Critical pathways in the analysis of breast masses.
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Results for “Pathway analysis”
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Comparing DNA damage-processing pathways by computer analysis of chromosome painting data.
Chromosome aberrations are large-scale illegitimate rearrangements of the genome. They are indicative of DNA damage and informative about damage processing pathways. Despite extensive investigations over many years, the mechanisms underlying aberration formation remain controversial. New experimental assays such as multiplex fluorescent in situ hybridyzation (mFISH) allow combinatorial "painting" of chromosomes and are promising for elucidating aberration formation mechanisms. Recently observed mFISH aberration patterns are so complex that computer and graph-theoretical methods are needed for their full analysis. An important part of the analysis is decomposing a chromosome rearrangement process into "cycles." A cycle of order n, characterized formally by the cyclic graph with 2n vertices, indicates that n chromatin breaks take part in a single irreducible reaction. We here describe algorithms for computing cycle structures from experimentally observed or computer-simulated mFISH aberration patterns. We show that analyzing cycles quantitatively can distinguish between different aberration formation mechanisms. In particular, we show that homology-based mechanisms do not generate the large number of complex aberrations, involving higher-order cycles, observed in irradiated human lymphocytes.
Algorithms↗
Transcriptome and proteome analysis identifies the pathways that increase hepatic lipid accumulation in zinc-deficient rats.
For identification of the underlying molecular changes in hepatic lipid metabolism in zinc deficiency, rats were force-fed a zinc-deficient diet. Subsequently DNA-microarray and proteome profiling was performed in combination with hepatic lipid analysis. Of 6200 target sequences analyzed, 268 transcripts showed altered expression levels in livers of zinc-deficient rats, with 43 genes thereof related to hepatic lipid metabolism. Northern blot analysis and quantitative real-time RT-PCR were employed to confirm changes in mRNA levels. Proteins involved in lipid metabolism were identified by proteome analysis. Functional gene clusters with uniform changes in transcript levels suggested that the pathways required for lipolysis and mitochondrial as well as peroxisomal fatty acid degradation were downregulated, whereas those needed for de novo fatty acid synthesis and triglyceride assembly were increased. Subsequent enzymatic analysis of liver tissues confirmed an almost 40% greater triacylglycerol concentration in zinc-depleted rats, as well as an altered fatty acid composition of the lipid fraction as determined by gas chromatography. Liver lipids of zinc-deficient rats had significantly greater proportions of cis-9-oleic acid, cis-11-vaccenic acid, caprylic acid, myristic acid, alpha-linolenic acid, and eicosapentaenoic acid, and significantly less stearic and arachidonic acids. These alterations in hepatic metabolism are discussed in the context of changes in mRNA and protein levels of enzymes and transporters responsible for fatty acid metabolism, sequestration, and their transcriptional control.
Animals↗
Analysis of the pathway structure of metabolic networks.
Metabolic networks comprise a multitude of enzymatic reactions carrying out various functions related to cell growth and product formation. Although such reactions are occasionally organized into biochemical pathways, a formal procedure is desired to identify the independent pathways in a bioreaction network and the degree of engagement of each individual reaction in these pathways. We present a procedure for the identification of the independent pathways of bioreaction networks of any size and complexity. The method makes use of the steady-state internal metabolite stoichiometry matrix and defines the independent pathways through the reaction membership of its kernel matrix. Examples from the aromatic amino acid biosynthetic pathway and central carbon metabolism of cells in culture are provided to illustrate the method. Applications to the analysis of the control structure of bioreaction networks are also discussed.
Adenosine Triphosphate↗
Global gene expression analysis identifies molecular pathways distinguishing blastocyst dormancy and activation.
Delayed implantation (embryonic diapause) occurs when the embryo at the blastocyst stage achieves a state of suspended animation. During this period, blastocyst growth is very slow, with minimal or no cell division. Nearly 100 mammals in seven different orders undergo delayed implantation, but the underlying molecular mechanisms that direct this process remain largely unknown. In mice, ovariectomy before preimplantation ovarian estrogen secretion on day 4 of pregnancy initiates blastocyst dormancy, which normally lasts for 1-2 weeks by continued progesterone treatment, although blastocyst survival decreases with time. An estrogen injection rapidly activates blastocysts and initiates their implantation in the progesterone-primed uterus. Using this model, here we show that among approximately 20,000 genes examined, only 229 are differentially expressed between dormant and activated blastocysts. The major functional categories of altered genes include the cell cycle, cell signaling, and energy metabolic pathways, particularly highlighting the importance of heparin-binding epidermal growth factor-like signaling in blastocyst-uterine crosstalk in implantation. The results provide evidence that the two different physiological states of the blastocyst, dormancy and activation, are molecularly distinguishable in a global perspective and underscore the importance of specific molecular pathways in these processes. This study has identified candidate genes that provide a scope for in-depth analysis of their functions and an opportunity for examining their relevance to blastocyst dormancy and activation in numerous other species for which microarray analysis is not available or possible due to very limited availability of blastocysts.
Animals↗
Integrated mechanistic and data-driven modelling for multivariate analysis of signalling pathways.
Mathematical models of highly interconnected and multivariate signalling networks provide useful tools to understand these complex systems. However, effective approaches to extracting multivariate regulation information from these models are still lacking. In this study, we propose a data-driven modelling framework to analyse large-scale multivariate datasets generated from mathematical models. We used an ordinary differential equation based model for the Fas apoptotic pathway as an example. The first step in our approach was to cluster simulation outputs generated from models with varied protein initial concentrations. Subsequently, decision tree analysis was applied, in which we used protein concentrations to predict the simulation outcomes. Our results suggest that no single subset of proteins can determine the pathway behaviour. Instead, different subsets of proteins with different concentrations ranges can be important. We also used the resulting decision tree to identify the minimal number of perturbations needed to change pathway behaviours. In conclusion, our framework provides a novel approach to understand the multivariate dependencies among molecules in complex networks, and can potentially be used to identify combinatorial targets for therapeutic interventions.
Apoptosis↗
Finite element analysis of current pathways with implanted electrodes.
A technique for numerical solution to complex electric field distribution problems has been devised. The specific application for which it was developed is the analysis of current density and isopotential line spacing from implanted neurostimulation electrodes. Three configurations of cerebellar stimulation electrodes in clinical use were studied for current spread to regions distant from the cerebellum using a planar model of the human head, neck, and upper torso in mid-saggital section. It was found that an array of cathodes on the superior cerebellar surface and an array of anodes on the inferior cerebellar surface causes significant current spread to the brainstem, a prediction confirmed by clinical observation in patients with previously implanted electrodes of this configuration. Results modelling other electrode configurations are also presented, along with a study of the effects of possible inaccuracies in available impedance data for neural tissue.
Brain Diseases↗
Optimizing bioconversion pathways through systems analysis and metabolic engineering.
We demonstrate a general approach for metabolic engineering of biocatalytic systems comprising the uses of a chemostat for strain improvement and radioisotopic tracers for the quantification of pathway fluxes. Flux determination allows the identification of target pathways for modification as validated by subsequent overexpression of the corresponding gene. We demonstrate this method in the indene bioconversion network of Rhodococcus modified for the overproduction of 1,2-indandiol, a key precursor for the AIDS drug Crixivan.
Biomedical Engineering↗
MetaModel: a program for modelling and control analysis of metabolic pathways on the IBM PC and compatibles.
MetaModel is a user-friendly program for calculating steady-state fluxes and metabolite concentrations of metabolic systems on the IBM PC and compatible computers. For any steady state that is obtained, one can then calculate a matrix of elasticity coefficients at that steady state, or a matrix of control and response coefficients. It thus offers a simple way to calculate the control structure of a pathway: it provides not only an educational tool that allows the student to verify empirically the classic summation relationships of metabolic control analysis but also a research tool for addressing 'what if?' questions about the behaviour of metabolic systems. Results can not only be printed or stored in a file, but can also be written to a special file that can be read by popular spreadsheet programs, thereby giving access to rapid, flexible and powerful methods for subsequent analysis and plotting of these results.
Algorithms↗
Phylogenetic analysis of metabolic pathways.
The information provided by completely sequenced genomes can yield insights into the multi-level organization of organisms and their evolution. At the lowest level of molecular organization individual enzymes are formed, often through assembly of multiple polypeptides. At a higher level, sets of enzymes group into metabolic networks. Much has been learned about the relationship of species from phylogenetic trees comparing individual enzymes. In this article we extend conventional phylogenetic analysis of individual enzymes in different organisms to the organisms' metabolic networks. For this purpose we suggest a method that combines sequence information with information about the underlying reaction networks. A distance between pathways is defined as incorporating distances between substrates and distances between corresponding enzymes. The new analysis is applied to electron-transfer and amino acid biosynthesis networks yielding a more comprehensive understanding of similarities and differences between organisms.
Animals↗
Analysis of flowering pathway integrators in Arabidopsis.
Flowering is regulated by an integrated network of several genetic pathways in Arabidopsis. The key genes integrating multiple flowering pathways are FT, SOC1 and LFY. To elucidate the interactions among these integrators, genetic analyses were performed. FT and SOC1 share the common upstream regulators CO, a key component in the long day pathway, and FLC, a flowering repressor integrating autonomous and vernalization pathways. However, the soc1 mutation further delayed the flowering time of long day pathway mutants including ft, demonstrating that SOC1 acts partially independently of FT. Although soc1 did not show an obvious defect in flower meristem determination on its own, it dramatically increased the number of coflorescences in a lfy mutant, which is indicative of a defect in floral initiation. Therefore, double mutant analysis shows that the three integrators have both overlapping and independent functions in the determination of flowering time and floral initiation. The expression analysis showed that FT regulates SOC1 expression, and SOC1 regulates LFY expression, but not vice versa, which is consistent with the fact that FT and LFY have the least overlapping functions among the three integrators. The triple mutation ft soc1 lfy did not block flowering completely under long days, indicating the presence of other integrators. Finally, vernalization accelerated flowering of flc ft soc1 and ft soc1 lfy triple mutants, which shows that the vernalization pathway also has targets other than FLC, FT, SOC1 and LFY. Our genetic analysis reveals the intricate nature of genetic networks for flowering.
Arabidopsis↗
Distribution of polycyclic aromatic hydrocarbons in the coastal region off Macao, China: assessment of input sources and transport pathways using compositional analysis.
The coastal region off Macao is a known depositional zone for persistent organic pollutants (POPs) in the Pearl River Delta and Estuary of southern China and an important gateway for the regional contributions of contamination to the globe. This paper presents a comprehensive assessment of the input sources and transport pathways of polycyclic aromatic hydrocarbons (PAHs) found in the coastal sediments of Macao, based on measurements of 48 2-7 ring PAHs and 7 sulfur/oxygenated (S/O) PAH derivatives in 45 sediment, 13 street dust, and 68 aerosol samples. Total sediment PAHs concentrations ranged from 294 to 12741 ng/g, categorized as moderate contamination compared to other regions of Asia and the world. In addition, the PAH compounds appeared to be bound more strongly to aromatics-rich soot particles than to natural organic matter, implying a prevailing atmospheric transport route for PAHs to Macao's coast. Compositional analysis and principal component analysis (PCA) suggested that different classes of PAHs in the coastal sediments of Macao may have been derived from different input sources via various transport pathways. For example, alkylated and S/O PAHs were likely derived from fossil fuel leakage and transported to sediments by both aerosols particles and street runoff. High-molecular-weight parent PAHs were predominantly originated from automobile exhausts and distributed by direct and indirect atmospheric deposition. Low-molecular-weight parent PAHs, on the other hand, may have stemmed from lower temperature combustion and fossil fuel (such as diesel) spillage from ships and boats and were transported to sediments by river runoff or direct discharge as well as by air-water exchange.
Air Pollutants↗
Functional transcriptomes: comparative analysis of biological pathways and processes in eukaryotes to infer genetic networks among transcripts.
Microarray technology enables us to monitor large changes in transcripts at any given time. The compilation of these data makes possible the comparison of such gene expression data on a genome-wide scale. As comparisons of genome sequence data yield new biological insights, comparative analyses of transcriptome data also promise new discoveries regarding metabolic pathways and cellular processes. The coordinated expression of genes shows that these genes physically interact with each other or are part of the same cascade. We have produced one of the largest expression profiles of adult mice and developmental tissues. These data, as well as the data on yeast from previous reports, were used to see whether coordinated expression (with high correlation coefficient) is closely coupled to the actual cascade on the pathway map.
Animals↗
Small cell carcinoma of the endometrium: report of a case with analysis of Wnt/beta-catenin pathway.
Small cell carcinoma of the endometrium (SCCE) is extremely rare. Previous reports indicate that SCCE frequently shows systemic spread and has a poor prognosis. Beta-catenin has been shown to be a key downstream effector of the Wnt signaling pathway, which regulates cell growth and survival. Decreased membranous expression of beta-catenin in cancers correlates with poor prognosis and is associated with dissemination of tumor cells and the formation of metastases. Recently, some different investigators demonstrated aberrant beta-catenin accumulation in neuroendocrine tumors arising in different organs, suggesting a role for the Wnt/beta-catenin signaling pathway during neuroendocrine tumorigenesis. Here, we report a new case of SCCE associated with peritoneal spreading and aggressive course; the patient died one month after surgery. This study also aimed at assessing the involvement of the Wnt signaling pathway in this rare neuroendocrine tumor. Interestingly, both intense nuclear beta-catenin accumulation and cyclin D1 immunoreactivity were restricted to carcinoma cells invading lymphatic vessels. However, mutation analysis failed to demonstrate any mutation in exon 3 of the beta-catenin gene or exon 15 of the APC gene in the present case. Although the mechanism of nuclear accumulation of beta-catenin is still unknown, the heterotopic nuclear localization of beta-catenin may play a role in the tumor invasion process and, subsequently, may be associated with the aggressive behavior of SCCE.
Biomarkers, Tumor↗
GH induced lipolysis stimulation in 3T3-L1 adipocytes stably expressing hGHR: analysis on signaling pathway and activity of 20K hGH.
We have constructed a cell line of 3T3-L1 which can efficiently express human GHR (3T3-L1-hGHR) after differentiation to adipocytes. The expressed hGHR was detected as two bands with approximate molecular sizes of 120K by Western analysis using hGHR specific monoclonal antibody. Maximum lipolytic activity induced by hGH in the 3T3-L1-hGHR was enhanced 10-fold as compared to that in 3T3-L1, suggesting that expressed hGHR is functionally active. Comparative analysis using bGH and hGH revealed that 70% of lipolysis stimulation by 1-10 ng/ml hGH could be attributed to hGHR-mediated response. Analyses on inhibition and phosphorylation of signaling molecules suggested that GH-induced lipolysis stimulation is dependent on gene expression and not mediated through PKA-, PKC-, PLA-, PLC-, nor MAPK-pathway but possibly through JAK-STATs pathway. Duration of STAT5 activation by hGH continued up to 48 h. We also revealed that 22 K hGH isoform, 20K hGH which has been reported as a weaker agonist for GH-induced lipolysis stimulation, possesses equipotent activity and shows stronger action in the presence of hGHBP as compared to 22 K hGH. Taken together we conclude that the hGH-induced lipolysis was not mediated through MAP-, PKA-, PKC-, nor PLA-pathway but might be mediated through STAT pathway and that 20K hGH might show higher lipolytic activity than 22 K hGH in adipose tissue that produces a large amount of GHBP.
3T3 Cells↗
Consecutive silver staining and autoradiography of 35S and 32P-labeled cellular proteins: application for the analysis of signal transducing pathways.
The methodology for the simultaneous analysis of protein synthesis concomitant with protein phosphorylation/dephosphorylation is described. The technique consists of metabolic labeling of rat liver epithelial (RLE) cells with [32P]orthophosphate and [35S]methionine, performing two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) of the mixed samples, followed by silver staining and subsequent autoradiography of the dried silver stained 2-D PAGE electrophoretograms using two films placed back-to-back. The first film, which is positioned in direct contact with the dried silver-stained gel, visualized both exposure to 35S and 32P while the second film recorded exposure to only 32P due to the differential energy levels of the two isotopes. The juxta-positioning of the silver-stained images with the two autoradiographic film images permits the unambiguous mapping of the phosphorylated polypeptides back to their corresponding silver-stained and methionine-labeled counterparts. This strategy provides quantitative information utilizing both silver staining (measure of constitutive levels of protein expression) and metabolic labeling to measure rates of protein synthesis and/or degradation and phosphorylation and/or dephosphorylation using [35S]methionine and [32P]orthophosphate, respectively. We have utilized this methodology for the in vitro analysis of transforming growth factor type beta 1 (TGF-beta 1)-mediated signal transduction in RLE cells and have identified three nuclear polypeptides, 1 (pI 4.95/M(r) 97 kDa), 2 (5.00/85 kDa) and 3 (4.90/84 kDa) whose phosphorylation status is rapidly and transiently modulated by TGF-beta 1. The methodology described should have wide applications in studies where it is desirous to measure protein synthesis and/or degradation concomitant with signal transduction pathways involving protein phosphorylation.
Animals↗
Molecular analysis integrating different pathways associated with androgen-independent progression in LuCaP 23.1 xenograft.
After therapeutic hormone deprivation, most prostate cancer (PrCa) cells develop androgen-independent (AI) growth. PrCa is highly heterogeneous and multifocal, suggesting that several molecular processes or pathways may be contributing to AI. The human LuCaP 23.1 xenograft model retains clinical hallmarks of PrCa, including heterogeneous growth, PSA production, androgen-responsiveness and progression to AI. In this work, we studied the effect of androgen depletion (castration) on the growth of LuCaP 23.1 xenografts. A total of 100 nude mice were implanted and analysed for their growth profiles before and after castration. By 11 and 15 weeks, tumours were harvested and assessed for molecular marker expression specific for PrCa. Prior to castration we found 37 fast growing (FG) tumours (948.9+/-76.9 mm(3)) and 63 slow growing (SG) tumours (229.6+/-18.4 mm(3)), a previously undescribed result for this PrCa model. Quantitative RT-PCR showed that in comparison to SGs, FGs contained high HER1, uPA and thymidilate synthetase (TS) expression with low levels of 5alpha-reductase 2 mRNA. All FG tumours progressed rapidly to AI growth 5 weeks after castration (FG-P). In SG castrated tumours, 66% of tumours (SG-P) showed retarded progression (by 12 weeks) to AI, whereas 34% responded to castration (SG-R). Molecular analysis permitted us to define distinct molecular profiles integrating different pathways associated with AI progression. FG-P, and a subgroup of SG-P tumours, presented significantly high levels of peptidylglycine alpha-amidating monooxygenase (PAM), HER1, HER2, TS, and uPA mRNA, all of which correlated with AR expression. The second subgroup of SG-P tumours showed overexpression of the antiapoptotic gene Bcl-2. A third subgroup of SG-P tumours showed significant expression of hypoxia-related gene (adrenomedullin) after castration. This work permitted to define distinct molecular profiles related to different AI growth in the LuCaP 23.1 xenograft.
Androgens↗
The spinal cord descending pathway for micturition: analysis in patients with spinal cord infarction.
We present three patients with urinary retention caused by spinal cord infarction of the deep white matter bilaterally within the ventral and lateral columns. This region corresponds to the watershed of the anterior spinal artery. We consider therefore that the descending pathway to the bladder lies in this area.
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