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Wong ET, Luettich K, Krishnan S, Wong SK, Lim WT, Yeo D, Büttner A, Leroy P, Vuillaume G, Boué S, Hoeng J, Vanscheeuwijck P, Peitsch MC. Reduced Chronic Toxicity and Carcinogenicity in A/J Mice in Response to Life-Time Exposure to Aerosol From a Heated Tobacco Product Compared With Cigarette Smoke. Toxicol Sci 2021; 178:44-70. [PMID: 32780830 PMCID: PMC7657344 DOI: 10.1093/toxsci/kfaa131] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
We conducted an inhalation study, in accordance with Organisation for Economic Co-operation and Development Test Guideline 453, exposing A/J mice to tobacco heating system (THS) 2.2 aerosol or 3R4F reference cigarette smoke (CS) for up to 18 months to evaluate chronic toxicity and carcinogenicity. All exposed mice showed lower thymus and spleen weight, blood lymphocyte counts, and serum lipid concentrations than sham mice, most likely because of stress and/or nicotine effects. Unlike THS 2.2 aerosol-exposed mice, CS-exposed mice showed increased heart weight, changes in red blood cell profiles and serum liver function parameters. Similarly, increased pulmonary inflammation, altered lung function, and emphysematous changes were observed only in CS-exposed mice. Histopathological changes in other respiratory tract organs were significantly lower in the THS 2.2 aerosol-exposed groups than in the CS-exposed group. Chronic exposure to THS 2.2 aerosol also did not increase the incidence or multiplicity of bronchioloalveolar adenomas or carcinomas relative to sham, whereas CS exposure did. Male THS 2.2 aerosol-exposed mice had a lower survival rate than sham mice, related to an increased incidence of urogenital issues that appears to be related to congenital factors rather than test item exposure. The lower impact of THS 2.2 aerosol exposure on tumor development and chronic toxicity is consistent with the significantly reduced levels of harmful and potentially harmful constituents in THS 2.2 aerosol relative to CS. The totality of the evidence from this study further supports the risk reduction potential of THS 2.2 for lung diseases in comparison with cigarettes.
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Affiliation(s)
- Ee Tsin Wong
- PMI R&D, Philip Morris International Research Laboratories Pte. Ltd, Science Park II, Singapore 117406, Singapore
| | - Karsta Luettich
- Department of Life Sciences, Systems Toxicology, PMI R&D, Philip Morris Products S.A, CH-2000 Neuchâtel, Switzerland
| | - Subash Krishnan
- PMI R&D, Philip Morris International Research Laboratories Pte. Ltd, Science Park II, Singapore 117406, Singapore
| | - Sin Kei Wong
- PMI R&D, Philip Morris International Research Laboratories Pte. Ltd, Science Park II, Singapore 117406, Singapore
| | - Wei Ting Lim
- PMI R&D, Philip Morris International Research Laboratories Pte. Ltd, Science Park II, Singapore 117406, Singapore
| | - Demetrius Yeo
- PMI R&D, Philip Morris International Research Laboratories Pte. Ltd, Science Park II, Singapore 117406, Singapore
| | | | - Patrice Leroy
- PMI R&D, Philip Morris International Research Laboratories Pte. Ltd, Science Park II, Singapore 117406, Singapore
| | - Grégory Vuillaume
- PMI R&D, Philip Morris International Research Laboratories Pte. Ltd, Science Park II, Singapore 117406, Singapore
| | - Stéphanie Boué
- PMI R&D, Philip Morris International Research Laboratories Pte. Ltd, Science Park II, Singapore 117406, Singapore
| | - Julia Hoeng
- PMI R&D, Philip Morris International Research Laboratories Pte. Ltd, Science Park II, Singapore 117406, Singapore
| | - Patrick Vanscheeuwijck
- PMI R&D, Philip Morris International Research Laboratories Pte. Ltd, Science Park II, Singapore 117406, Singapore
| | - Manuel C Peitsch
- PMI R&D, Philip Morris International Research Laboratories Pte. Ltd, Science Park II, Singapore 117406, Singapore
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Boué S, Goedertier D, Hoeng J, Kuczaj A, Majeed S, Mathis C, May A, Phillips B, Peitsch MC, Radtke F, Schlage WK, Tan WT, Vanscheeuwijck P. State-of-the-art methods and devices for the generation, exposure, and collection of aerosols from heat-not-burn tobacco products. Toxicology Research and Application 2020. [DOI: 10.1177/2397847319897869] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Tobacco harm reduction is increasingly recognized as a promising approach to accelerate the decline in smoking prevalence and smoking-related population harm. Potential modified risk tobacco products (MRTPs) must undergo a rigorous premarket toxicological risk assessment. The ability to reproducibly generate, collect, and use aerosols is critical for the characterization, and preclinical assessment of aerosol-based candidate MRTPs (cMRTPs), such as noncombusted cigarettes, also referred to as heated tobacco products, tobacco heating products, or heat-not-burn (HNB) tobacco products. HNB tobacco products generate a nicotine-containing aerosol by heating tobacco instead of burning it. The aerosols generated by HNB products are qualitatively and quantitatively highly different from cigarette smoke (CS). This constitutes technical and experimental challenges comparing the toxicity of HNB aerosols with CS. The methods and experimental setups that have been developed for the study of CS cannot be directly transposed to the study of HNB aerosols. Significant research efforts are dedicated to the development, characterization, and validation of experimental setups and methods suitable for HNB aerosols. They are described in this review, with a particular focus on the Tobacco Heating System version 2.2. This is intended to support further studies, the objective evaluation and verification of existing evidence, and the development of scientifically substantiated HNB MRTPs.
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Affiliation(s)
- Stéphanie Boué
- Philip Morris International (PMI) Research & Development, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Didier Goedertier
- Philip Morris International (PMI) Research & Development, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Julia Hoeng
- Philip Morris International (PMI) Research & Development, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Arkadiusz Kuczaj
- Philip Morris International (PMI) Research & Development, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Shoaib Majeed
- Philip Morris International (PMI) Research & Development, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Carole Mathis
- Philip Morris International (PMI) Research & Development, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Anne May
- Consultants in Science, Epalinges, Switzerland
| | - Blaine Phillips
- Philip Morris International (PMI) Research & Development, Philip Morris International Research Laboratories Pte. Ltd, Science Park II, Singapore
| | - Manuel C Peitsch
- Philip Morris International (PMI) Research & Development, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Falk Radtke
- Philip Morris International (PMI) Research & Development, Philip Morris Products S.A., Neuchâtel, Switzerland
| | | | - Wei Teck Tan
- Philip Morris International (PMI) Research & Development, Philip Morris International Research Laboratories Pte. Ltd, Science Park II, Singapore
| | - Patrick Vanscheeuwijck
- Philip Morris International (PMI) Research & Development, Philip Morris Products S.A., Neuchâtel, Switzerland
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Boué S, Goedertier D, Hoeng J, Iskandar A, Kuczaj AK, Marescotti D, Mathis C, May A, Phillips B, Peitsch MC, Schlage WK, Sciuscio D, Tan WT, Vanscheeuwijck P. State-of-the-art methods and devices for generation, exposure, and collection of aerosols from e-vapor products. Toxicology Research and Application 2020. [DOI: 10.1177/2397847320979751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
E-vapor products (EVP) have become popular alternatives for cigarette smokers who would otherwise continue to smoke. EVP research is challenging and complex, mostly because of the numerous and rapidly evolving technologies and designs as well as the multiplicity of e-liquid flavors and solvents available on the market. There is an urgent need to standardize all stages of EVP assessment, from the production of a reference product to e-vapor generation methods and from physicochemical characterization methods to nonclinical and clinical exposure studies. The objective of this review is to provide a detailed description of selected experimental setups and methods for EVP aerosol generation and collection and exposure systems for their in vitro and in vivo assessment. The focus is on the specificities of the product that constitute challenges and require development of ad hoc assessment frameworks, equipment, and methods. In so doing, this review aims to support further studies, objective evaluation, comparison, and verification of existing evidence, and, ultimately, formulation of standardized methods for testing EVPs.
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Affiliation(s)
- Stéphanie Boué
- Philip Morris International (PMI) Research & Development, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Didier Goedertier
- Philip Morris International (PMI) Research & Development, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Julia Hoeng
- Philip Morris International (PMI) Research & Development, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Anita Iskandar
- Philip Morris International (PMI) Research & Development, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Arkadiusz K Kuczaj
- Philip Morris International (PMI) Research & Development, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Diego Marescotti
- Philip Morris International (PMI) Research & Development, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Carole Mathis
- Philip Morris International (PMI) Research & Development, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Anne May
- Consultants in Science, Epalinges, Switzerland
| | - Blaine Phillips
- Philip Morris International (PMI) Research & Development, Philip Morris International Research Laboratories Pte. Ltd, Science Park II, Singapore
| | - Manuel C Peitsch
- Philip Morris International (PMI) Research & Development, Philip Morris Products S.A., Neuchâtel, Switzerland
| | | | - Davide Sciuscio
- Philip Morris International (PMI) Research & Development, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Wei Teck Tan
- Philip Morris International (PMI) Research & Development, Philip Morris International Research Laboratories Pte. Ltd, Science Park II, Singapore
| | - Patrick Vanscheeuwijck
- Philip Morris International (PMI) Research & Development, Philip Morris Products S.A., Neuchâtel, Switzerland
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Boué S, Schlage WK, Page D, Hoeng J, Peitsch MC. Toxicological assessment of Tobacco Heating System 2.2: Findings from an independent peer review. Regul Toxicol Pharmacol 2019; 104:115-127. [PMID: 30878573 DOI: 10.1016/j.yrtph.2019.03.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/12/2019] [Accepted: 03/09/2019] [Indexed: 01/09/2023]
Abstract
Offering safer alternatives to cigarettes, such as e-cigarettes and heated tobacco products, to smokers who are not willing to quit could reduce the harm caused by smoking. Extensive and rigorous scientific studies are conducted to assess the relative risk of such potentially modified risk tobacco products compared with that of smoking cigarettes. In addition to the peer review of publications reporting individual studies, we aimed to gauge the plausibility of the evidence to the scientific community and appreciate likely necessary additions prior to regulatory submission. Therefore, we sponsored a two-tier peer review organized by an independent third party who identified, recruited, and managed 7 panels of 5-12 experts whose identity remains unknown to us. The reviewers had access to all publications and raw data from preclinical and clinical studies via a web portal. The reviewers were asked questions regarding study design, methods, quality of data, and interpretation of results to judge the validity of the conclusions regarding the relative effects of the Tobacco Heating System 2.2 compared with cigarettes. Once their conclusions were submitted, the experts had the opportunity to participate in an anonymized online debate with their fellow panel members. We present here the results obtained from this innovative peer review effort which revealed supportive or very supportive of the study methods and results, and support the robustness of the studies and validity of the conclusions.
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Affiliation(s)
- Stéphanie Boué
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland.
| | - Walter K Schlage
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland
| | - David Page
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland
| | - Julia Hoeng
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland
| | - Manuel C Peitsch
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000, Neuchâtel, Switzerland
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Abstract
Low rates of reproducibility and translatability of data from nonclinical research have been reported. Major causes of irreproducibility include oversights in study design, failure to characterize reagents and protocols, a lack of access to detailed methods and data, and an absence of universally accepted and applied standards and guidelines. Specific areas of concern include uncharacterized antibodies and cell lines, the use of inappropriate sampling and testing protocols, a lack of transparency and access to raw data, and deficiencies in the translatability of findings to the clinic from studies using animal models of disease. All stakeholders—academia, industry, funding agencies, regulators, nonprofit entities, and publishers—are encouraged to play active roles in addressing these challenges by formulating and promoting access to best practices and standard operating procedures and validating data collaboratively at each step of the biomedical research life cycle.
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Affiliation(s)
- Stéphanie Boué
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Michael Byrne
- Global Biological Standards Institute (GBSI), Washington, DC, USA
| | - A Wallace Hayes
- Michigan State University, Institute for Integrative Toxicology, East Lansing, MI, USA.,University of South Florida, College of Public Health, Tampa, FL, USA
| | - Julia Hoeng
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
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Poussin C, Sierro N, Boué S, Battey J, Scotti E, Belcastro V, Peitsch MC, Ivanov NV, Hoeng J. Interrogating the microbiome: experimental and computational considerations in support of study reproducibility. Drug Discov Today 2018; 23:1644-1657. [PMID: 29890228 DOI: 10.1016/j.drudis.2018.06.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 05/03/2018] [Accepted: 06/06/2018] [Indexed: 12/12/2022]
Abstract
The microbiome is an important factor in human health and disease and is investigated to develop novel therapeutics. Metagenomics leverages advances in sequencing technologies and computational analysis to identify and quantify the microorganisms present in a sample. This field has, however, not yet reached maturity and the international metagenomics community, aware of the current limitations and of the necessity for standardization, has started investigating sources of variability in experimental and computational workflows. The first studies have already resulted in the identification of crucial steps and factors affecting metagenomics data quality, quantification and interpretation. This review summarizes experimental and computational considerations for interrogating the microbiome and establishing reproducible and robust analysis workflows.
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Affiliation(s)
- Carine Poussin
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Nicolas Sierro
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Stéphanie Boué
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - James Battey
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Elena Scotti
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Vincenzo Belcastro
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Manuel C Peitsch
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Nikolai V Ivanov
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Julia Hoeng
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland.
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Scotti E, Boué S, Sasso GL, Zanetti F, Belcastro V, Poussin C, Sierro N, Battey J, Gimalac A, Ivanov NV, Hoeng J. Exploring the microbiome in health and disease. Toxicology Research and Application 2017. [DOI: 10.1177/2397847317741884] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The analysis of human microbiome is an exciting and rapidly expanding field of research. In the past decade, the biological relevance of the microbiome for human health has become evident. Microbiome comprises a complex collection of microorganisms, with their genes and metabolites, colonizing different body niches. It is now well known that the microbiome interacts with its host, assisting in the bioconversion of nutrients and detoxification, supporting immunity, protecting against pathogenic microbes, and maintaining health. Remarkable new findings showed that our microbiome not only primarily affects the health and function of the gastrointestinal tract but also has a strong influence on general body health through its close interaction with the nervous system and the lung. Therefore, a perfect and sensitive balanced interaction of microbes with the host is required for a healthy body. In fact, growing evidence suggests that the dynamics and function of the indigenous microbiota can be influenced by many factors, including genetics, diet, age, and toxicological agents like cigarette smoke, environmental contaminants, and drugs. The disruption of this balance, that is called dysbiosis, is associated with a plethora of diseases, including metabolic diseases, inflammatory bowel disease, chronic obstructive pulmonary disease, periodontitis, skin diseases, and neurological disorders. The importance of the host microbiome for the human health has also led to the emergence of novel therapeutic approaches focused on the intentional manipulation of the microbiota, either by restoring missing functions or eliminating harmful roles. In the present review, we outline recent studies devoted to elucidate not only the role of microbiome in health conditions and the possible link with various types of diseases but also the influence of various toxicological factors on the microbial composition and function.
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Affiliation(s)
- Elena Scotti
- PMI R&D, Philip Morris Products S.A., Neuchatel, Switzerland (Part of Philip Morris International group of companies)
| | - Stéphanie Boué
- PMI R&D, Philip Morris Products S.A., Neuchatel, Switzerland (Part of Philip Morris International group of companies)
| | - Giuseppe Lo Sasso
- PMI R&D, Philip Morris Products S.A., Neuchatel, Switzerland (Part of Philip Morris International group of companies)
| | - Filippo Zanetti
- PMI R&D, Philip Morris Products S.A., Neuchatel, Switzerland (Part of Philip Morris International group of companies)
| | - Vincenzo Belcastro
- PMI R&D, Philip Morris Products S.A., Neuchatel, Switzerland (Part of Philip Morris International group of companies)
| | - Carine Poussin
- PMI R&D, Philip Morris Products S.A., Neuchatel, Switzerland (Part of Philip Morris International group of companies)
| | - Nicolas Sierro
- PMI R&D, Philip Morris Products S.A., Neuchatel, Switzerland (Part of Philip Morris International group of companies)
| | - James Battey
- PMI R&D, Philip Morris Products S.A., Neuchatel, Switzerland (Part of Philip Morris International group of companies)
| | - Anne Gimalac
- PMI R&D, Philip Morris Products S.A., Neuchatel, Switzerland (Part of Philip Morris International group of companies)
| | - Nikolai V Ivanov
- PMI R&D, Philip Morris Products S.A., Neuchatel, Switzerland (Part of Philip Morris International group of companies)
| | - Julia Hoeng
- PMI R&D, Philip Morris Products S.A., Neuchatel, Switzerland (Part of Philip Morris International group of companies)
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Poussin C, Belcastro V, Martin F, Boué S, Peitsch MC, Hoeng J. Crowd-Sourced Verification of Computational Methods and Data in Systems Toxicology: A Case Study with a Heat-Not-Burn Candidate Modified Risk Tobacco Product. Chem Res Toxicol 2017; 30:934-945. [PMID: 28085253 DOI: 10.1021/acs.chemrestox.6b00345] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Systems toxicology intends to quantify the effect of toxic molecules in biological systems and unravel their mechanisms of toxicity. The development of advanced computational methods is required for analyzing and integrating high throughput data generated for this purpose as well as for extrapolating predictive toxicological outcomes and risk estimates. To ensure the performance and reliability of the methods and verify conclusions from systems toxicology data analysis, it is important to conduct unbiased evaluations by independent third parties. As a case study, we report here the results of an independent verification of methods and data in systems toxicology by crowdsourcing. The sbv IMPROVER systems toxicology computational challenge aimed to evaluate computational methods for the development of blood-based gene expression signature classification models with the ability to predict smoking exposure status. Participants created/trained models on blood gene expression data sets including smokers/mice exposed to 3R4F (a reference cigarette) or noncurrent smokers/Sham (mice exposed to air). Participants applied their models on unseen data to predict whether subjects classify closer to smoke-exposed or nonsmoke exposed groups. The data sets also included data from subjects that had been exposed to potential modified risk tobacco products (MRTPs) or that had switched to a MRTP after exposure to conventional cigarette smoke. The scoring of anonymized participants' predictions was done using predefined metrics. The top 3 performers' methods predicted class labels with area under the precision recall scores above 0.9. Furthermore, although various computational approaches were used, the crowd's results confirmed our own data analysis outcomes with regards to the classification of MRTP-related samples. Mice exposed directly to a MRTP were classified closer to the Sham group. After switching to a MRTP, the confidence that subjects belonged to the smoke-exposed group decreased significantly. Smoking exposure gene signatures that contributed to the group separation included a core set of genes highly consistent across teams such as AHRR, LRRN3, SASH1, and P2RY6. In conclusion, crowdsourcing constitutes a pertinent approach, in complement to the classical peer review process, to independently and unbiasedly verify computational methods and data for risk assessment using systems toxicology.
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Affiliation(s)
- Carine Poussin
- PMI R&D, Philip Morris Products S.A. , Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland (Part of Philip Morris International group of companies)
| | - Vincenzo Belcastro
- PMI R&D, Philip Morris Products S.A. , Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland (Part of Philip Morris International group of companies)
| | - Florian Martin
- PMI R&D, Philip Morris Products S.A. , Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland (Part of Philip Morris International group of companies)
| | - Stéphanie Boué
- PMI R&D, Philip Morris Products S.A. , Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland (Part of Philip Morris International group of companies)
| | - Manuel C Peitsch
- PMI R&D, Philip Morris Products S.A. , Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland (Part of Philip Morris International group of companies)
| | - Julia Hoeng
- PMI R&D, Philip Morris Products S.A. , Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland (Part of Philip Morris International group of companies)
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Szostak J, Boué S, Talikka M, Guedj E, Martin F, Phillips B, Ivanov NV, Peitsch MC, Hoeng J. Aerosol from Tobacco Heating System 2.2 has reduced impact on mouse heart gene expression compared with cigarette smoke. Food Chem Toxicol 2017; 101:157-167. [PMID: 28111298 DOI: 10.1016/j.fct.2017.01.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 01/10/2017] [Accepted: 01/18/2017] [Indexed: 02/05/2023]
Abstract
Experimental studies clearly demonstrate a causal effect of cigarette smoking on cardiovascular disease. To reduce the individual risk and population harm caused by smoking, alternative products to cigarettes are being developed. We recently reported on an apolipoprotein E-deficient (Apoe-/-) mouse inhalation study that compared the effects of exposure to aerosol from a candidate modified risk tobacco product, Tobacco Heating System 2.2 (THS2.2), and smoke from the reference cigarette (3R4F) on pulmonary and vascular biology. Here, we applied a transcriptomics approach to evaluate the impact of the exposure to 3R4F smoke and THS2.2 aerosol on heart tissues from the same cohort of mice. The systems response profiles demonstrated that 3R4F smoke exposure led to time-dependent transcriptomics changes (False Discovery Rate (FDR) < 0.05; 44 differentially expressed genes at 3-months; 491 at 8-months). Analysis of differentially expressed genes in the heart tissue indicated that 3R4F exposure induced the downregulation of genes involved in cytoskeleton organization and the contractile function of the heart, notably genes that encode beta actin (Actb), actinin alpha 4 (Actn4), and filamin C (Flnc). This was accompanied by the downregulation of genes related to the inflammatory response. None of these effects were observed in the group exposed to THS2.2 aerosol.
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Affiliation(s)
- Justyna Szostak
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland.
| | - Stéphanie Boué
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland.
| | - Marja Talikka
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland.
| | - Emmanuel Guedj
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland.
| | - Florian Martin
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland.
| | - Blaine Phillips
- Philip Morris International Research Laboratories Pte Ltd, Science Park II, Singapore.
| | - Nikolai V Ivanov
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland.
| | - Manuel C Peitsch
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland.
| | - Julia Hoeng
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland.
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Boué S, Exner T, Ghosh S, Belcastro V, Dokler J, Page D, Boda A, Bonjour F, Hardy B, Vanscheeuwijck P, Hoeng J, Peitsch M. Supporting evidence-based analysis for modified risk tobacco products through a toxicology data-sharing infrastructure. F1000Res 2017; 6:12. [PMID: 29123642 PMCID: PMC5657032 DOI: 10.12688/f1000research.10493.2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/25/2017] [Indexed: 01/24/2023] Open
Abstract
The US FDA defines modified risk tobacco products (MRTPs) as products that aim to reduce harm or the risk of tobacco-related disease associated with commercially marketed tobacco products. Establishing a product’s potential as an MRTP requires scientific substantiation including toxicity studies and measures of disease risk relative to those of cigarette smoking. Best practices encourage verification of the data from such studies through sharing and open standards. Building on the experience gained from the OpenTox project, a proof-of-concept database and website (
INTERVALS) has been developed to share results from both
in vivo inhalation studies and
in vitro studies conducted by Philip Morris International R&D to assess candidate MRTPs. As datasets are often generated by diverse methods and standards, they need to be traceable, curated, and the methods used well described so that knowledge can be gained using data science principles and tools. The data-management framework described here accounts for the latest standards of data sharing and research reproducibility. Curated data and methods descriptions have been prepared in ISA-Tab format and stored in a database accessible via a search portal on the INTERVALS website. The portal allows users to browse the data by study or mechanism (e.g., inflammation, oxidative stress) and obtain information relevant to study design, methods, and the most important results. Given the successful development of the initial infrastructure, the goal is to grow this initiative and establish a public repository for 21
st-century preclinical systems toxicology MRTP assessment data and results that supports open data principles.
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Affiliation(s)
- Stéphanie Boué
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | | | | | | | - Joh Dokler
- Douglas Connect GmbH, Zeiningen, Switzerland
| | - David Page
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Akash Boda
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Filipe Bonjour
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Barry Hardy
- Douglas Connect GmbH, Zeiningen, Switzerland
| | | | - Julia Hoeng
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Manuel Peitsch
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
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12
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Boué S, Exner T, Ghosh S, Belcastro V, Dokler J, Page D, Boda A, Bonjour F, Hardy B, Vanscheeuwijck P, Hoeng J, Peitsch M. Supporting evidence-based analysis for modified risk tobacco products through a toxicology data-sharing infrastructure. F1000Res 2017; 6:12. [PMID: 29123642 DOI: 10.12688/f1000research.10493.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/03/2017] [Indexed: 12/11/2022] Open
Abstract
The US FDA defines modified risk tobacco products (MRTPs) as products that aim to reduce harm or the risk of tobacco-related disease associated with commercially marketed tobacco products. Establishing a product's potential as an MRTP requires scientific substantiation including toxicity studies and measures of disease risk relative to those of cigarette smoking. Best practices encourage verification of the data from such studies through sharing and open standards. Building on the experience gained from the OpenTox project, a proof-of-concept database and website ( INTERVALS) has been developed to share results from both in vivo inhalation studies and in vitro studies conducted by Philip Morris International R&D to assess candidate MRTPs. As datasets are often generated by diverse methods and standards, they need to be traceable, curated, and the methods used well described so that knowledge can be gained using data science principles and tools. The data-management framework described here accounts for the latest standards of data sharing and research reproducibility. Curated data and methods descriptions have been prepared in ISA-Tab format and stored in a database accessible via a search portal on the INTERVALS website. The portal allows users to browse the data by study or mechanism (e.g., inflammation, oxidative stress) and obtain information relevant to study design, methods, and the most important results. Given the successful development of the initial infrastructure, the goal is to grow this initiative and establish a public repository for 21 st-century preclinical systems toxicology MRTP assessment data and results that supports open data principles.
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Affiliation(s)
- Stéphanie Boué
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | | | | | | | - Joh Dokler
- Douglas Connect GmbH, Zeiningen, Switzerland
| | - David Page
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Akash Boda
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Filipe Bonjour
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Barry Hardy
- Douglas Connect GmbH, Zeiningen, Switzerland
| | | | - Julia Hoeng
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Manuel Peitsch
- PMI R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
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13
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Boué S, Hardy B, Hayes W, Belcastro V, Exner T, Dokler J, Hoeng J, Peitsch M. Sharing systems toxicology data for inhalation toxicology. Toxicol Lett 2016. [DOI: 10.1016/j.toxlet.2016.07.598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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14
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Poussin C, Belcastro V, Boué S, Martin F, Sewer A, Titz B, Cannesson L, Peitsch M, Hoeng J. The systems toxicology challenge: Marker of exposure response identification in blood. Toxicol Lett 2016. [DOI: 10.1016/j.toxlet.2016.07.415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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15
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Hirschman L, Fort K, Boué S, Kyrpides N, Islamaj Doğan R, Cohen KB. Crowdsourcing and curation: perspectives from biology and natural language processing. Database (Oxford) 2016; 2016:baw115. [PMID: 27504010 PMCID: PMC4976298 DOI: 10.1093/database/baw115] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 07/11/2016] [Indexed: 12/27/2022]
Abstract
Crowdsourcing is increasingly utilized for performing tasks in both natural language processing and biocuration. Although there have been many applications of crowdsourcing in these fields, there have been fewer high-level discussions of the methodology and its applicability to biocuration. This paper explores crowdsourcing for biocuration through several case studies that highlight different ways of leveraging 'the crowd'; these raise issues about the kind(s) of expertise needed, the motivations of participants, and questions related to feasibility, cost and quality. The paper is an outgrowth of a panel session held at BioCreative V (Seville, September 9-11, 2015). The session consisted of four short talks, followed by a discussion. In their talks, the panelists explored the role of expertise and the potential to improve crowd performance by training; the challenge of decomposing tasks to make them amenable to crowdsourcing; and the capture of biological data and metadata through community editing.Database URL: http://www.mitre.org/publications/technical-papers/crowdsourcing-and-curation-perspectives.
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Affiliation(s)
| | - Karën Fort
- University of Paris-Sorbonne/STIH Team, Paris, France
| | - Stéphanie Boué
- Philip Morris International R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | | | - Rezarta Islamaj Doğan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
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16
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Namasivayam AA, Morales AF, Lacave ÁMF, Tallam A, Simovic B, Alfaro DG, Bobbili DR, Martin F, Androsova G, Shvydchenko I, Park J, Calvo JV, Hoeng J, Peitsch MC, Racero MGV, Biryukov M, Talikka M, Pérez MB, Rohatgi N, Díaz-Díaz N, Mandarapu R, Ruiz RA, Davidyan S, Narayanasamy S, Boué S, Guryanova S, Arbas SM, Menon S, Xiang Y. Community-Reviewed Biological Network Models for Toxicology and Drug Discovery Applications. Gene Regul Syst Bio 2016; 10:51-66. [PMID: 27429547 PMCID: PMC4944831 DOI: 10.4137/grsb.s39076] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 03/31/2016] [Accepted: 04/12/2016] [Indexed: 12/13/2022]
Abstract
Biological network models offer a framework for understanding disease by describing the relationships between the mechanisms involved in the regulation of biological processes. Crowdsourcing can efficiently gather feedback from a wide audience with varying expertise. In the Network Verification Challenge, scientists verified and enhanced a set of 46 biological networks relevant to lung and chronic obstructive pulmonary disease. The networks were built using Biological Expression Language and contain detailed information for each node and edge, including supporting evidence from the literature. Network scoring of public transcriptomics data inferred perturbation of a subset of mechanisms and networks that matched the measured outcomes. These results, based on a computable network approach, can be used to identify novel mechanisms activated in disease, quantitatively compare different treatments and time points, and allow for assessment of data with low signal. These networks are periodically verified by the crowd to maintain an up-to-date suite of networks for toxicology and drug discovery applications.
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Affiliation(s)
| | - Aishwarya Alex Namasivayam
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, Esch-sur-Alzette, Luxembourg
| | | | | | - Aravind Tallam
- TWINCORE, Zentrum für Experimentelle und Klinische Infektionsforschung, Hannover, Germany
| | | | | | - Dheeraj Reddy Bobbili
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, Esch-sur-Alzette, Luxembourg
| | - Florian Martin
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud, Neuchâtel, Switzerland (part of Philip Morris International group of companies)
| | - Ganna Androsova
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, Esch-sur-Alzette, Luxembourg
| | - Irina Shvydchenko
- Kuban State University of Physical Education, Sport and Tourism, Krasnodar, Russia
| | | | - Jorge Val Calvo
- Center for Molecular Biology, "Severo Ochoa" - Spanish National Research Council, Madrid, Spain
| | - Julia Hoeng
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud, Neuchâtel, Switzerland (part of Philip Morris International group of companies)
| | - Manuel C Peitsch
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud, Neuchâtel, Switzerland (part of Philip Morris International group of companies)
| | | | - Maria Biryukov
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, Esch-sur-Alzette, Luxembourg
| | - Marja Talikka
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud, Neuchâtel, Switzerland (part of Philip Morris International group of companies)
| | | | - Neha Rohatgi
- Center for Systems Biology, University of Iceland, Reykjavik, Iceland
| | | | - Rajesh Mandarapu
- Prakhya Research Laboratories, Lakshminagar, Selaiyur, Chennai, Tamil Nadu, India
| | | | - Sergey Davidyan
- Institute of Biochemical Physics Russian Academy of Sciences, Moscow, Russia
| | - Shaman Narayanasamy
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, Esch-sur-Alzette, Luxembourg
| | - Stéphanie Boué
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud, Neuchâtel, Switzerland (part of Philip Morris International group of companies)
| | - Svetlana Guryanova
- Institute of Bioorganic Chemistry Russian Academy of Sciences, Moscow, Russia
| | - Susana Martínez Arbas
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Campus Belval, Esch-sur-Alzette, Luxembourg
| | - Swapna Menon
- AnalyzeDat Consulting Services, Edapally Byepass Junction, Kochi, Kerala, India
| | - Yang Xiang
- Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud, Neuchâtel, Switzerland (part of Philip Morris International group of companies)
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Phillips B, Veljkovic E, Boué S, Schlage WK, Vuillaume G, Martin F, Titz B, Leroy P, Buettner A, Elamin A, Oviedo A, Cabanski M, De León H, Guedj E, Schneider T, Talikka M, Ivanov NV, Vanscheeuwijck P, Peitsch MC, Hoeng J. An 8-Month Systems Toxicology Inhalation/Cessation Study in Apoe-/- Mice to Investigate Cardiovascular and Respiratory Exposure Effects of a Candidate Modified Risk Tobacco Product, THS 2.2, Compared With Conventional Cigarettes. Toxicol Sci 2016; 151:462-4. [PMID: 27225756 PMCID: PMC7297302 DOI: 10.1093/toxsci/kfw062] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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18
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Lo Sasso G, Schlage WK, Boué S, Veljkovic E, Peitsch MC, Hoeng J. The Apoe(-/-) mouse model: a suitable model to study cardiovascular and respiratory diseases in the context of cigarette smoke exposure and harm reduction. J Transl Med 2016; 14:146. [PMID: 27207171 PMCID: PMC4875735 DOI: 10.1186/s12967-016-0901-1] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 05/07/2016] [Indexed: 02/03/2023] Open
Abstract
Atherosclerosis-prone apolipoprotein E-deficient (Apoe(-/-)) mice display poor lipoprotein clearance with subsequent accumulation of cholesterol ester-enriched particles in the blood, which promote the development of atherosclerotic plaques. Therefore, the Apoe(-/-) mouse model is well established for the study of human atherosclerosis. The systemic proinflammatory status of Apoe(-/-) mice also makes them good candidates for studying chronic obstructive pulmonary disease, characterized by pulmonary inflammation, airway obstruction, and emphysema, and which shares several risk factors with cardiovascular diseases, including smoking. Herein, we review the results from published studies using Apoe(-/-) mice, with a particular focus on work conducted in the context of cigarette smoke inhalation studies. The findings from these studies highlight the suitability of this animal model for researching the effects of cigarette smoking on atherosclerosis and emphysema.
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Affiliation(s)
- Giuseppe Lo Sasso
- />Philip Morris International R&D, Philip Morris Products S.A. (Part of Philip Morris International Group of Companies), Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | | | - Stéphanie Boué
- />Philip Morris International R&D, Philip Morris Products S.A. (Part of Philip Morris International Group of Companies), Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Emilija Veljkovic
- />Philip Morris International R&D, Philip Morris Products S.A. (Part of Philip Morris International Group of Companies), Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Manuel C. Peitsch
- />Philip Morris International R&D, Philip Morris Products S.A. (Part of Philip Morris International Group of Companies), Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Julia Hoeng
- />Philip Morris International R&D, Philip Morris Products S.A. (Part of Philip Morris International Group of Companies), Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
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19
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Lo Sasso G, Titz B, Nury C, Boué S, Phillips B, Belcastro V, Schneider T, Dijon S, Baumer K, Peric D, Dulize R, Elamin A, Guedj E, Buettner A, Leroy P, Kleinhans S, Vuillaume G, Veljkovic E, Ivanov NV, Martin F, Vanscheeuwijck P, Peitsch MC, Hoeng J. Effects of cigarette smoke, cessation and switching to a candidate modified risk tobacco product on the liver in Apoe -/- mice--a systems toxicology analysis. Inhal Toxicol 2016; 28:226-40. [PMID: 27027324 DOI: 10.3109/08958378.2016.1150368] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 01/14/2016] [Accepted: 02/01/2016] [Indexed: 12/11/2022]
Abstract
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.
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Affiliation(s)
- Giuseppe Lo Sasso
- a Philip Morris International Research and Development , Neuchatel , Switzerland
| | - Bjoern Titz
- a Philip Morris International Research and Development , Neuchatel , Switzerland
| | - Catherine Nury
- a Philip Morris International Research and Development , Neuchatel , Switzerland
| | - Stéphanie Boué
- a Philip Morris International Research and Development , Neuchatel , Switzerland
| | - Blaine Phillips
- b Philip Morris International Research Laboratories , Singapore , Singapore , and
| | - Vincenzo Belcastro
- a Philip Morris International Research and Development , Neuchatel , Switzerland
| | - Thomas Schneider
- a Philip Morris International Research and Development , Neuchatel , Switzerland
| | - Sophie Dijon
- a Philip Morris International Research and Development , Neuchatel , Switzerland
| | - Karine Baumer
- a Philip Morris International Research and Development , Neuchatel , Switzerland
| | - Daruisz Peric
- a Philip Morris International Research and Development , Neuchatel , Switzerland
| | - Remi Dulize
- a Philip Morris International Research and Development , Neuchatel , Switzerland
| | - Ashraf Elamin
- a Philip Morris International Research and Development , Neuchatel , Switzerland
| | - Emmanuel Guedj
- a Philip Morris International Research and Development , Neuchatel , Switzerland
| | | | - Patrice Leroy
- a Philip Morris International Research and Development , Neuchatel , Switzerland
| | - Samuel Kleinhans
- a Philip Morris International Research and Development , Neuchatel , Switzerland
| | - Gregory Vuillaume
- a Philip Morris International Research and Development , Neuchatel , Switzerland
| | - Emilija Veljkovic
- a Philip Morris International Research and Development , Neuchatel , Switzerland
| | - Nikolai V Ivanov
- a Philip Morris International Research and Development , Neuchatel , Switzerland
| | - Florian Martin
- a Philip Morris International Research and Development , Neuchatel , Switzerland
| | | | - Manuel C Peitsch
- a Philip Morris International Research and Development , Neuchatel , Switzerland
| | - Julia Hoeng
- a Philip Morris International Research and Development , Neuchatel , Switzerland
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20
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Titz B, Boué S, Phillips B, Talikka M, Vihervaara T, Schneider T, Nury C, Elamin A, Guedj E, Peck MJ, Schlage WK, Cabanski M, Leroy P, Vuillaume G, Martin F, Ivanov NV, Veljkovic E, Ekroos K, Laaksonen R, Vanscheeuwijck P, Peitsch MC, Hoeng J. Effects of Cigarette Smoke, Cessation, and Switching to Two Heat-Not-Burn Tobacco Products on Lung Lipid Metabolism in C57BL/6 and Apoe-/- Mice-An Integrative Systems Toxicology Analysis. Toxicol Sci 2016; 149:441-57. [PMID: 26582801 PMCID: PMC4725611 DOI: 10.1093/toxsci/kfv244] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
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.
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Affiliation(s)
- Bjoern Titz
- *Philip Morris International Research and Development, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland; *Philip Morris International Research and Development, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland;
| | - Stéphanie Boué
- *Philip Morris International Research and Development, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Blaine Phillips
- Philip Morris International Research Laboratories, 50 Science Park Road, Singapore, Singapore; and
| | - Marja Talikka
- *Philip Morris International Research and Development, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | | | - Thomas Schneider
- *Philip Morris International Research and Development, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Catherine Nury
- *Philip Morris International Research and Development, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Ashraf Elamin
- *Philip Morris International Research and Development, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Emmanuel Guedj
- *Philip Morris International Research and Development, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Michael J Peck
- *Philip Morris International Research and Development, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Walter K Schlage
- *Philip Morris International Research and Development, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Maciej Cabanski
- *Philip Morris International Research and Development, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Patrice Leroy
- *Philip Morris International Research and Development, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Gregory Vuillaume
- *Philip Morris International Research and Development, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Florian Martin
- *Philip Morris International Research and Development, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Nikolai V Ivanov
- *Philip Morris International Research and Development, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Emilija Veljkovic
- *Philip Morris International Research and Development, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Kim Ekroos
- Zora Biosciences Oy, Biologinkuja 1, 02150 Espoo, Finland
| | | | - Patrick Vanscheeuwijck
- *Philip Morris International Research and Development, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Manuel C Peitsch
- *Philip Morris International Research and Development, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Julia Hoeng
- *Philip Morris International Research and Development, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland;
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21
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Phillips B, Veljkovic E, Boué S, Schlage WK, Vuillaume G, Martin F, Titz B, Leroy P, Buettner A, Elamin A, Oviedo A, Cabanski M, De León H, Guedj E, Schneider T, Talikka M, Ivanov NV, Vanscheeuwijck P, Peitsch MC, Hoeng J. An 8-Month Systems Toxicology Inhalation/Cessation Study in Apoe-/- Mice to Investigate Cardiovascular and Respiratory Exposure Effects of a Candidate Modified Risk Tobacco Product, THS 2.2, Compared With Conventional Cigarettes. Toxicol Sci 2016; 149:411-32. [PMID: 26609137 PMCID: PMC4725610 DOI: 10.1093/toxsci/kfv243] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Smoking cigarettes is a major risk factor in the development and progression of cardiovascular disease (CVD) and chronic obstructive pulmonary disease (COPD). Modified risk tobacco products (MRTPs) are being developed to reduce smoking-related health risks. The goal of this study was to investigate hallmarks of COPD and CVD over an 8-month period in apolipoprotein E-deficient mice exposed to conventional cigarette smoke (CS) or to the aerosol of a candidate MRTP, tobacco heating system (THS) 2.2. In addition to chronic exposure, cessation or switching to THS2.2 after 2 months of CS exposure was assessed. Engaging a systems toxicology approach, exposure effects were investigated using physiology and histology combined with transcriptomics, lipidomics, and proteomics. CS induced nasal epithelial hyperplasia and metaplasia, lung inflammation, and emphysematous changes (impaired pulmonary function and alveolar damage). Atherogenic effects of CS exposure included altered lipid profiles and aortic plaque formation. Exposure to THS2.2 aerosol (nicotine concentration matched to CS, 29.9 mg/m(3)) neither induced lung inflammation or emphysema nor did it consistently change the lipid profile or enhance the plaque area. Cessation or switching to THS2.2 reversed the inflammatory responses and halted progression of initial emphysematous changes and the aortic plaque area. Biological processes, including senescence, inflammation, and proliferation, were significantly impacted by CS but not by THS2.2 aerosol. Both, cessation and switching to THS2.2 reduced these perturbations to almost sham exposure levels. In conclusion, in this mouse model cessation or switching to THS2.2 retarded the progression of CS-induced atherosclerotic and emphysematous changes, while THS2.2 aerosol alone had minimal adverse effects.
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Affiliation(s)
- Blaine Phillips
- *Philip Morris International Research Laboratories Pte Ltd, The Kendall #02-07, Science Park II, Singapore 117406
| | - Emilija Veljkovic
- Philip Morris International R&D, Philip Morris Products S.A., 2000 Neuchâtel, Switzerland
| | - Stéphanie Boué
- Philip Morris International R&D, Philip Morris Products S.A., 2000 Neuchâtel, Switzerland
| | - Walter K Schlage
- WK Schlage Biology Consulting, 51429 Bergisch Gladbach, Germany; and
| | - Gregory Vuillaume
- Philip Morris International R&D, Philip Morris Products S.A., 2000 Neuchâtel, Switzerland
| | - Florian Martin
- Philip Morris International R&D, Philip Morris Products S.A., 2000 Neuchâtel, Switzerland
| | - Bjoern Titz
- Philip Morris International R&D, Philip Morris Products S.A., 2000 Neuchâtel, Switzerland
| | - Patrice Leroy
- Philip Morris International R&D, Philip Morris Products S.A., 2000 Neuchâtel, Switzerland
| | | | - Ashraf Elamin
- Philip Morris International R&D, Philip Morris Products S.A., 2000 Neuchâtel, Switzerland
| | - Alberto Oviedo
- *Philip Morris International Research Laboratories Pte Ltd, The Kendall #02-07, Science Park II, Singapore 117406
| | - Maciej Cabanski
- Philip Morris International R&D, Philip Morris Products S.A., 2000 Neuchâtel, Switzerland
| | - Héctor De León
- Philip Morris International R&D, Philip Morris Products S.A., 2000 Neuchâtel, Switzerland
| | - Emmanuel Guedj
- Philip Morris International R&D, Philip Morris Products S.A., 2000 Neuchâtel, Switzerland
| | - Thomas Schneider
- Philip Morris International R&D, Philip Morris Products S.A., 2000 Neuchâtel, Switzerland
| | - Marja Talikka
- Philip Morris International R&D, Philip Morris Products S.A., 2000 Neuchâtel, Switzerland
| | - Nikolai V Ivanov
- Philip Morris International R&D, Philip Morris Products S.A., 2000 Neuchâtel, Switzerland
| | - Patrick Vanscheeuwijck
- Philip Morris International R&D, Philip Morris Products S.A., 2000 Neuchâtel, Switzerland
| | - Manuel C Peitsch
- Philip Morris International R&D, Philip Morris Products S.A., 2000 Neuchâtel, Switzerland
| | - Julia Hoeng
- Philip Morris International R&D, Philip Morris Products S.A., 2000 Neuchâtel, Switzerland;
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22
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Ansari S, Baumer K, Boué S, Dijon S, Dulize R, Ekroos K, Elamin A, Foong C, Guedj E, Hoeng J, Ivanov NV, Krishnan S, Leroy P, Martin F, Merg C, Peck MJ, Peitsch MC, Phillips B, Schlage WK, Schneider T, Talikka M, Titz B, Vanscheeuwijck P, Veljkovic E, Vihervaara T, Vuillaume G, Woon CQ. Comprehensive systems biology analysis of a 7-month cigarette smoke inhalation study in C57BL/6 mice. Sci Data 2016; 3:150077. [PMID: 26731301 PMCID: PMC4700839 DOI: 10.1038/sdata.2015.77] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 11/19/2015] [Indexed: 12/12/2022] Open
Abstract
Smoking of combustible cigarettes has a major impact on human health. Using a systems toxicology approach in a model of chronic obstructive pulmonary disease (C57BL/6 mice), we assessed the health consequences in mice of an aerosol derived from a prototype modified risk tobacco product (pMRTP) as compared to conventional cigarettes. We investigated physiological and histological endpoints in parallel with transcriptomics, lipidomics, and proteomics profiles in mice exposed to a reference cigarette (3R4F) smoke or a pMRTP aerosol for up to 7 months. We also included a cessation group and a switching-to-pMRTP group (after 2 months of 3R4F exposure) in addition to the control (fresh air-exposed) group, to understand the potential risk reduction of switching to pMRTP compared with continuous 3R4F exposure and cessation. The present manuscript describes the study design, setup, and implementation, as well as the generation, processing, and quality control analysis of the toxicology and ‘omics’ datasets that are accessible in public repositories for further analyses.
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Affiliation(s)
- Sam Ansari
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | - Karine Baumer
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | - Stéphanie Boué
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | - Sophie Dijon
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | - Remi Dulize
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | - Kim Ekroos
- Zora Biosciences Oy, Biologinkuja 1, Espoo 02150, Finland
| | - Ashraf Elamin
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | - Clement Foong
- Philip Morris International Research Laboratories, 50 Science Park Road, Science Park II, Singapore, Singapore 117406
| | - Emmanuel Guedj
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | - Julia Hoeng
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | - Nikolai V Ivanov
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | - Subash Krishnan
- Philip Morris International Research Laboratories, 50 Science Park Road, Science Park II, Singapore, Singapore 117406
| | - Patrice Leroy
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | - Florian Martin
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | - Celine Merg
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | - Michael J Peck
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | - Manuel C Peitsch
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | - Blaine Phillips
- Philip Morris International Research Laboratories, 50 Science Park Road, Science Park II, Singapore, Singapore 117406
| | - Walter K Schlage
- Biology consultant, Max-Baermann-Str. 21, 51429 Bergisch Gladbach, Germany
| | - Thomas Schneider
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | - Marja Talikka
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | - Bjoern Titz
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | - Patrick Vanscheeuwijck
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | - Emilija Veljkovic
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | | | - Gregory Vuillaume
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | - Ching Qing Woon
- Philip Morris International Research Laboratories, 50 Science Park Road, Science Park II, Singapore, Singapore 117406
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23
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Phillips B, Esposito M, Verbeeck J, Boué S, Iskandar A, Vuillaume G, Leroy P, Krishnan S, Kogel U, Utan A, Schlage WK, Bera M, Veljkovic E, Hoeng J, Peitsch MC, Vanscheeuwijck P. Toxicity of aerosols of nicotine and pyruvic acid (separate and combined) in Sprague-Dawley rats in a 28-day OECD 412 inhalation study and assessment of systems toxicology. Inhal Toxicol 2015; 27:405-31. [PMID: 26295358 DOI: 10.3109/08958378.2015.1046000] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Toxicity of nebulized nicotine (Nic) and nicotine/pyruvic acid mixtures (Nic/Pyr) was characterized in a 28-day Organization for Economic Co-operation and Development 412 inhalation study with additional transcriptomic and lipidomic analyses. Sprague-Dawley rats were nose-only exposed, 6 h/day, 5 days/week to filtered air, saline, nicotine (50 µg/l), sodium pyruvate (NaPyr, 33.9 µg/l) or equimolar Nic/Pyr mixtures (18, 25 and 50 µg nicotine/l). Saline and NaPyr caused no health effects, but rats exposed to nicotine-containing aerosols had decreased body weight gains and concentration-dependent increases in liver weight. Blood neutrophil counts were increased and lymphocyte counts decreased in rats exposed to nicotine; activities of alkaline phosphatase and alanine aminotransferase were increased, and levels of cholesterol and glucose decreased. The only histopathologic finding in non-respiratory tract organs was increased liver vacuolation and glycogen content. Respiratory tract findings upon nicotine exposure (but also some phosphate-buffered saline aerosol effects) were observed only in the larynx and were limited to adaptive changes. Gene expression changes in the lung and liver were very weak. Nic and Nic/Pyr caused few significant changes (including Cyp1a1 gene upregulation). Changes were predominantly related to energy metabolism and fatty acid metabolism but did not indicate an obvious toxicity-related response. Nicotine exposure lowered plasma lipids, including cholesteryl ester (CE) and free cholesterol and, in the liver, phospholipids and sphingolipids. Nic, NaPyr and Nic/Pyr decreased hepatic triacylglycerol and CE. In the lung, Nic and Nic/Pyr increased CE levels. These data suggest that only minor biologic effects related to inhalation of Nic or Nic/Pyr aerosols were observed in this 28-day study.
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Affiliation(s)
- Blaine Phillips
- a Philip Morris International Research Laboratories Pte Ltd , Science Park II , Singapore and
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24
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Boué S, Talikka M, Westra JW, Hayes W, Di Fabio A, Park J, Schlage WK, Sewer A, Fields B, Ansari S, Martin F, Veljkovic E, Kenney R, Peitsch MC, Hoeng J. Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems. Database (Oxford) 2015; 2015:bav030. [PMID: 25887162 PMCID: PMC4401337 DOI: 10.1093/database/bav030] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 03/09/2015] [Indexed: 01/28/2023]
Abstract
With the wealth of publications and data available, powerful and transparent computational approaches are required to represent measured data and scientific knowledge in a computable and searchable format. We developed a set of biological network models, scripted in the Biological Expression Language, that reflect causal signaling pathways across a wide range of biological processes, including cell fate, cell stress, cell proliferation, inflammation, tissue repair and angiogenesis in the pulmonary and cardiovascular context. This comprehensive collection of networks is now freely available to the scientific community in a centralized web-based repository, the Causal Biological Network database, which is composed of over 120 manually curated and well annotated biological network models and can be accessed at http://causalbionet.com. The website accesses a MongoDB, which stores all versions of the networks as JSON objects and allows users to search for genes, proteins, biological processes, small molecules and keywords in the network descriptions to retrieve biological networks of interest. The content of the networks can be visualized and browsed. Nodes and edges can be filtered and all supporting evidence for the edges can be browsed and is linked to the original articles in PubMed. Moreover, networks may be downloaded for further visualization and evaluation. Database URL:http://causalbionet.com
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Affiliation(s)
- Stéphanie Boué
- Philip Morris International R&D, Philip Morris Products S.A. Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland, Selventa, One Alewife Center, Cambridge, MA 02140, USA and Applied Dynamic Solutions, LLC, 220 Davidson Avenue, Suite 100, Somerset, NJ 08873, USA
| | - Marja Talikka
- Philip Morris International R&D, Philip Morris Products S.A. Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland, Selventa, One Alewife Center, Cambridge, MA 02140, USA and Applied Dynamic Solutions, LLC, 220 Davidson Avenue, Suite 100, Somerset, NJ 08873, USA
| | - Jurjen Willem Westra
- Philip Morris International R&D, Philip Morris Products S.A. Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland, Selventa, One Alewife Center, Cambridge, MA 02140, USA and Applied Dynamic Solutions, LLC, 220 Davidson Avenue, Suite 100, Somerset, NJ 08873, USA
| | - William Hayes
- Philip Morris International R&D, Philip Morris Products S.A. Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland, Selventa, One Alewife Center, Cambridge, MA 02140, USA and Applied Dynamic Solutions, LLC, 220 Davidson Avenue, Suite 100, Somerset, NJ 08873, USA
| | - Anselmo Di Fabio
- Philip Morris International R&D, Philip Morris Products S.A. Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland, Selventa, One Alewife Center, Cambridge, MA 02140, USA and Applied Dynamic Solutions, LLC, 220 Davidson Avenue, Suite 100, Somerset, NJ 08873, USA
| | - Jennifer Park
- Philip Morris International R&D, Philip Morris Products S.A. Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland, Selventa, One Alewife Center, Cambridge, MA 02140, USA and Applied Dynamic Solutions, LLC, 220 Davidson Avenue, Suite 100, Somerset, NJ 08873, USA
| | - Walter K Schlage
- Philip Morris International R&D, Philip Morris Products S.A. Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland, Selventa, One Alewife Center, Cambridge, MA 02140, USA and Applied Dynamic Solutions, LLC, 220 Davidson Avenue, Suite 100, Somerset, NJ 08873, USA
| | - Alain Sewer
- Philip Morris International R&D, Philip Morris Products S.A. Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland, Selventa, One Alewife Center, Cambridge, MA 02140, USA and Applied Dynamic Solutions, LLC, 220 Davidson Avenue, Suite 100, Somerset, NJ 08873, USA
| | - Brett Fields
- Philip Morris International R&D, Philip Morris Products S.A. Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland, Selventa, One Alewife Center, Cambridge, MA 02140, USA and Applied Dynamic Solutions, LLC, 220 Davidson Avenue, Suite 100, Somerset, NJ 08873, USA
| | - Sam Ansari
- Philip Morris International R&D, Philip Morris Products S.A. Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland, Selventa, One Alewife Center, Cambridge, MA 02140, USA and Applied Dynamic Solutions, LLC, 220 Davidson Avenue, Suite 100, Somerset, NJ 08873, USA
| | - Florian Martin
- Philip Morris International R&D, Philip Morris Products S.A. Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland, Selventa, One Alewife Center, Cambridge, MA 02140, USA and Applied Dynamic Solutions, LLC, 220 Davidson Avenue, Suite 100, Somerset, NJ 08873, USA
| | - Emilija Veljkovic
- Philip Morris International R&D, Philip Morris Products S.A. Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland, Selventa, One Alewife Center, Cambridge, MA 02140, USA and Applied Dynamic Solutions, LLC, 220 Davidson Avenue, Suite 100, Somerset, NJ 08873, USA
| | - Renee Kenney
- Philip Morris International R&D, Philip Morris Products S.A. Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland, Selventa, One Alewife Center, Cambridge, MA 02140, USA and Applied Dynamic Solutions, LLC, 220 Davidson Avenue, Suite 100, Somerset, NJ 08873, USA
| | - Manuel C Peitsch
- Philip Morris International R&D, Philip Morris Products S.A. Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland, Selventa, One Alewife Center, Cambridge, MA 02140, USA and Applied Dynamic Solutions, LLC, 220 Davidson Avenue, Suite 100, Somerset, NJ 08873, USA
| | - Julia Hoeng
- Philip Morris International R&D, Philip Morris Products S.A. Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland, Selventa, One Alewife Center, Cambridge, MA 02140, USA and Applied Dynamic Solutions, LLC, 220 Davidson Avenue, Suite 100, Somerset, NJ 08873, USA
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25
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De León H, Boué S, Schlage WK, Boukharov N, Westra JW, Gebel S, VanHooser A, Talikka M, Fields RB, Veljkovic E, Peck MJ, Mathis C, Hoang V, Poussin C, Deehan R, Stolle K, Hoeng J, Peitsch MC. A vascular biology network model focused on inflammatory processes to investigate atherogenesis and plaque instability. J Transl Med 2014; 12:185. [PMID: 24965703 PMCID: PMC4227037 DOI: 10.1186/1479-5876-12-185] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 06/09/2014] [Indexed: 12/20/2022] Open
Abstract
Background Numerous inflammation-related pathways have been shown to play important roles in atherogenesis. Rapid and efficient assessment of the relative influence of each of those pathways is a challenge in the era of “omics” data generation. The aim of the present work was to develop a network model of inflammation-related molecular pathways underlying vascular disease to assess the degree of translatability of preclinical molecular data to the human clinical setting. Methods We constructed and evaluated the Vascular Inflammatory Processes Network (V-IPN), a model representing a collection of vascular processes modulated by inflammatory stimuli that lead to the development of atherosclerosis. Results Utilizing the V-IPN as a platform for biological discovery, we have identified key vascular processes and mechanisms captured by gene expression profiling data from four independent datasets from human endothelial cells (ECs) and human and murine intact vessels. Primary ECs in culture from multiple donors revealed a richer mapping of mechanisms identified by the V-IPN compared to an immortalized EC line. Furthermore, an evaluation of gene expression datasets from aortas of old ApoE-/- mice (78 weeks) and human coronary arteries with advanced atherosclerotic lesions identified significant commonalities in the two species, as well as several mechanisms specific to human arteries that are consistent with the development of unstable atherosclerotic plaques. Conclusions We have generated a new biological network model of atherogenic processes that demonstrates the power of network analysis to advance integrative, systems biology-based knowledge of cross-species translatability, plaque development and potential mechanisms leading to plaque instability.
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Affiliation(s)
- Héctor De León
- Philip Morris International R&D, Philip Morris Products S,A,, Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland.
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26
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Poussin C, Mathis C, Alexopoulos LG, Messinis DE, Dulize RHJ, Belcastro V, Melas IN, Sakellaropoulos T, Rhrissorrakrai K, Bilal E, Meyer P, Talikka M, Boué S, Norel R, Rice JJ, Stolovitzky G, Ivanov NV, Peitsch MC, Hoeng J. The species translation challenge-a systems biology perspective on human and rat bronchial epithelial cells. Sci Data 2014; 1:140009. [PMID: 25977767 PMCID: PMC4322580 DOI: 10.1038/sdata.2014.9] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 04/25/2014] [Indexed: 11/19/2022] Open
Abstract
The biological responses to external cues such as drugs, chemicals, viruses and hormones, is an essential question in biomedicine and in the field of toxicology, and cannot be easily studied in humans. Thus, biomedical research has continuously relied on animal models for studying the impact of these compounds and attempted to 'translate' the results to humans. In this context, the SBV IMPROVER (Systems Biology Verification for Industrial Methodology for PROcess VErification in Research) collaborative initiative, which uses crowd-sourcing techniques to address fundamental questions in systems biology, invited scientists to deploy their own computational methodologies to make predictions on species translatability. A multi-layer systems biology dataset was generated that was comprised of phosphoproteomics, transcriptomics and cytokine data derived from normal human (NHBE) and rat (NRBE) bronchial epithelial cells exposed in parallel to more than 50 different stimuli under identical conditions. The present manuscript describes in detail the experimental settings, generation, processing and quality control analysis of the multi-layer omics dataset accessible in public repositories for further intra- and inter-species translation studies.
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Affiliation(s)
- Carine Poussin
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
- These authors contributed equally to this work
| | - Carole Mathis
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
- These authors contributed equally to this work
| | - Leonidas G Alexopoulos
- ProtATonce Ltd, Scientific Park Lefkippos, Patriarchou Grigoriou & Neapoleos, 15343 Ag. Paraskevi, Attiki, Greece
- National Technical University of Athens, Heroon Polytechniou 9, Zografou 15780, Greece
- These authors contributed equally to this work
| | - Dimitris E Messinis
- ProtATonce Ltd, Scientific Park Lefkippos, Patriarchou Grigoriou & Neapoleos, 15343 Ag. Paraskevi, Attiki, Greece
- National Technical University of Athens, Heroon Polytechniou 9, Zografou 15780, Greece
| | - Rémi H J Dulize
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Vincenzo Belcastro
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Ioannis N Melas
- ProtATonce Ltd, Scientific Park Lefkippos, Patriarchou Grigoriou & Neapoleos, 15343 Ag. Paraskevi, Attiki, Greece
- National Technical University of Athens, Heroon Polytechniou 9, Zografou 15780, Greece
| | | | | | - Erhan Bilal
- IBM Computational Biology Center, Yorktown Heights, NY 10598, USA
| | - Pablo Meyer
- IBM Computational Biology Center, Yorktown Heights, NY 10598, USA
| | - Marja Talikka
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Stéphanie Boué
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Raquel Norel
- IBM Computational Biology Center, Yorktown Heights, NY 10598, USA
| | - John J Rice
- IBM Computational Biology Center, Yorktown Heights, NY 10598, USA
| | | | - Nikolai V Ivanov
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Manuel C Peitsch
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Julia Hoeng
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
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27
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Boué S, De León H, Schlage WK, Peck MJ, Weiler H, Berges A, Vuillaume G, Martin F, Friedrichs B, Lebrun S, Meurrens K, Schracke N, Moehring M, Steffen Y, Schueller J, Vanscheeuwijck P, Peitsch MC, Hoeng J. Cigarette smoke induces molecular responses in respiratory tissues of ApoE−/− mice that are progressively deactivated upon cessation. Toxicology 2013; 314:112-24. [DOI: 10.1016/j.tox.2013.09.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 09/24/2013] [Accepted: 09/24/2013] [Indexed: 12/25/2022]
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28
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De Lucca AJ, Carter-Wientjes CH, Boué S, Bhatnagar D. Volatile trans-2-hexenal, a soybean aldehyde, inhibits Aspergillus flavus growth and aflatoxin production in corn. J Food Sci 2011; 76:M381-6. [PMID: 22417509 DOI: 10.1111/j.1750-3841.2011.02250.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
UNLABELLED Trans-2-hexenal, a volatile aldehyde, is produced by soybean (Glycine max [L.] Merr) and other plants via the lipoxygenase pathway. In vitro tests showed it significantly (P < 0.001) reduced Aspergillus flavus germinating conidial viability at 10 μM, with approximately 95% viability reduction observed at 20 μM. The viability of nongerminated conidia was not reduced. To test the effectiveness of this volatile to prevent fungal growth in stored corn, trans-2-hexenal was pumped intermittently into glass jars containing corn. Experiments were performed to determine the ability of 2 different pump cycle time-courses to prevent A. flavus growth on sterile corn (23% moisture). Intermittently (30-min pumping period) over 7 d, this volatile was pumped through 350 g of corn kernels inoculated with 1 mL of 3 × 10⁴ conidia of A. flavus. Controls consisted of (1) sterile corn, (2) corn inoculated with A. flavus with no pumped air, and (3) corn inoculated with A. flavus with intermittently pumped air. Aflatoxin B₁ (AFB₁), viability counts, and aldehyde concentration in the headspace were performed in each experiment. To determine whether an increased time period between volatile pumping would prevent A. flavus growth, a 2nd series of experiments were performed that were similar to the 1st series except that trans-2-hexenal (only) was pumped for a 30-min period every 12 h. Experiments were performed 3 times for each time course. Both experiments showed that intermittent pumping of volatile trans-2-hexenal significantly (P < 0.001) prevented A. flavus growth and aflatoxin B₁ production over a 7-d period. PRACTICAL APPLICATION Results from this study indicate that intermittent pumping of volatile trans-2-hexenal could be used to protect stored corn from A. flavus growth and aflatoxin contamination.
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Affiliation(s)
- A J De Lucca
- Southern Regional Research Center, Agricultural Research Service, U.S. Dept. of Agriculture, 1100 Robert E. Lee Blvd., New Orleans, LA 70124, USA.
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29
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Vassena R, Boué S, González-Roca E, Aran B, Auer H, Veiga A, Izpisua Belmonte JC. Waves of early transcriptional activation and pluripotency program initiation during human preimplantation development. Development 2011; 138:3699-709. [PMID: 21775417 DOI: 10.1242/dev.064741] [Citation(s) in RCA: 196] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The events regulating human preimplantation development are still largely unknown owing to a scarcity of material, ethical and legal limitations and a lack of reliable techniques to faithfully amplify the transcriptome of a single cell. Nonetheless, human embryology is gathering renewed interest due to its close relationship with both stem cell biology and epigenetic reprogramming to pluripotency and their importance in regenerative medicine. Carefully timed genome-wide transcript analyses of single oocytes and embryos uncovered a series of successive waves of embryonic transcriptional initiation that start as early as the 2-cell stage. In addition, we identified the hierarchical activation of genes involved in the regulation of pluripotency. Finally, we developed HumER, a database of human preimplantation gene expression, to serve the scientific community. Importantly, our work links early transcription in the human embryo with the correct execution of the pluripotency program later in development and paves the way for the identification of factors to improve epigenetic reprogramming.
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Affiliation(s)
- Rita Vassena
- Center for Regenerative Medicine in Barcelona, CMR[B], Dr Aiguader 88, 08003, Barcelona, Spain
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30
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Boué S, Paramonov I, Barrero MJ, Izpisúa Belmonte JC. Analysis of human and mouse reprogramming of somatic cells to induced pluripotent stem cells. What is in the plate? PLoS One 2010; 5. [PMID: 20862250 PMCID: PMC2941458 DOI: 10.1371/journal.pone.0012664] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Accepted: 08/15/2010] [Indexed: 01/22/2023] Open
Abstract
After the hope and controversy brought by embryonic stem cells two decades ago for regenerative medicine, a new turn has been taken in pluripotent cells research when, in 2006, Yamanaka's group reported the reprogramming of fibroblasts to pluripotent cells with the transfection of only four transcription factors. Since then many researchers have managed to reprogram somatic cells from diverse origins into pluripotent cells, though the cellular and genetic consequences of reprogramming remain largely unknown. Furthermore, it is still unclear whether induced pluripotent stem cells (iPSCs) are truly functionally equivalent to embryonic stem cells (ESCs) and if they demonstrate the same differentiation potential as ESCs. There are a large number of reprogramming experiments published so far encompassing genome-wide transcriptional profiling of the cells of origin, the iPSCs and ESCs, which are used as standards of pluripotent cells and allow us to provide here an in-depth analysis of transcriptional profiles of human and mouse cells before and after reprogramming. When compared to ESCs, iPSCs, as expected, share a common pluripotency/self-renewal network. Perhaps more importantly, they also show differences in the expression of some genes. We concentrated our efforts on the study of bivalent domain-containing genes (in ESCs) which are not expressed in ESCs, as they are supposedly important for differentiation and should possess a poised status in pluripotent cells, i.e. be ready to but not yet be expressed. We studied each iPSC line separately to estimate the quality of the reprogramming and saw a correlation of the lowest number of such genes expressed in each respective iPSC line with the stringency of the pluripotency test achieved by the line. We propose that the study of expression of bivalent domain-containing genes, which are normally silenced in ESCs, gives a valuable indication of the quality of the iPSC line, and could be used to select the best iPSC lines out of a large number of lines generated in each reprogramming experiment.
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Affiliation(s)
- Stéphanie Boué
- Center for Regenerative Medicine in Barcelona (CMRB), Barcelona, Spain
| | - Ida Paramonov
- Center for Regenerative Medicine in Barcelona (CMRB), Barcelona, Spain
| | | | - Juan Carlos Izpisúa Belmonte
- Center for Regenerative Medicine in Barcelona (CMRB), Barcelona, Spain
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, California, United States of America
- * E-mail:
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31
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Edel MJ, Boué S, Menchon C, Sánchez-Danés A, Izpisua Belmonte JC. Rem2 GTPase controls proliferation and apoptosis of neurons during embryo development. Cell Cycle 2010; 9:3414-22. [PMID: 20729629 DOI: 10.4161/cc.9.17.12719] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We have recently found that Rem2 GTPase, highly expressed in human embryonic stem cells (hESC), maintains the cell cycle and controls proper differentiation towards ectoderm, suggesting a role in neuronal development. We describe here the use of the zebrafish (Danio rerio) model to determine the physiological significance of Rem2 during embryogenesis. We show that Rem2 RNA is highly expressed in zebrafish embryos up to 2 hours of development followed by a decrease in expression until 48 hours when afterwards Rem2 is switched on again until 5 days. In situ expression analysis reveals that Rem2 is expressed exclusively in the tectum of the brain and eye of the zebrafish. Rem2 morpholino demonstrates impaired embryo development resulting in loss of neural tissue. We show that the mechanism of action of Rem2 is to control apoptosis and proliferation, peaking at 36 hours of development. Rem2 is down-regulated under general differentiation conditions of hESC and is lower expressed in most differentiated cells; however, it is upregulated with neuronal development. This suggests that Rem2 is critical for neuronal development during embryogenesis by regulating proliferation and apoptosis. We propose a model in which Rem2 GTPase is a key regulator maintaining pluripotency during early stages of embryogenesis and survival of neurons during later embryonic development.
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Affiliation(s)
- Michael J Edel
- Center of Regenerative Medicine in Barcelona, Barcelona, Spain
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Boué S, Gielen M, Nasielski J. Composés Organométalliques IV. Spectres de résonance magnétique nucléaire protonique de dérivés organostanniques (CH3)3SnR′ (). ACTA ACUST UNITED AC 2010. [DOI: 10.1002/bscb.19670761102] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Boué S, Gielen M, Nasielski J. Organometallic compounds. VI . Electron impact fragmentation of some mixed and symmetrical tetraalkyltins. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/bscb.19680770105] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Boué S, Gielen M, Nasielski J, Lieutenant JP, Spielmann R. Organometallic Compounds. XI. Synthesis and Properties of a Series of Racemic Tetraalkyltins. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/bscb.19690780117] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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36
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Abstract
In mammals, after a myocardial infarction episode, the damaged myocardium is replaced by scar tissue with negligible cardiomyocyte proliferation. Zebrafish, in contrast, display an extensive regenerative capacity, as they are able to restore completely lost cardiac tissue after partial ventricular amputation. Although questions about the early signals that drive the regenerative response and the relative role of each cardiac cell type in this process still need to be answered, the zebrafish is emerging as a very valuable tool to understand heart regeneration and to devise strategies that may be of potential value to treat human cardiac disease. Here, we performed a genome-wide transcriptome profile analysis focusing on the early time points of zebrafish heart regeneration and compared our results with those of previously published data. Our analyses confirmed the differential expression of several transcripts and identified additional genes whose expression is differentially regulated during zebrafish heart regeneration. We validated the microarray data by conventional and/or quantitative reverse transcriptase-polymerase chain reaction (RT-PCR). For a subset of these genes, their expression pattern was analyzed by in-situ hybridization and shown to be upregulated in the regenerating area of the heart. Our results offer new insights into the biology of heart regeneration in the zebrafish and, together with future experiments in mammals, may be of potential interest for clinical applications.
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Affiliation(s)
- Eduard Sleep
- Center for Regenerative Medicine, Barcelona, Spain
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Benjak A, Boué S, Forneck A, Casacuberta JM. Recent amplification and impact of MITEs on the genome of grapevine (Vitis vinifera L.). Genome Biol Evol 2009; 1:75-84. [PMID: 20333179 PMCID: PMC2817404 DOI: 10.1093/gbe/evp009] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2009] [Indexed: 01/07/2023] Open
Abstract
Miniature inverted-repeat transposable elements (MITEs) are a particular type of defective class II transposons present in genomes as highly homogeneous populations of small elements. Their high copy number and close association to genes make their potential impact on gene evolution particularly relevant. Here, we present a detailed analysis of the MITE families directly related to grapevine "cut-and-paste" transposons. Our results show that grapevine MITEs have transduplicated and amplified genomic sequences, including gene sequences and fragments of other mobile elements. Our results also show that although some of the MITE families were already present in the ancestor of the European and American Vitis wild species, they have been amplified and have been actively transposing accompanying grapevine domestication and breeding. We show that MITEs are abundant in grapevine and some of them are frequently inserted within the untranslated regions of grapevine genes. MITE insertions are highly polymorphic among grapevine cultivars, which frequently generate transcript variability. The data presented here show that MITEs have greatly contributed to the grapevine genetic diversity which has been used for grapevine domestication and breeding.
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Affiliation(s)
- Andrej Benjak
- Department of Plant Molecular Genetics, Center for Research in Agricultural Genomics (Consejo Superior Investigaciones Científicas-Institut de Recerca I Tecnologia Agrícola-Universitat Autònoma de Barcelona), Barcelona, Spain
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Koscielny G, Texier VL, Gopalakrishnan C, Kumanduri V, Riethoven JJ, Nardone F, Stanley E, Fallsehr C, Hofmann O, Kull M, Harrington E, Boué S, Eyras E, Plass M, Lopez F, Ritchie W, Moucadel V, Ara T, Pospisil H, Herrmann A, G. Reich J, Guigó R, Bork P, Doeberitz MVK, Vilo J, Hide W, Apweiler R, Thanaraj TA, Gautheret D. ASTD: The Alternative Splicing and Transcript Diversity database. Genomics 2009; 93:213-20. [DOI: 10.1016/j.ygeno.2008.11.003] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2008] [Revised: 11/03/2008] [Accepted: 11/05/2008] [Indexed: 10/21/2022]
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Aasen T, Raya A, Barrero MJ, Garreta E, Consiglio A, Gonzalez F, Vassena R, Bilić J, Pekarik V, Tiscornia G, Edel M, Boué S, Belmonte JCI. Efficient and rapid generation of induced pluripotent stem cells from human keratinocytes. Nat Biotechnol 2008; 26:1276-84. [PMID: 18931654 DOI: 10.1038/nbt.1503] [Citation(s) in RCA: 946] [Impact Index Per Article: 59.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2008] [Accepted: 09/29/2008] [Indexed: 12/13/2022]
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Abstract
Nowadays understanding alternative splicing is one of the greatest challenges in biology, because it is a genetic process much more important than thought at the time of its discovery. In this paper, we explain the approach of using the different available databases and software tools to start a large scale investigation of alternative splice forms. To collect information about alternative splicing we investigated known data in the databases using different computational methods. The investigations proceeded from the genomic sequence data to structural protein data. Then, we interpreted those data to find the relationship between alternative splice forms and protein function and structure. We found some interesting features of alternative splicing which are presented here. We discuss the results of one chosen example. They concern the coverage quality of the protein sequence of a known structure, an EST analysis, the validation of splice variants, the determination of the alternative splice type, and finally the link between alternative splicing and disease.
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Affiliation(s)
- Stéphanie Boué
- Max-Planck-Institute for Molecular Genetics, Department Computational Molecular Biology, Berlin, Germany
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Abstract
Transcript diversity generated by alternative splicing and associated mechanisms contributes heavily to the functional complexity of biological systems. The numerous examples of the mechanisms and functional implications of these events are scattered throughout the scientific literature. Thus, it is crucial to have a tool that can automatically extract the relevant facts and collect them in a knowledge base that can aid the interpretation of data from high-throughput methods. We have developed and applied a composite text-mining method for extracting information on transcript diversity from the entire MEDLINE database in order to create a database of genes with alternative transcripts. It contains information on tissue specificity, number of isoforms, causative mechanisms, functional implications, and experimental methods used for detection. We have mined this resource to identify 959 instances of tissue-specific splicing. Our results in combination with those from EST-based methods suggest that alternative splicing is the preferred mechanism for generating transcript diversity in the nervous system. We provide new annotations for 1,860 genes with the potential for generating transcript diversity. We assign the MeSH term “alternative splicing” to 1,536 additional abstracts in the MEDLINE database and suggest new MeSH terms for other events. We have successfully extracted information about transcript diversity and semiautomatically generated a database, LSAT, that can provide a quantitative understanding of the mechanisms behind tissue-specific gene expression. LSAT (Literature Support for Alternative Transcripts) is publicly available at http://www.bork.embl.de/LSAT/. Given the functional complexity of higher eukaryotes, the relatively small number of genes in the human and other mammalian genomes came as a surprise to the scientific community. Later it was discovered that the majority of genes are subject to alternative splicing (“cutting and pasting”) or associated mechanisms that ultimately increase the diversity of transcripts that code for proteins. Studies exploring transcript diversity are currently dominated by high-throughput experiments and computational methods; however, the quality of such data should be assessed against a reliable reference set based on single-gene studies. Unfortunately, the latter type of information is scattered throughout the scientific literature. The authors have thus developed a computational approach for extracting information on alternative transcripts from MEDLINE abstracts and used it to create a database, LSAT. LSAT (Literature Support for Alternative Transcripts) provides information for more than 4,000 genes from about 14,000 abstracts. This database can provide a quantitative understanding of the mechanisms behind tissue-specific gene expression based on single-gene studies, which we show agrees well with EST-based studies (these studies involve tissue-specific splicing detected by the analysis of libraries of expressed sequence tags [ESTs]). These results indicate that mechanisms like alternative splicing, alternative promoters, and alternative polyadenylation work in concert to generate and regulate transcript diversity. More generally, information extraction of complex biological process seems feasible and can also complement large-scale data generation in other areas to assign functions to genes.
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Affiliation(s)
- Parantu K Shah
- Structural and Computational Biology Program, European Molecular Biology Laboratory, Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, Berlin-Buch, Germany
| | - Lars J Jensen
- Structural and Computational Biology Program, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Stéphanie Boué
- Structural and Computational Biology Program, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Peer Bork
- Structural and Computational Biology Program, European Molecular Biology Laboratory, Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, Berlin-Buch, Germany
- * To whom correspondence should be addressed. E-mail:
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Zenkouar M, Boué S, Vander Donckt E. Pressure- and solvent-dependent fluorescence quenching of pyrene by p-chlorobenzonitrile analysed by the simplex algorithm: A powerful computer approach to the problem. J Photochem Photobiol A Chem 1988. [DOI: 10.1016/1010-6030(88)80099-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Srinivasan R, Boué S. Einige Eigenschaften einer dreigliedrigen cyclischen Diradikalzwischenstufe. Angew Chem Int Ed Engl 1972. [DOI: 10.1002/ange.19720840732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Boué S, Gielen M, Nasielski J, Autin J, Limbourg M. On the reported selectivity of the bromination of mixed tetraalkyltins in carbon tetrachloride. J Organomet Chem 1968. [DOI: 10.1016/s0022-328x(00)86353-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Boué S, Gielen M, Nasielski J. Mécanismes de rupture de la liason corbone-étain par les halogènes II. Substitution radicalaire en solution. J Organomet Chem 1967. [DOI: 10.1016/s0022-328x(00)91017-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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