrain organization begun to become more widely appreciated. The modern view, reviewed in the present article, recognizes that the avian basal ganglia occupies no more of the telencephalon than is typically the case in mammals, and that it plays a role in motor control and motor learning as in mammals. Moreover, the vast majority of the telencephalon in birds is pallial in nature and, as true of cerebral cortex in mammals, provides the substrate for the substantial perceptual and cognitive abilities evident among birds. While the evolutionary relationship of the pallium of the avian telencephalon and its thalamic input to mammalian cerebral cortex and its thalamic input remains a topic of intense interest, the evidence currently favors the view that they had a common origin from forerunners in the stem amniotes ancestral to birds and mammals.

Animals↗