Hermida L.,Philip Morris International Research and Development |
Poussin C.,Philip Morris International Research and Development |
Stadler M.B.,Friedrich Miescher Institute for Biomedical Research |
Stadler M.B.,University of Basel |
And 14 more authors.
BMC Genomics | Year: 2013
Background: High-throughput omics technologies such as microarrays and next-generation sequencing (NGS) have become indispensable tools in biological research. Computational analysis and biological interpretation of omics data can pose significant challenges due to a number of factors, in particular the systems integration required to fully exploit and compare data from different studies and/or technology platforms. In transcriptomics, the identification of differentially expressed genes when studying effect(s) or contrast(s) of interest constitutes the starting point for further downstream computational analysis (e.g. gene over-representation/enrichment analysis, reverse engineering) leading to mechanistic insights. Therefore, it is important to systematically store the full list of genes with their associated statistical analysis results (differential expression, t-statistics, p-value) corresponding to one or more effect(s) or contrast(s) of interest (shortly termed as " contrast data" ) in a comparable manner and extract gene sets in order to efficiently support downstream analyses and further leverage data on a long-term basis. Filling this gap would open new research perspectives for biologists to discover disease-related biomarkers and to support the understanding of molecular mechanisms underlying specific biological perturbation effects (e.g. disease, genetic, environmental, etc.).Results: To address these challenges, we developed Confero, a contrast data and gene set platform for downstream analysis and biological interpretation of omics data. The Confero software platform provides storage of contrast data in a simple and standard format, data transformation to enable cross-study and platform data comparison, and automatic extraction and storage of gene sets to build new a priori knowledge which is leveraged by integrated and extensible downstream computational analysis tools. Gene Set Enrichment Analysis (GSEA) and Over-Representation Analysis (ORA) are currently integrated as an analysis module as well as additional tools to support biological interpretation. Confero is a standalone system that also integrates with Galaxy, an open-source workflow management and data integration system. To illustrate Confero platform functionality we walk through major aspects of the Confero workflow and results using the Bioconductor estrogen package dataset.Conclusion: Confero provides a unique and flexible platform to support downstream computational analysis facilitating biological interpretation. The system has been designed in order to provide the researcher with a simple, innovative, and extensible solution to store and exploit analyzed data in a sustainable and reproducible manner thereby accelerating knowledge-driven research. Confero source code is freely available from http://sourceforge.net/projects/confero/. © 2013 Hermida et al.; licensee BioMed Central Ltd.
Konig A.,University of Oxford |
Konig A.,University of Luxembourg |
Kuiper H.A.,Wageningen University |
Marvin H.J.P.,Wageningen University |
And 19 more authors.
Food Control | Year: 2010
Three main changes to current risk analysis processes are proposed to improve their transparency, openness, and accountability. First, the addition of a formal framing stage would allow interested parties, experts and officials to work together as needed to gain an initial shared understanding of the issue, the objectives of regulatory action, and alternative risk management measures. Second, the scope of the risk assessment is expanded to include the assessment of health and environmental benefits as well as risks, and the explicit consideration of economic- and social-impacts of risk management action and their distribution. Moreover approaches were developed for deriving improved information from genomic, proteomic and metabolomic profiling methods and for probabilistic modelling of health impacts for risk assessment purposes. Third, in an added evaluation stage, interested parties, experts, and officials may compare and weigh the risks, costs, and benefits and their distribution. As part of a set of recommendations on risk communication, we propose that reports on each stage should be made public. © 2010 Elsevier Ltd.
Weitkunat R.,Philip Morris International Research and Development |
Lee P.N.,P N Lee Statistics and Computing Ltd |
Baker G.,Philip Morris International Research and Development |
Sponsiello-Wang Z.,Philip Morris International Research and Development |
And 2 more authors.
Regulatory Toxicology and Pharmacology | Year: 2015
Based on the Food and Drug Administration's Modified Risk Tobacco Product (MRTP) Application draft guideline, Philip Morris International (PMI) has developed a Population Health Impact Model to estimate the reduction in the number of deaths over a period following the introduction of an MRTP. Such a model is necessary to assess the effect that its introduction would have on population health, given the lack of epidemiological data available prior to marketing authorization on any risks from MRTPs. The model is based on publicly available data on smoking prevalence and on the relationships between smoking-related disease-specific mortality and various aspects of the smoking of conventional cigarettes (CCs), together with an estimate of exposure from the MRTP relative to that from CCs, and allows the exploration of possible scenarios regarding the effect of MRTP introduction on the prevalence of CC and MRTP use, individually and in combination. By comparing mortality attributable in a scenario where the MRTP is introduced with one where it is not, the model can estimate the mortality attributable to CCs and the MRTP, as well as the reduction in the deaths attributable to the introduction of the MRTP. © 2015 The Authors.
Winkelmann C.,Philip Morris International Research and Development |
Winkelmann C.,Philip Morris Products SA |
Nordlund M.,Philip Morris International Research and Development |
Nordlund M.,Philip Morris Products SA |
And 5 more authors.
International Journal for Numerical Methods in Fluids | Year: 2014
The dynamics of a single-species aerosol composed of droplets in air is described in terms of nucleation, evaporation, condensation, and coagulation processes. We present a comprehensive overview of the Euler-Euler formulation, which gives rise to a model in which fast nucleation that initiates aerosol droplets co-exists with comparably slow condensation. The latter process is responsible for the subsequent growth of the droplets. To accurately represent the dynamical consequences of the fast nucleation process, while retaining numerical efficiency, a new second-order time-integration method for the nucleation, evaporation, and condensation processes is proposed and analyzed. The new time-integration method takes the form of a 'corrected Euler forward' method. It includes rapid nucleation bursts and their possible cessation within a time step Δt. If the current nucleation burst persists for longer than the next time step, it is included fully, whereas cessation of the nucleation burst within the next Δt implies corrections to the effective rates in the algorithm. The identification of these two situations corresponds to the physical mechanism by which nucleation of a supersaturated vapor is halted because of the progressing condensation onto the already formed droplets. The resulting time-integration method is shown to be second-order accurate in time, whereas the computational costs per time step were found to be increased by less than 25% compared with the Euler forward method. The new method is also applied in combination with advective transport of the aerosol forming vapor to investigate a front of rapid nucleation. Adopting robust first-order upwinding for the spatial discretization, we arrive at a flexible method that shows an overall first-order convergence in Δt. For the full, spatially dependent system motivated by an aerosol of water droplets in air, the computational benefits of the new time-integration method over the Euler forward scheme, are a factor of about 10 improvements in accuracy at a given Δt and a similar factor in computing time when keeping the same level of accuracy. © 2013 John Wiley & Sons, Ltd.
Lo Sasso G.,Philip Morris International Research and Development |
Titz B.,Philip Morris International Research and Development |
Nury C.,Philip Morris International Research and Development |
Boue S.,Philip Morris International Research and Development |
And 18 more authors.
Inhalation Toxicology | Year: 2016
The liver is one of the most important organs involved in elimination of xenobiotic and potentially toxic substances. Cigarette smoke (CS) contains more than 7000 chemicals, including those that exert biological effects and cause smoking-related diseases. Though CS is not directly hepatotoxic, a growing body of evidence suggests that it may exacerbate pre-existing chronic liver disease. In this study, we integrated toxicological endpoints with molecular measurements and computational analyses to investigate effects of exposures on the livers of Apoe−/− mice. Mice were exposed to 3R4F reference CS, to an aerosol from the Tobacco Heating System (THS) 2.2, a candidate modified risk tobacco product (MRTP) or to filtered air (Sham) for up to 8 months. THS2.2 takes advantage of a “heat-not-burn” technology that, by heating tobacco, avoids pyrogenesis and pyrosynthesis. After CS exposure for 2 months, some groups were either switched to the MRTP or filtered air. While no group showed clear signs of hepatotoxicity, integrative analysis of proteomics and transcriptomics data showed a CS-dependent impairment of specific biological networks. These networks included lipid and xenobiotic metabolism and iron homeostasis that likely contributed synergistically to exacerbating oxidative stress. In contrast, most proteomic and transcriptomic changes were lower in mice exposed to THS2.2 and in the cessation and switching groups compared to the CS group. Our findings elucidate the complex biological responses of the liver to CS exposure. Furthermore, they provide evidence that THS2.2 aerosol has reduced biological effects, as compared with CS, on the livers of Apoe−/− mice. © 2016 Taylor & Francis.
Martin F.,Philip Morris International Research and Development |
Talikka M.,Philip Morris International Research and Development |
Hoeng J.,Philip Morris International Research and Development |
Peitsch M.C.,Philip Morris International Research and Development
Human and Experimental Toxicology | Year: 2015
Gene expression profiling data can be used in toxicology to assess both the level and impact of toxicant exposure, aligned with a vision of 21st century toxicology. Here, we present a whole blood-derived gene signature that can distinguish current smokers from either nonsmokers or former smokers with high specificity and sensitivity. Such a signature that can be measured in a surrogate tissue (whole blood) may help in monitoring smoking exposure as well as discontinuation of exposure when the primarily impacted tissue (e.g., lung) is not readily accessible. The signature consisted of LRRN3, SASH1, PALLD, RGL1, TNFRSF17, CDKN1C, IGJ, RRM2, ID3, SERPING1, and FUCA1. Several members of this signature have been previously described in the context of smoking. The signature translated well across species and could distinguish mice that were exposed to cigarette smoke from ones exposed to air only or had been withdrawn from cigarette smoke exposure. Finally, the small signature of only 11 genes could be converted into a polymerase chain reaction-based assay that could serve as a marker to monitor compliance with a smoking abstinence protocol. © The Author(s) 2015.
Agne B.,University of Neuchatel |
Andres C.,University of Neuchatel |
Montandon C.,University of Neuchatel |
Christ B.,University of Zürich |
And 6 more authors.
Plant Physiology | Year: 2010
The translocon at the outer membrane of the chloroplast assists the import of a large class of preproteins with amino-terminal transit sequences. The preprotein receptors Toc159 and Toc33 in Arabidopsis (Arabidopsis thaliana) are specific for the accumulation of abundant photosynthetic proteins. The receptors are homologous GTPases known to be regulated by phosphorylation within their GTP-binding domains. In addition to the central GTP-binding domain, Toc159 has an acidic N-terminal domain (A-domain) and a C-terminal membrane-anchoring domain (M-domain). The A-domain of Toc159 is dispensable for its in vivo activity in Arabidopsis and prone to degradation in pea (Pisum sativum). Therefore, it has been suggested to have a regulatory function. Here, we show that in Arabidopsis, the A-domain is not simply degraded but that it accumulates as a soluble, phosphorylated protein separated from Toc159. However, the physiological relevance of this process is unclear. The data show that the A-domain of Toc159 as well as those of its homologs Toc132 and Toc120 are targets of a casein kinase 2-like activity. © 2010 American Society of Plant Biologists.
PubMed | Philip Morris International Research and Development, Zora Biosciences Oy and Philip Morris International Research Laboratories
Type: Journal Article | Journal: Toxicological sciences : an official journal of the Society of Toxicology | Year: 2016
The impact of cigarette smoke (CS), a major cause of lung diseases, on the composition and metabolism of lung lipids is incompletely understood. Here, we integrated quantitative lipidomics and proteomics to investigate exposure effects on lung lipid metabolism in a C57BL/6 and an Apolipoprotein E-deficient (Apoe(-/-)) mouse study. In these studies, mice were exposed to high concentrations of 3R4F reference CS, aerosol from potential modified risk tobacco products (MRTPs) or filtered air (Sham) for up to 8 months. The 2 assessed MRTPs, the prototypical MRTP for C57BL/6 mice and the Tobacco Heating System 2.2 for Apoe(-/-) mice, utilize heat-not-burn technologies and were each matched in nicotine concentrations to the 3R4F CS. After 2 months of CS exposure, some groups were either switched to the MRTP or underwent cessation. In both mouse strains, CS strongly affected several categories of lung lipids and lipid-related proteins. Candidate surfactant lipids, surfactant proteins, and surfactant metabolizing proteins were increased. Inflammatory eicosanoids, their metabolic enzymes, and several ceramide classes were elevated. Overall, CS induced a coordinated lipid response controlled by transcription regulators such as SREBP proteins and supported by other metabolic adaptations. In contrast, most of these changes were absent in the mice exposed to the potential MRTPs, in the cessation group, and the switching group. Our findings demonstrate the complex biological response of the lungs to CS exposure and support the benefits of cessation or switching to a heat-not-burn product using a design such as those employed in this study.
PubMed | Biology Consultant and Philip Morris International Research and Development
Type: Journal Article | Journal: Chemical research in toxicology | Year: 2016
Cigarette smoke (CS) has been reported to increase predisposition to oral cancer and is also recognized as a risk factor for many conditions including periodontal diseases, gingivitis, and other benign mucosal disorders. Smoking cessation remains the most effective approach for minimizing the risk of smoking-related diseases. However, reduction of harmful constituents by heating rather than combusting tobacco, without modifying the amount of nicotine, is a promising new paradigm in harm reduction. In this study, we compared effects of exposure to aerosol derived from a candidate modified risk tobacco product, the tobacco heating system (THS) 2.2, with those of CS generated from the 3R4F reference cigarette. Human organotypic oral epithelial tissue cultures (EpiOral, MatTek Corporation) were exposed for 28 min to 3R4F CS or THS2.2 aerosol, both diluted with air to comparable nicotine concentrations (0.32 or 0.51 mg nicotine/L aerosol/CS for 3R4F and 0.31 or 0.46 mg/L for THS2.2). We also tested one higher concentration (1.09 mg/L) of THS2.2. A systems toxicology approach was employed combining cellular assays (i.e., cytotoxicity and cytochrome P450 activity assays), comprehensive molecular investigations of the buccal epithelial transcriptome (mRNA and miRNA) by means of computational network biology, measurements of secreted proinflammatory markers, and histopathological analysis. We observed that the impact of 3R4F CS was greater than THS2.2 aerosol in terms of cytotoxicity, morphological tissue alterations, and secretion of inflammatory mediators. Analysis of the transcriptomic changes in the exposed oral cultures revealed significant perturbations in various network models such as apoptosis, necroptosis, senescence, xenobiotic metabolism, oxidative stress, and nuclear factor (erythroid-derived 2)-like 2 (NFE2L2) signaling. The stress responses following THS2.2 aerosol exposure were markedly decreased, and the exposed cultures recovered more completely compared with those exposed to 3R4F CS.
PubMed | Philip Morris International Research and Development
Type: Journal Article | Journal: Human & experimental toxicology | Year: 2015
Gene expression profiling data can be used in toxicology to assess both the level and impact of toxicant exposure, aligned with a vision of 21st century toxicology. Here, we present a whole blood-derived gene signature that can distinguish current smokers from either nonsmokers or former smokers with high specificity and sensitivity. Such a signature that can be measured in a surrogate tissue (whole blood) may help in monitoring smoking exposure as well as discontinuation of exposure when the primarily impacted tissue (e.g., lung) is not readily accessible. The signature consisted of LRRN3, SASH1, PALLD, RGL1, TNFRSF17, CDKN1C, IGJ, RRM2, ID3, SERPING1, and FUCA1. Several members of this signature have been previously described in the context of smoking. The signature translated well across species and could distinguish mice that were exposed to cigarette smoke from ones exposed to air only or had been withdrawn from cigarette smoke exposure. Finally, the small signature of only 11 genes could be converted into a polymerase chain reaction-based assay that could serve as a marker to monitor compliance with a smoking abstinence protocol.