Systems Approach to Refining Genome Annotation Reed, Jennifer L.; Patel, Trina R.; Chen, Keri H. ...
Proceedings of the National Academy of Sciences - PNAS,
11/2006, Letnik:
103, Številka:
46
Journal Article
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Genome-scale models of Escherichia coli K-12 MG1655 metabolism have been able to predict growth phenotypes in most, but not all, defined growth environments. Here we introduce the use of an ...optimization-based algorithm that predicts the missing reactions that are required to reconcile computation and experiment when they disagree. The computer-generated hypotheses for missing reactions were verified experimentally in five cases, leading to the functional assignment of eight ORFs (yjjLMN, yeaTU, dctA, idnT, and putP) with two new enzymatic activities and four transport functions. This study thus demonstrates the use of systems analysis to discover metabolic and transport functions and their genetic basis by a combination of experimental and computational approaches.
We applied whole-genome resequencing of Escherichia coli to monitor the acquisition and fixation of mutations that conveyed a selective growth advantage during adaptation to a glycerol-based growth ...medium. We identified 13 different de novo mutations in five different E. coli strains and monitored their fixation over a 44-d period of adaptation. We obtained proof that the observed spontaneous mutations were responsible for improved fitness by creating single, double and triple site-directed mutants that had growth rates matching those of the evolved strains. The success of this new genome-scale approach indicates that real-time evolution studies will now be practical in a wide variety of contexts.
Macitentan (Opsumit®) is a novel dual endothelin receptor antagonist (ERA) with sustained receptor binding properties developed by Actelion Pharmaceuticals Ltd. In October 2013, oral macitentan 10 mg ...once daily received its first global approval in the US, followed closely by Canada, for the treatment of pulmonary arterial hypertension (PAH). The drug has also received a positive opinion in the EU from the Committee for Medicinal Products for Human Use for the treatment of PAH, and is under regulatory review in several other countries for the same indication. Endothelin (ET)-1 influences pathological changes via two ET receptor subtypes (ETA and ETB), to which it binds with high affinity. ET-1 is implicated in several forms of vascular disease making it a valid target for the treatment of pulmonary vascular diseases such as PAH. Clinical development is underway for other indications, including Eisenmenger syndrome, ischaemic digital ulcers secondary to systemic sclerosis, and glioblastoma. Macitentan was also evaluated in idiopathic pulmonary fibrosis; however, a phase 2 trial did not meet its primary endpoint and further investigation in this indication was discontinued. Macitentan was developed by modifying the structure of bosentan in the search for an optimal dual ERA with improved efficacy and tolerability compared with other ERAs. This article summarizes the milestones in the development of macitentan leading to this first approval for PAH.
Siltuximab: first global approval Markham, Anthony; Patel, Trina
Drugs (New York, N.Y.),
07/2014, Letnik:
74, Številka:
10
Journal Article
Recenzirano
The anti-interleukin-6 (IL-6) chimeric monoclonal antibody siltuximab is the first drug to be approved for the treatment of multicentric Castleman's disease (MCD) in the US and European union (EU), ...having gained approval under the FDA priority review program in the US and from an accelerated assessment and recommendation by the Committee for Medicinal Products for Human Use (CHMP) in the EU. Development of the drug is continuing in smoldering multiple myeloma. This article summarizes the milestones in the development of siltuximab leading to this first approval for MCD.
A non-lacquer 10% topical solution of efinaconazole, developed by Valeant Pharmaceuticals International, received its first global approval in Canada in October 2013 for the treatment of ...onychomycosis. The product is under regulatory review in the US and Japan. The mechanism of anti-fungal activity of efinaconazole, a small-molecule triazole compound, appears to be similar to that of other anti-fungal triazoles, namely ergosterol synthesis inhibition. In particular, it appears to inhibit 14α demethylase, an enzyme involved in the conversion of lanosterol to ergosterol, resulting in secondary degenerative changes. This article summarizes the milestones in the development of efinaconazole leading to this first approval for onychomycosis.
By exploiting a genome-wide collection of bacterial single-gene deletion mutants, we have studied the toxicological pathways of a 60-nm cationic (amino-functionalized) polystyrene nanomaterial ...(PS-NH2) in bacterial cells. The IC50 of commercially available 60 nm PS-NH2 was determined to be 158 μg/mL, the IC5 is 108 μg/mL, and the IC90 is 190 μg/mL for the parent E. coli strain of the gene deletion library. Over 4000 single nonessential gene deletion mutants of Escherichia coli were screened for the growth phenotype of each strain in the presence and absence of PS-NH2. This revealed that genes clusters in the lipopolysaccharide biosynthetic pathway, outer membrane transport channels, ubiquinone biosynthetic pathways, flagellar movement, and DNA repair systems are all important to how this organism responds to cationic nanomaterials. These results, coupled with those from confirmatory assays described herein, suggest that the primary mechanisms of toxicity of the 60-nm PS-NH2 nanomaterial in E. coli are destabilization of the outer membrane and production of reactive oxygen species. The methodology reported herein should prove generally useful for identifying pathways that are involved in how cells respond to a broad range of nanomaterials and for determining the mechanisms of cellular toxicity of different types of nanomaterials.
New generation in vitro high-throughput screening (HTS) assays for the assessment of engineered nanomaterials provide an opportunity to learn how these particles interact at the cellular level, ...particularly in relation to injury pathways. These types of assays are often characterized by small sample sizes, high measurement error and high dimensionality, as multiple cytotoxicity outcomes are measured across an array of doses and durations of exposure. In this paper we propose a probability model for the toxicity profiling of engineered nanomaterials. A hierarchical structure is used to account for the multivariate nature of the data by modeling dependence between outcomes and thereby combining information across cytotoxicity pathways. In this framework we are able to provide a flexible surface-response model that provides inference and generalizations of various classical risk assessment parameters. We discuss applications of this model to data on eight nanoparticles evaluated in relation to four cytotoxicity parameters.
The development of high throughput screening (HTS) assays in the field of nanotoxicology provide new opportunities for the hazard assessment and ranking of engineered nanomaterials (ENMs). It is ...often necessary to rank lists of materials based on multiple risk assessment parameters, often aggregated across several measures of toxicity and possibly spanning an array of experimental platforms. Bayesian models coupled with the optimization of loss functions have been shown to provide an effective framework for conducting inference on ranks. In this article we present various loss-function-based ranking approaches for comparing ENM within experiments and toxicity parameters. Additionally, we propose a framework for the aggregation of ranks across different sources of evidence while allowing for differential weighting of this evidence based on its reliability and importance in risk ranking. We apply these methods to high throughput toxicity data on two human cell-lines, exposed to eight different nanomaterials, and measured in relation to four cytotoxicity outcomes. This article has supplementary material online.
Until recently, very little research has been conducted to assess the potential human health hazards associated with engineered nanomaterials (ENMs). In-vitro high-throughput screening (HTS) assays ...for the assessment of engineered nanomaterials provide new opportunities to learn how these particles interact at the cellular level, and may aid in reducing the demand for in-vivo testing. The large number of potential factors that could link nanomaterials to adverse human health impacts, create an imperative need to develop a stronger foundation for quantitative risk assessment in nanotoxicology. In this dissertation we propose a probability model for the analysis of high-throughput cellular assays. In particular, we develop a method that builds a balance between model complexity and interpretability as a tool to be used by subject-matter specialists for assessing cytotoxicity. The resulting multivariate surface-response model allows for joint inference on dose and time kinetics, and associated classical risk assessment parameters of interest. We illustrate the proposed methodology by profiling a multivariate screening study of eight metal-oxide nanomaterials. Next, we present loss-function-based methods for the hazard ranking of engineered nanomaterials. Specifically, we provide a decision-making tool for prioritizing extensive in-vivo testing of emerging nanomaterials. The proposed framework allows for the aggregation of ranks across different sources of evidence while allowing for differential weighting of this evidence based on its reliability and importance in risk ranking. We illustrate the methodology by ranking particles from a multivariate cytotoxicity screening study of eight metal oxides, conducted in two human cell-lines. Finally, we propose methodology for modeling the relationship between physicochemical properties of ENMs and their observed cytotoxicity, as an initial step in the development of a framework for predictive nanotoxicology. In particular, the proposed approach introduces a new measure of toxicity that is seamlessly integrated into a multi-dimensional model that accounts for dose and duration kinetics jointly using a flexible smooth surface fit. Moreover, the designed approach is appropriate for small sample size, and includes data integration and a framework for advanced dimension reduction through variable selection. The proposed method was applied to a library of 24 engineered nanomaterials.
New generation in vitro high-throughput screening (HTS) assays for the assessment of engineered nanomaterials provide an opportunity to learn how these particles interact at the cellular level, ...particularly in relation to injury pathways. These types of assays are often characterized by small sample sizes, high measurement error and high dimensionality, as multiple cytotoxicity outcomes are measured across an array of doses and durations of exposure. In this paper we propose a probability model for the toxicity profiling of engineered nanomaterials. A hierarchical structure is used to account for the multivariate nature of the data by modeling dependence between outcomes and thereby combining information across cytotoxicity pathways. In this framework we are able to provide a flexible surface-response model that provides inference and generalizations of various classical risk assessment parameters. We discuss applications of this model to data on eight nanoparticles evaluated in relation to four cytotoxicity parameters.
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