R 59-022

Microscopic observation drug-susceptibility assay vs. Xpert((R)) MTB/RIF for the diagnosis of tuberculosis in a rural African setting: a cost-utility analysis.[Pubmed:28380276]

Trop Med Int Health. 2017 Jun;22(6):734-743.

OBJECTIVE: To compare the cost-utility of microscopic observation drug-susceptibility assay (MODS) and Xpert((R)) MTB/RIF implementation for tuberculosis (TB) diagnosis in rural northern Mozambique. METHODS: Stochastic transmission compartmental TB model from the healthcare provider perspective with parameter input from direct measurements, systematic literature reviews and expert opinion. MODS and Xpert((R)) MTB/RIF were evaluated as replacement test of smear microscopy (SM) or as an add-on test after a negative SM. Costs were calculated in 2013 USD, effects in disability-adjusted life years (DALY). Willingness to pay threshold (WPT) was established at once the per capita Gross National Income of Mozambique. RESULTS: MODS as an add-on test to negative SM produced an incremental cost-effectiveness ratio (ICER) of 5647.89USD/DALY averted. MODS as a substitute for SM yielded an ICER of 5374.58USD/DALY averted. Xpert((R)) MTB/RIF as an add-on test to negative SM yielded ICER of 345.71USD/DALY averted. Xpert((R)) MTB/RIF as a substitute for SM obtained an ICER of 122.13USD/DALY averted. TB prevalence and risk of infection were the main factors impacting MODS and Xpert((R)) MTB/RIF ICER in the one-way sensitivity analysis. In the probabilistic sensitivity analysis, Xpert((R)) MTB/RIF was most likely to have an ICER below the WPT, whereas MODS was not. CONCLUSION: Our cost-utility analysis favours the implementation of Xpert((R)) MTB/RIF as a replacement of SM for all TB suspects in this rural high TB/HIV prevalence African setting.

cnAnalysis450k: an R package for comparative analysis of 450k/EPIC Illumina methylation array derived copy number data.[Pubmed:28379302]

Bioinformatics. 2017 Aug 1;33(15):2266-2272.

Motivation: Detailed copy number (CN) variation data can be obtained from 450k or EPIC Illumina methylation assays. However, the effects of different preprocessing strategies (normalization, transformation and selection of gain/loss cutoff values) on variant calling have not been evaluated systematically. Results: We provide an R package which allows to directly compare any preprocessed CN data. It provides its own CN alteration detection methodology: segments are identified through detection of changes in variance of CN data and are subsequently filtered for significance. Meaningful cutoffs for gain/loss definition can be identified automatically through analysis of the resulting DeltaCN distributions of all analyzed samples. Three exemplary datasets (2x450k, 1xEPIC) were selected for comparative analyses of Raw, Illumina, SWAN, Quantile, Noob, Funnorm and Dasen normalizations. Importantly, all CN data distributions were skewed (-0.66 to -1.2) therefore requiring different gain/loss cutoffs. Depending on the normalization method, prominent baseline differences between samples could be observed. We present a workflow, which alleviates both issues: Z-transformation removes baseline differences between samples, and automatic cutoff selection circumvents the problems accompanying the skewed distributions. Additional filtering of candidates by significance yields comparable results for most enumerated normalization methods except for SWAN. In contrast, manual cutoff determination results in highly variable numbers of variant calls, highly dependent on the selected normalization method. Taken together, we present a workflow which allows to robustly identify copy number alterations in methylation array data fairly independent of the applied normalization. Availability and Implementation: The cnAnalysis450k package is available on github ( https://github.com/mknoll/cnAnalysis450k ). Contact: m.knoll@dkfz.de. Supplementary information: Supplementary data are available at Bioinformatics online.

Novel diacylglycerol kinase inhibitor selectively suppressed an U46619-induced enhancement of mouse portal vein contraction under high glucose conditions.[Pubmed:15289283]

Br J Pharmacol. 2004 Sep;143(1):166-78.

1. Diacylglycerol kinase (DG kinase) is a key enzyme in vascular contraction; however, alterations of the regulatory mechanisms in vascular dysfunction are poorly understood. In this study, the effect of a novel DG kinase inhibitor, stemphone, on vascular contraction was investigated. 2. The conventional DG kinase inhibitor, 6-[2-(4-[(4-fluorophenyl)phenyl-methylene]-1-piperidinyl)ethyl]-7-methyl-5H-thiaz olo [3,2-alpha] pyrimidine-5-one (R59022) (0.1-30 microm), inhibited thromboxane A(2) analogue 9,11-dideoxy-11alpha,9alpha-epoxymethanoprostaglandin F(2alpha) (U46619)-induced sustained contractions in mouse aorta and porcine coronary artery in a dose-dependent manner. Treatment with stemphone did not affect contractions in these tissues. However, stemphone significantly inhibited (>0.3 microm) U46619-induced spontaneous phasic contraction in mouse portal vein. This inhibitory effect was not detected following R59022 treatment in portal vein. Therefore, stemphone demonstrated selectivity in terms of portal vein contraction. 3. Under high glucose (22.2 mm) conditions, U46619-induced contraction was enhanced in these three types of vascular tissue. Inhibitory effects of R59022 were attenuated under these conditions; however, effects of stemphone were observed. These results indicated that stemphone could inhibit portal vein contraction under high glucose conditions, for example, diabetes. These data suggested the possibility that DG kinase may be a target of hyperportal pressure. 4. Total mass of DG was enhanced under high glucose conditions. DG was derived from incorporated glucose via de novo synthesis in the absence of phospholipase C pathway mediation. This enhanced DG under high glucose conditions activated a calcium-independent protein kinase C (PKC). This PKC was associated with calcium-independent DG kinase activation. Treatment with stemphone also inhibited calcium-independent DG kinase. These signal transduction pathways were distinguishable from a DG-PKC pathway under normal glucose conditions. 5. The present investigation suggested that stemphone selectively inhibited overcontraction of portal vein induced by high glucose levels. This phenomenon was attributable to inhibition of calcium-independent DG kinase activation that occurred under high glucose conditions mediated by both DG synthesized from glucose and calcium-independent PKC activation.

Neutrophil chemotaxis induced by the diacylglycerol kinase inhibitor R59022.[Pubmed:8392381]

Biochim Biophys Acta. 1993 Jul 28;1178(1):97-102.

The diacylglycerol kinase inhibitor R59022 induced chemotaxis in neutrophils. The response to R59022 was primarily chemotactic and only very little chemokinetic. Pretreatment with the protein kinase C inhibitors staurosporine and AMG-C16 inhibited chemotaxis induced by R59022 indicating the involvement of protein kinase C. In contrast, chemotaxis induced by fMet-Leu-Phe was only slightly inhibited by staurosporine and AMG16. The effects of R59022 were comparable to the effects of the protein kinase C activators DiC8 and PMA and suggest an involvement of protein kinase C. Pretreatment with pertussis toxin inhibited R59022-induced migration, fMet-Leu-Phe-induced migration, and random migration. GTP gamma S, which stimulates migration of electropermeabilized neutrophils by itself, causes an additive increase of migration in electropermeabilized neutrophils stimulated with a suboptimal concentration R59022, but causes a synergistic increase of migration in cells stimulated with a suboptimal concentration fMet-Leu-Phe. The effects of GTP gamma S on migration are completely inhibited by AMG-C16. This suggests that the GTP-binding protein involved in R59022-activated migration is the G protein that is associated with random migration.

A diacylglycerol kinase inhibitor, R59022, potentiates secretion by and aggregation of thrombin-stimulated human platelets.[Pubmed:2821994]

Biochem J. 1987 May 1;243(3):809-13.

The diacylglycerol kinase inhibitor R59022 (10 microM) potentiates secretion and aggregation responses in human platelets challenged with sub-maximal concentrations of thrombin. Potentiation correlates closely with increased formation of diacylglycerol, increased phosphorylation of a 40 kDa protein, a known substrate for protein kinase C, and with decreased formation of phosphatidic acid, the product of diacylglycerol kinase. Phosphorylation of myosin light chains, formation of inositol phosphates and the mobilization of Ca2+ by thrombin are not affected by R59022 (10 microM). These data support a role for protein kinase C in platelet aggregation and secretion, and provide further evidence that endogenous diacylglycerols bring about the activation of this enzyme. These data also add further argument against a role for phosphatidic acid in platelet activation.

R 59 022, a diacylglycerol kinase inhibitor. Its effect on diacylglycerol and thrombin-induced C kinase activation in the intact platelet.[Pubmed:2999135]

J Biol Chem. 1985 Dec 15;260(29):15762-70.

R 59 022 (6-[2-[4-[(4-fluorophenyl) phenylmethylene)-1-piperidinyl]ethyl]-7-methyl-5H-thiazolo[3,2-alpha] pyrimidin-5-one) was found to inhibit diacylglycerol kinase in human red blood cell membranes at concentrations where polyphosphoinositide phosphodiesterase, phosphatidylinositol kinase, and phosphatidylinositol 4-phosphate kinase activity remained unaffected. The concentration needed for half-maximal inhibition (IC50) was 2.8 +/- 1.5 X 10(-6) M for the kinase acting on endogenous diacylglycerol and 3.3 +/- 0.4 X 10(-6) M when 1-oleoyl-2-acetylglycerol (OAG) was added exogenously as substrate. In intact platelets, R 59 022 inhibits the phosphorylation of OAG to 1-oleoyl-2-acetylglyceryl-3-phosphoric acid (OAPA) (IC50: 3.8 +/- 1.2 X 10(-6) M); concomitantly the stimulation of protein kinase C activity by OAG was amplified. When in platelets inositol lipid turnover is accelerated by thrombin, further addition of R 59 022 results in a marked elevation of diacylglycerol levels, a decreased formation of phosphatidic acid and an increased protein kinase C activity as compared with the controls. It is concluded that in studies on the signal-transducing system coupled to inositol lipid metabolism R 59 022 might occupy a role comparable to cyclic AMP phosphodiesterase inhibitors, since it potentiates the effect of the putative second messenger diacylglycerol by preventing its rapid metabolism.

R 59-022 (DKGI-I) is a diacylglycerol kinase inhibitor (IC50=2.8 μM). R 59-022 is a 5-HTR antagonist, and activates protein kinase C (PKC). R 59-022 potentiates thrombin-induced diacylglycerol production in platelets and inhibits phosphatidic acid production in neutrophils.

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