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Stobernack T, Dommershausen N, Alcolea-Rodríguez V, Ledwith R, Bañares MA, Haase A, Pink M, Dumit VI. Advancing Nanomaterial Toxicology Screening Through Efficient and Cost-Effective Quantitative Proteomics. SMALL METHODS 2024:e2400420. [PMID: 38813751 DOI: 10.1002/smtd.202400420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/17/2024] [Indexed: 05/31/2024]
Abstract
Proteomic investigations yield high-dimensional datasets, yet their application to large-scale toxicological assessments is hindered by reproducibility challenges due to fluctuating measurement conditions. To address these limitations, this study introduces an advanced tandem mass tag (TMT) labeling protocol. Although labeling approaches shorten data acquisition time by multiplexing samples compared to traditional label-free quantification (LFQ) methods in general, the associated costs may surge significantly with large sample sets, for example, in toxicological screenings. However, the introduced advanced protocol offers an efficient, cost-effective alternative, reducing TMT reagent usage (by a factor of ten) and requiring minimal biological material (1 µg), while demonstrating increased reproducibility compared to LFQ. To demonstrate its effectiveness, the advanced protocol is employed to assess the toxicity of nine benchmark nanomaterials (NMs) on A549 lung epithelial cells. While LFQ measurements identify 3300 proteins, they proved inadequate to reveal NM toxicity. Conversely, despite detecting 2600 proteins, the TMT protocol demonstrates superior sensitivity by uncovering alterations induced by NM treatment. In contrast to previous studies, the introduced advanced protocol allows simultaneous and straightforward assessment of multiple test substances, enabling prioritization, ranking, and grouping for hazard evaluation. Additionally, it fosters the development of New Approach Methodologies (NAMs), contributing to innovative methodologies in toxicological research.
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Affiliation(s)
- Tobias Stobernack
- German Federal Institute for Risk Assessment (BfR), Department of Chemical and Product Safety, Max-Dohrn-Straße 8-10, 10589, Berlin, Germany
| | - Nils Dommershausen
- German Federal Institute for Risk Assessment (BfR), Department of Chemical and Product Safety, Max-Dohrn-Straße 8-10, 10589, Berlin, Germany
| | - Víctor Alcolea-Rodríguez
- German Federal Institute for Risk Assessment (BfR), Department of Chemical and Product Safety, Max-Dohrn-Straße 8-10, 10589, Berlin, Germany
- Spanish National Research Council - Institute of Catalysis and Petrochemistry (ICP-CSIC), Spectroscopy and Industrial Catalysis group, Marie Curie, 2, Madrid, 28049, Spain
| | - Rico Ledwith
- German Federal Institute for Risk Assessment (BfR), Department of Chemical and Product Safety, Max-Dohrn-Straße 8-10, 10589, Berlin, Germany
| | - Miguel A Bañares
- Spanish National Research Council - Institute of Catalysis and Petrochemistry (ICP-CSIC), Spectroscopy and Industrial Catalysis group, Marie Curie, 2, Madrid, 28049, Spain
| | - Andrea Haase
- German Federal Institute for Risk Assessment (BfR), Department of Chemical and Product Safety, Max-Dohrn-Straße 8-10, 10589, Berlin, Germany
| | - Mario Pink
- German Federal Institute for Risk Assessment (BfR), Department of Chemical and Product Safety, Max-Dohrn-Straße 8-10, 10589, Berlin, Germany
| | - Verónica I Dumit
- German Federal Institute for Risk Assessment (BfR), Department of Chemical and Product Safety, Max-Dohrn-Straße 8-10, 10589, Berlin, Germany
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Liu X, Wu S, Peng Y, Gao L, Huang X, Deng R, Lu J. Delineation of renal protein profiles in aristolochic acid I-induced nephrotoxicity in mice by label-free quantitative proteomics. Front Pharmacol 2024; 15:1341854. [PMID: 38783935 PMCID: PMC11111959 DOI: 10.3389/fphar.2024.1341854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 04/15/2024] [Indexed: 05/25/2024] Open
Abstract
Introduction: Aristolochic acid nephropathy (AAN) is a kidney injury syndrome caused by aristolochic acids exposure. Our study used label-free quantitative proteomics to delineate renal protein profiles and identify key proteins after exposure to different doses of aristolochic acid I (AAI). Methods: Male C57BL/6 mice received AAI (1.25 mg/kg/d, 2.5 mg/kg/d, or 5 mg/kg/d) or vehicle for 5 days. Results and discussion: The results showed that AAI induced dose-dependent nephrotoxicity. Differences in renal protein profiles between the control and AAI groups increased with AAI dose. Comparing the control with the low-, medium-, and high-dose AAI groups, we found 58, 210, and 271 differentially expressed proteins, respectively. Furthermore, protein-protein interaction network analysis identified acyl-CoA synthetase medium-chain family member 3 (Acsm3), cytochrome P450 family 2 subfamily E member 1 (Cyp2e1), microsomal glutathione S-transferase 1 (Mgst1), and fetuin B (Fetub) as the key proteins. Proteomics revealed that AAI decreased Acsm3 and Cyp2e1 while increasing Mgst1 and Fetub expression in mice kidneys, which was further confirmed by Western blotting. Collectively, in AAI-induced nephrotoxicity, renal protein profiles were dysregulated and exacerbated with increasing AAI dose. Acsm3, Cyp2e1, Mgst1, and Fetub may be the potential therapeutic targets for AAN.
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Affiliation(s)
- Xinhui Liu
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, China
| | - Shanshan Wu
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, China
- The Fourth Clinical Medical College, Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, China
| | - Yu Peng
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, China
- The Fourth Clinical Medical College, Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, China
| | - Liwen Gao
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, China
- The Fourth Clinical Medical College, Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, China
| | - Xi Huang
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, China
- The Fourth Clinical Medical College, Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, China
| | - Ruyu Deng
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, China
- Shenzhen Traditional Chinese Medicine Hospital Affiliated to Nanjing University of Chinese Medicine, Shenzhen, Guangdong, China
| | - Jiandong Lu
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, Guangdong, China
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Liu Y, Lian G, Chen T. A novel multi-omics data analysis of dose-dependent and temporal changes in regulatory pathways due to chemical perturbation: a case study on caffeine. Toxicol Mech Methods 2024; 34:164-175. [PMID: 37794615 DOI: 10.1080/15376516.2023.2265462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/26/2023] [Indexed: 10/06/2023]
Abstract
Comprehensive analysis of multi-omics data can reveal alterations in regulatory pathways induced by cellular exposure to chemicals by characterizing biological processes at the molecular level. Data-driven omics analysis, conducted in a dose-dependent or dynamic manner, can facilitate comprehending toxicity mechanisms. This study introduces a novel multi-omics data analysis designed to concurrently examine dose-dependent and temporal patterns of cellular responses to chemical perturbations. This analysis, encompassing preliminary exploration, pattern deconstruction, and network reconstruction of multi-omics data, provides a comprehensive perspective on the dynamic behaviors of cells exposed to varying levels of chemical stimuli. Importantly, this analysis is adaptable to any number of omics layers, including site-specific phosphoproteomics. We implemented this analysis on multi-omics data obtained from HepG2 cells exposed to a range of caffeine doses over varying durations and identified six response patterns, along with their associated biomolecules and pathways. Our study demonstrates the effectiveness of the proposed multi-omics data analysis in capturing multidimensional patterns of cellular response to chemical perturbation, enhancing understanding of pathway regulation for chemical risk assessment.
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Affiliation(s)
- Yufan Liu
- School of Chemistry and Chemical Engineering, University of Surrey, Guildford, UK
| | - Guoping Lian
- School of Chemistry and Chemical Engineering, University of Surrey, Guildford, UK
- Unilever R&D Colworth, Bedford, UK
| | - Tao Chen
- School of Chemistry and Chemical Engineering, University of Surrey, Guildford, UK
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4
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Chen H, Williams KE, Kwan EY, Kapidzic M, Puckett KA, San A, Fisher SJ, Robinson JF. Proteomic analyses of primary human villous trophoblasts exposed to flame retardant BDE-47 using SWATH-MS. Toxicology 2023; 494:153583. [PMID: 37385330 PMCID: PMC10864010 DOI: 10.1016/j.tox.2023.153583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/08/2023] [Accepted: 06/21/2023] [Indexed: 07/01/2023]
Abstract
Polybrominated diphenyl ethers (PBDEs) are a class of brominated flame retardants and recognized developmental toxicants that are detectable in placental tissues. Higher levels of in utero PBDE exposure have been associated with an increased risk of adverse birth outcomes. During pregnancy, cytotrophoblasts (CTBs) from the placenta play critical roles in the formation of the maternal-fetal interface via uterine invasion and vascular remodeling. The differentiation of these cells towards an invasive phenotype is crucial for proper placental development. We previously have shown that BDE-47 can impact CTB viability and hinder the ability of these cells to migrate and invade. To expand on potential toxicological mechanisms, we utilized quantitative proteomic approaches to identify changes in the global proteome of mid-gestation primary human CTBs after exposure to BDE-47. Using sequential window acquisition of all theoretical fragment-ion spectra (SWATH), we identified 3024 proteins in our CTB model of differentiation/invasion. Over 200 proteins were impacted as a function of BDE-47 exposure (1 μM and 5 μM) across the treatment period (15, 24, and 39 h). The differentially expressed molecules displayed time- and concentration-dependent changes in expression and were enriched in pathways associated with aggregatory and adhesive processes. Network analysis identified CYFIP1, a molecule previously unexplored in a placental context, to be dysregulated at BDE-47 concentrations previously seen to impact CTB migration/invasion. Our SWATH-MS dataset thus demonstrates BDE-47 impacts the global proteome of differentiating CTBs and serves as a valuable resource for further understanding of the relationship between environmental chemical exposures and placental development and function. AVAILABILITY OF DATA AND MATERIAL: Raw chromatograms are deposited on the MassIVE proteomic database (https://massive.ucsd.edu) under accession number MSV000087870. Normalized relative abundances are also available as Table S1.
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Affiliation(s)
- Hao Chen
- Center for Reproductive Sciences and Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco (UCSF), San Francisco, CA, USA.
| | - Katherine E Williams
- Center for Reproductive Sciences and Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Elaine Y Kwan
- Center for Reproductive Sciences and Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Mirhan Kapidzic
- Center for Reproductive Sciences and Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Kenisha A Puckett
- Center for Reproductive Sciences and Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Ali San
- Center for Reproductive Sciences and Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Susan J Fisher
- Center for Reproductive Sciences and Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Joshua F Robinson
- Center for Reproductive Sciences and Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco (UCSF), San Francisco, CA, USA
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Nury C, Merg C, Eb-Levadoux Y, Bovard D, Porchet M, Maranzano F, Loncarevic I, Tavalaei S, Lize E, Demenescu RL, Yepiskoposyan H, Hoeng J, Ivanov NV, Renggli K, Titz B. Toxicoproteomics reveals an effect of clozapine on autophagy in human liver spheroids. Toxicol Mech Methods 2022:1-10. [DOI: 10.1080/15376516.2022.2156005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Catherine Nury
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Celine Merg
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Yvan Eb-Levadoux
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - David Bovard
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Matthieu Porchet
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Fabio Maranzano
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Isidora Loncarevic
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Shahrzad Tavalaei
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Eleonore Lize
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | | | - Hasmik Yepiskoposyan
- 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
| | - Nikolai V Ivanov
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Kasper Renggli
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Bjoern Titz
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
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González-Penagos CE, Zamora-Briseño JA, Améndola-Pimenta M, Elizalde-Contreras JM, Árcega-Cabrera F, Cruz-Quintana Y, Santana-Piñeros AM, Cañizárez-Martínez MA, Pérez-Vega JA, Ruiz-May E, Rodríguez-Canul R. Integrative description of changes occurring on zebrafish embryos exposed to water-soluble crude oil components and its mixture with a chemical surfactant. Toxicol Appl Pharmacol 2022; 445:116033. [PMID: 35452689 DOI: 10.1016/j.taap.2022.116033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/09/2022] [Accepted: 04/13/2022] [Indexed: 11/16/2022]
Abstract
The effects of crude oil spills are an ongoing problem for wildlife and human health in both marine and freshwater aquatic environments. Bioassays of model organisms are a convenient way to assess the potential risks of the substances involved in oil spills. Zebrafish embryos (ZFE) are a useful to reach a fast and detailed description of the toxicity of the pollutants, including both the components of the crude oil itself and substances that are commonly used for crude oil spill mitigation (e.g. surfactants). Here, we evaluated the survival rate, as well as histological, morphological, and proteomic changes in ZFE exposed to Water Accumulated Fraction (WAF) of light crude oil and in mixture with dioctyl sulfosuccinate sodium (DOSS, e.g. CEWAF: Chemically Enhanced WAF), a surfactant that is frequently used in chemical dispersant formulations. Furthermore, we compared de hydrocarbon concentration of WAF and CEWAF of the sublethal dilution. In histological, morphological, and gene expression variables, the ZFE exposed to WAF showed less changes than those exposed to CEWAF. Proteomic changes were more dramatic in ZFE exposed to WAF, with important alterations in spliceosomal and ribosomal proteins, as well as proteins related to eye and retinal photoreceptor development and heart function. We also found that the concentration of high molecular weight hydrocarbons in water was slighly higher in presence of DOSS, but the low molecular weight hydrocarbons concentration was higher in WAF. These results provide an important starting point for identifying useful crude-oil exposure biomarkers in fish species.
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Affiliation(s)
- Carlos Eduardo González-Penagos
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN) Unidad Mérida, Antigua carretera a Progreso Km. 6, CP 97310 Mérida, Yucatán, Mexico
| | - Jesús Alejandro Zamora-Briseño
- Laboratorio de Entomología Molecular, Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, El Instituto de Ecología, Carretera antigua a Coatepec 351, El Haya, Xalapa, Veracruz, CP 91070, Mexico
| | - Monica Améndola-Pimenta
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN) Unidad Mérida, Antigua carretera a Progreso Km. 6, CP 97310 Mérida, Yucatán, Mexico
| | - José Miguel Elizalde-Contreras
- Laboratorio de Entomología Molecular, Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, El Instituto de Ecología, Carretera antigua a Coatepec 351, El Haya, Xalapa, Veracruz, CP 91070, Mexico
| | - Flor Árcega-Cabrera
- Unidad de Química Sisal, Facultad de Química, Universidad Nacional Autónoma de México, Puerto de Abrigo S/N, Sisal, Yucatán 97356, Mexico
| | - Yanis Cruz-Quintana
- Grupo de Investigación en Sanidad Acuícola, Inocuidad y Salud Ambiental, Facultad de Ciencias Veterinarias, Departamento de Acuicultura y Pesca, Universidad Técnica de Manabí, Ciudadela Universitaria, Bahía de Caráquez, Manabí 130104, Ecuador
| | - Ana María Santana-Piñeros
- Grupo de Investigación en Sanidad Acuícola, Inocuidad y Salud Ambiental, Facultad de Ciencias Veterinarias, Departamento de Acuicultura y Pesca, Universidad Técnica de Manabí, Ciudadela Universitaria, Bahía de Caráquez, Manabí 130104, Ecuador
| | - Mayra Alejandra Cañizárez-Martínez
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN) Unidad Mérida, Antigua carretera a Progreso Km. 6, CP 97310 Mérida, Yucatán, Mexico
| | - Juan Antonio Pérez-Vega
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN) Unidad Mérida, Antigua carretera a Progreso Km. 6, CP 97310 Mérida, Yucatán, Mexico
| | - Eliel Ruiz-May
- Laboratorio de Entomología Molecular, Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, El Instituto de Ecología, Carretera antigua a Coatepec 351, El Haya, Xalapa, Veracruz, CP 91070, Mexico.
| | - Rossanna Rodríguez-Canul
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN) Unidad Mérida, Antigua carretera a Progreso Km. 6, CP 97310 Mérida, Yucatán, Mexico.
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Ventura C, Torres V, Vieira L, Gomes B, Rodrigues AS, Rueff J, Penque D, Silva MJ. New “Omics” Approaches as Tools to Explore Mechanistic Nanotoxicology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1357:179-194. [DOI: 10.1007/978-3-030-88071-2_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Titz B, Sewer A, Luettich K, Wong ET, Guedj E, Nury C, Schneider T, Xiang Y, Trivedi K, Vuillaume G, Leroy P, Büttner A, Martin F, Ivanov NV, Vanscheeuwijck P, Hoeng J, Peitsch MC. Respiratory Effects of Exposure to Aerosol From the Candidate Modified-Risk Tobacco Product THS 2.2 in an 18-Month Systems Toxicology Study With A/J Mice. Toxicol Sci 2021; 178:138-158. [PMID: 32780831 PMCID: PMC7657339 DOI: 10.1093/toxsci/kfaa132] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Smoking cessation is the most effective measure for reducing the risk of smoking-related diseases. However, switching to less harmful products (modified-risk tobacco products [MRTP]) can be an alternative to help reduce the risk for adult smokers who would otherwise continue to smoke. In an 18-month chronic carcinogenicity/toxicity study in A/J mice (OECD Test Guideline 453), we assessed the aerosol of Tobacco Heating System 2.2 (THS 2.2), a candidate MRTP based on the heat-not-burn principle, compared with 3R4F cigarette smoke (CS). To capture toxicity- and disease-relevant mechanisms, we complemented standard toxicology endpoints with in-depth systems toxicology analyses. In this part of our publication series, we report on integrative assessment of the apical and molecular exposure effects on the respiratory tract (nose, larynx, and lungs). Across the respiratory tract, we found changes in inflammatory response following 3R4F CS exposure (eg, antimicrobial peptide response in the nose), with both shared and distinct oxidative and xenobiotic responses. Compared with 3R4F CS, THS 2.2 aerosol exerted far fewer effects on respiratory tract histology, including adaptive tissue changes in nasal and laryngeal epithelium and inflammation and emphysematous changes in the lungs. Integrative analysis of molecular changes confirmed the substantially lower impact of THS 2.2 aerosol than 3R4F CS on toxicologically and disease-relevant molecular processes such as inflammation, oxidative stress responses, and xenobiotic metabolism. In summary, this work exemplifies how apical and molecular endpoints can be combined effectively for toxicology assessment and further supports findings on the reduced respiratory health risks of THS 2.2 aerosol.
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Affiliation(s)
- Bjoern Titz
- PMI R&D, Philip Morris Products S.A, CH-2000 Neuchâtel, Switzerland
| | - Alain Sewer
- PMI R&D, Philip Morris Products S.A, CH-2000 Neuchâtel, Switzerland
| | - Karsta Luettich
- PMI R&D, Philip Morris Products S.A, CH-2000 Neuchâtel, Switzerland
| | - Ee Tsin Wong
- Philip Morris International Research Laboratories Pte. Ltd, Singapore 117406
| | - Emmanuel Guedj
- PMI R&D, Philip Morris Products S.A, CH-2000 Neuchâtel, Switzerland
| | - Catherine Nury
- PMI R&D, Philip Morris Products S.A, CH-2000 Neuchâtel, Switzerland
| | | | - Yang Xiang
- PMI R&D, Philip Morris Products S.A, CH-2000 Neuchâtel, Switzerland
| | - Keyur Trivedi
- PMI R&D, Philip Morris Products S.A, CH-2000 Neuchâtel, Switzerland
| | | | - Patrice Leroy
- PMI R&D, Philip Morris Products S.A, CH-2000 Neuchâtel, Switzerland
| | | | - Florian Martin
- PMI R&D, Philip Morris Products S.A, CH-2000 Neuchâtel, Switzerland
| | - Nikolai V Ivanov
- PMI R&D, Philip Morris Products S.A, CH-2000 Neuchâtel, Switzerland
| | | | - Julia Hoeng
- PMI R&D, Philip Morris Products S.A, CH-2000 Neuchâtel, Switzerland
| | - Manuel C Peitsch
- PMI R&D, Philip Morris Products S.A, CH-2000 Neuchâtel, Switzerland
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9
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Zhang S, Li C, Feng T, Cao S, Zhou H, Li L, Hu Q, Mao X, Ji S. Proteomics analysis in the kidney of mice following oral feeding Realgar. JOURNAL OF ETHNOPHARMACOLOGY 2021; 275:114118. [PMID: 33878415 DOI: 10.1016/j.jep.2021.114118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/03/2021] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Realgar, a famous traditional Chinese mineral medicine, has been toxic to the renal system. However, the underlying mechanism of Realgar nephrotoxicity is still unclear. AIM OF THE STUDY This study aimed to investigate the potential mechanism of Realgar-induced nephrotoxicity by using a label-free quantitative proteomic method. MATERIALS AND METHODS 36 mice were randomly divided into four groups: Control group, 0.5-, 1.0, and 2.0 g/kg Realgar group. After one week, serum biochemical parameters and renal histopathological examination were performed. Label-free quantitative proteomics was used to identify differentially expressed proteins which were subsequently analyzed with bioinformatics methods. Western blot was utilized to verify the six representative protein expressions. RESULTS The results showed that 2.0 g/kg Realgar significantly increased blood urea nitrogen and induced the formation of tube cast of renal tubules, while the lower-dose of 0.5 g/kg and 1.0 g/kg Realgar showed no changes. Label-free proteomic analysis identified 3138 proteins, and 272 of those proteins were screened for significant changes in a dose-dependent manner. Functional enrichment analysis suggested that these proteins could affect the apoptotic process and oxidative stress. Representative proteins in the 2.0 g/kg Realgar group, including Cat, Bad, Cycs, Nqo1, Podxl, and Hmox1, were verified by western blot. CONCLUSIONS The results in this study suggest that apoptosis and oxidative stress might be related to the Realgar-induced nephrotoxicity in mice. Moreover, the strategy of proteomics could contribute to the understanding of the mechanisms of nephrotoxicity in mice exposed to Realgar.
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Affiliation(s)
- Sheng Zhang
- Tianjin University of Traditional Chinese Medicine, Tianjin, 300139, China; NMPA Key Laboratory for Quality Control of Traditional Chinese Medicine, Shanghai Institute for Food and Drug Control, Shanghai, 201203, China.
| | - Chao Li
- NMPA Key Laboratory for Quality Control of Traditional Chinese Medicine, Shanghai Institute for Food and Drug Control, Shanghai, 201203, China; Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Tingting Feng
- NMPA Key Laboratory for Quality Control of Traditional Chinese Medicine, Shanghai Institute for Food and Drug Control, Shanghai, 201203, China
| | - Shuai Cao
- NMPA Key Laboratory for Quality Control of Traditional Chinese Medicine, Shanghai Institute for Food and Drug Control, Shanghai, 201203, China
| | - Heng Zhou
- NMPA Key Laboratory for Quality Control of Traditional Chinese Medicine, Shanghai Institute for Food and Drug Control, Shanghai, 201203, China
| | - Liming Li
- NMPA Key Laboratory for Quality Control of Traditional Chinese Medicine, Shanghai Institute for Food and Drug Control, Shanghai, 201203, China
| | - Qing Hu
- NMPA Key Laboratory for Quality Control of Traditional Chinese Medicine, Shanghai Institute for Food and Drug Control, Shanghai, 201203, China
| | - Xiuhong Mao
- NMPA Key Laboratory for Quality Control of Traditional Chinese Medicine, Shanghai Institute for Food and Drug Control, Shanghai, 201203, China
| | - Shen Ji
- Tianjin University of Traditional Chinese Medicine, Tianjin, 300139, China; NMPA Key Laboratory for Quality Control of Traditional Chinese Medicine, Shanghai Institute for Food and Drug Control, Shanghai, 201203, China.
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10
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Application of Q-TOF-MS based metabonomics techniques to analyze the plasma metabolic profile changes on rats following death due to acute intoxication of phorate. Int J Legal Med 2021; 135:1437-1447. [PMID: 33987742 DOI: 10.1007/s00414-021-02532-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 02/10/2021] [Indexed: 11/27/2022]
Abstract
Organophosphorus pesticides (OPS) are widely used in the world, and many poisoning cases were caused by them. Phorate intoxication is especially common in China. However, there are currently few methods for discriminating phorate poisoning death from phorate exposure after death and interpretation of false-positive results due to the lack of effective biomarkers. In this study, we investigated the metabonomics of rat plasma at different dose levels of acute phorate intoxication using ultra-performance liquid chromatography quadrupole-time of flight mass spectrometry (UPLC-Q-TOF-MS) analysis. A total of 11 endogenous metabolites were significantly changed in the groups exposed to phorate at LD50 level and three times of LD50 (3LD50) level compared with the control group, which could be potential biomarkers of acute phorate intoxication. Plasma metabonomics analysis showed that diethylthiophosphate (DETP) could be a useful biomarker of acute phorate intoxication. The levels of uric acid, acylcarnitine, succinate, gluconic acid, and phosphatidylcholine (PC) (36:2) were increased, while pyruvate level was decreased in all groups exposed to phorate. The levels of ceramides (Cer) (d 18:0/16:0), palmitic acid, and lysophosphatidylcholine (lysoPC) (18:1) were only changed after 3LD50 dosage. The results of this study indicate that the dose-dependent relationship exists between metabolomic profile change and toxicities associated with apoptosis, fatty acid metabolism disorder, energy metabolism disorder especially tricarboxylic acid (TCA) cycle, as well as liver, kidney, and nervous system functions after acute exposure of phorate. This study shows that metabonomics is a useful tool in identifying biomarkers for the forensic toxicology study of phorate poisoning.
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11
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Kogel U, Wong ET, Szostak J, Tan WT, Lucci F, Leroy P, Titz B, Xiang Y, Low T, Wong SK, Guedj E, Ivanov NV, Schlage WK, Peitsch MC, Kuczaj A, Vanscheeuwijck P, Hoeng J. Impact of whole-body versus nose-only inhalation exposure systems on systemic, respiratory, and cardiovascular endpoints in a 2-month cigarette smoke exposure study in the ApoE -/- mouse model. J Appl Toxicol 2021; 41:1598-1619. [PMID: 33825214 PMCID: PMC8519037 DOI: 10.1002/jat.4149] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 11/09/2022]
Abstract
Cigarette smoking is one major modifiable risk factor in the development and progression of chronic obstructive pulmonary disease and cardiovascular disease. To characterize and compare cigarette smoke (CS)-induced disease endpoints after exposure in either whole-body (WB) or nose-only (NO) exposure systems, we exposed apolipoprotein E-deficient mice to filtered air (Sham) or to the same total particulate matter (TPM) concentration of mainstream smoke from 3R4F reference cigarettes in NO or WB exposure chambers (EC) for 2 months. At matching TPM concentrations, we observed similar concentrations of carbon monoxide, acetaldehyde, and acrolein, but higher concentrations of nicotine and formaldehyde in NOEC than in WBEC. In both exposure systems, CS exposure led to the expected adaptive changes in nasal epithelia, altered lung function, lung inflammation, and pronounced changes in the nasal epithelial transcriptome and lung proteome. Exposure in the NOEC caused generally more severe histopathological changes in the nasal epithelia and a higher stress response as indicated by body weight decrease and lower blood lymphocyte counts compared with WB exposed mice. Erythropoiesis, and increases in total plasma triglyceride levels and atherosclerotic plaque area were observed only in CS-exposed mice in the WBEC group but not in the NOEC group. Although the composition of CS in the breathing zone is not completely comparable in the two exposure systems, the CS-induced respiratory disease endpoints were largely confirmed in both systems, with a higher magnitude of severity after NO exposure. CS-accelerated atherosclerosis and other pro-atherosclerotic factors were only significant in WBEC.
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Affiliation(s)
- Ulrike Kogel
- Philip Morris International Research and Development, Philip Morris Products S.A., Neuchatel, Switzerland
| | - Ee Tsin Wong
- Philip Morris International Research Laboratories Pte. Ltd., Science Park II, Singapore
| | - Justyna Szostak
- Philip Morris International Research and Development, Philip Morris Products S.A., Neuchatel, Switzerland
| | - Wei Teck Tan
- Philip Morris International Research Laboratories Pte. Ltd., Science Park II, Singapore
| | - Francesco Lucci
- Philip Morris International Research and Development, Philip Morris Products S.A., Neuchatel, Switzerland
| | - Patrice Leroy
- Philip Morris International Research and Development, Philip Morris Products S.A., Neuchatel, Switzerland
| | - Bjoern Titz
- Philip Morris International Research and Development, Philip Morris Products S.A., Neuchatel, Switzerland
| | - Yang Xiang
- Philip Morris International Research and Development, Philip Morris Products S.A., Neuchatel, Switzerland
| | - Tiffany Low
- Philip Morris International Research Laboratories Pte. Ltd., Science Park II, Singapore
| | - Sin Kei Wong
- Philip Morris International Research Laboratories Pte. Ltd., Science Park II, Singapore
| | - Emmanuel Guedj
- Philip Morris International Research and Development, Philip Morris Products S.A., Neuchatel, Switzerland
| | - Nikolai V Ivanov
- Philip Morris International Research and Development, Philip Morris Products S.A., Neuchatel, Switzerland
| | - Walter K Schlage
- Biology Consultant, Max-Baermann-Str. 21, Bergisch Gladbach, Germany
| | - Manuel C Peitsch
- Philip Morris International Research and Development, Philip Morris Products S.A., Neuchatel, Switzerland
| | - Arkadiusz Kuczaj
- Philip Morris International Research and Development, Philip Morris Products S.A., Neuchatel, Switzerland
| | - Patrick Vanscheeuwijck
- Philip Morris International Research and Development, Philip Morris Products S.A., Neuchatel, Switzerland
| | - Julia Hoeng
- Philip Morris International Research and Development, Philip Morris Products S.A., Neuchatel, Switzerland
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12
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Talikka M, Belcastro V, Boué S, Marescotti D, Hoeng J, Peitsch MC. Applying Systems Toxicology Methods to Drug Safety. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11522-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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13
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Wang Z, Karkossa I, Großkopf H, Rolle-Kampczyk U, Hackermüller J, von Bergen M, Schubert K. Comparison of quantitation methods in proteomics to define relevant toxicological information on AhR activation of HepG2 cells by BaP. Toxicology 2020; 448:152652. [PMID: 33278487 DOI: 10.1016/j.tox.2020.152652] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/19/2020] [Accepted: 11/27/2020] [Indexed: 02/06/2023]
Abstract
The application of quantitative proteomics provides a new and promising tool for standardized toxicological research. However, choosing a suitable quantitative method still puzzles many researchers because the optimal method needs to be determined. In this study, we investigated the advantages and limitations of two of the most commonly used global quantitative proteomics methods, namely label-free quantitation (LFQ) and tandem mass tags (TMT). As a case study, we exposed hepatocytes (HepG2) to the environmental contaminant benzo[a]pyrene (BaP) using a concentration of 2 μM. Our results revealed that both methods yield a similar proteome coverage, in which for LFQ a wider range of fold changes was observed but with less significant p-values compared to TMT. We detected 37 and 47 significantly enriched pathways by LFQ and TMT, respectively, with 17 overlapping pathways. To define the minimally required effort in proteomics as a benchmark, we artificially reduced the LFQ, and TMT data sets stepwise and compared the pathway enrichment. Thereby, we found that fewer proteins are necessary for detecting significant enrichment of pathways in TMT compared to LFQ, which might be explained by the higher reproducibility of the TMT data that was observed. In summary, we showed that the TMT approach is the preferable one when investigating toxicological questions because it offers a high reproducibility and sufficient proteome coverage in a comparably short time.
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Affiliation(s)
- Zhipeng Wang
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Isabel Karkossa
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Henning Großkopf
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Ulrike Rolle-Kampczyk
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Jörg Hackermüller
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany; Institute of Biochemistry, Leipzig University, Leipzig, Germany
| | - Kristin Schubert
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany.
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14
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Liang X, Martyniuk CJ, Simmons DBD. Are we forgetting the "proteomics" in multi-omics ecotoxicology? COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 36:100751. [PMID: 33142247 DOI: 10.1016/j.cbd.2020.100751] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 07/19/2020] [Accepted: 09/23/2020] [Indexed: 12/12/2022]
Abstract
Proteomics plays a significant role in discerning the effects of chemical exposures in animal taxa. Multi-omics applications have become more pervasive in toxicology, however questions remain about whether proteomics is being utilized by the community to its full potential - are we placing too much stock in transcriptomics and other omics approaches for developing adverse outcome pathways? Proteins are more relevant than transcripts because they are direct mediators of the resulting phenotype. There is also rarely perfect stoichiometry between transcript and protein abundance and transcript abundance may not accurately predict physiologic response. Proteins direct all levels of phenotype: structural proteins dictate physical form, enzymes catalyze biochemical reactions, and proteins act as signaling proteins, antibodies, transporters, ion pumps, and transcription factors to control gene expression. Molecular initiating events (MIEs) of AOPs predominantly occur at the level of the protein (e.g. ligand-receptor binding) and proteomics can elucidate novel MIEs and mapping KEs in AOPs. This critical review highlights the need for proteomics in multi-omics studies in environmental toxicology and outlines steps required for inclusion and wider acceptance in chemical risk assessment. We also present case studies of multi-omics approaches that utilize proteomics and discuss some of the challenges and opportunities for proteomics in comparative ecotoxicology. Our intention is not to minimize the importance of other omics technologies, as each has strengths and limitations, but rather to encourage researchers to consider proteomics-based methods in multi-omics studies and AOP development.
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Affiliation(s)
- Xuefang Liang
- Inner Mongolia Key Laboratory of Environmental Pollution Control & Waste Resource Reuse, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Christopher J Martyniuk
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, UF Genetics Institute, University of Florida, Gainesville, FL, USA
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15
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Titz B, Szostak J, Sewer A, Phillips B, Nury C, Schneider T, Dijon S, Lavrynenko O, Elamin A, Guedj E, Tsin Wong E, Lebrun S, Vuillaume G, Kondylis A, Gubian S, Cano S, Leroy P, Keppler B, Ivanov NV, Vanscheeuwijck P, Martin F, Peitsch MC, Hoeng J. Multi-omics systems toxicology study of mouse lung assessing the effects of aerosols from two heat-not-burn tobacco products and cigarette smoke. Comput Struct Biotechnol J 2020; 18:1056-1073. [PMID: 32419906 PMCID: PMC7218232 DOI: 10.1016/j.csbj.2020.04.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 04/19/2020] [Indexed: 12/15/2022] Open
Abstract
Multi-omics systems toxicology study, comprising five omics data modalities. Multi-Omics Factor Analysis and multi-modality functional network interpretation. Cigarettes smoke (CS) induced complex immunoregulatory interactions across molecular layers. Aerosols from two heat-not-burn tobacco products had less impact on lungs than CS.
Cigarette smoke (CS) causes adverse health effects and, for smoker who do not quit, modified risk tobacco products (MRTPs) can be an alternative to reduce the risk of developing smoking-related diseases. Standard toxicological endpoints can lack sensitivity, with systems toxicology approaches yielding broader insights into toxicological mechanisms. In a 6-month systems toxicology study on ApoE−/− mice, we conducted an integrative multi-omics analysis to assess the effects of aerosols from the Carbon Heated Tobacco Product (CHTP) 1.2 and Tobacco Heating System (THS) 2.2—a potential and a candidate MRTP based on the heat-not-burn (HnB) principle—compared with CS at matched nicotine concentrations. Molecular exposure effects in the lungs were measured by mRNA/microRNA transcriptomics, proteomics, metabolomics, and lipidomics. Integrative data analysis included Multi-Omics Factor Analysis and multi-modality functional network interpretation. Across all five data modalities, CS exposure was associated with an increased inflammatory and oxidative stress response, and lipid/surfactant alterations. Upon HnB aerosol exposure these effects were much more limited or absent, with reversal of CS-induced effects upon cessation and switching to CHTP 1.2. Functional network analysis revealed CS-induced complex immunoregulatory interactions across the investigated molecular layers (e.g., itaconate, quinolinate, and miR-146) and highlighted the engagement of the heme–Hmox–bilirubin oxidative stress axis by CS. This work exemplifies how multi-omics approaches can be leveraged within systems toxicology studies and the generated multi-omics data set can facilitate the development of analysis methods and can yield further insights into the effects of toxicological exposures on the lung of mice.
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Key Words
- CHTP, Carbon Heated Tobacco Product
- COPD, chronic obstructive pulmonary disease
- CS, cigarette smoke
- Cigarette smoking
- Inhalation toxicology
- LC, liquid chromatography
- MOFA, Multi-Omics Factor Analysis
- MS, mass spectrometry
- Modified risk tobacco product (MRTP)
- Multi-omics
- PCSF, prize-collecting Steiner forest
- ROS, reactive oxygen species
- Systems toxicology
- THS, Tobacco Heating System
- cMRTP, candidate modified risk tobacco product
- sGCCA, sparse generalized canonical correlation analysis
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Affiliation(s)
- Bjoern Titz
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Justyna Szostak
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Alain Sewer
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Blaine Phillips
- Philip Morris International Research Laboratories Pte. Ltd., Science Park II, Singapore
| | - Catherine Nury
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Thomas Schneider
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Sophie Dijon
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Oksana Lavrynenko
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Ashraf Elamin
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Emmanuel Guedj
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Ee Tsin Wong
- Philip Morris International Research Laboratories Pte. Ltd., Science Park II, Singapore
| | - Stefan Lebrun
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Grégory Vuillaume
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Athanasios Kondylis
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Sylvain Gubian
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Stephane Cano
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Patrice Leroy
- 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
| | | | - Florian Martin
- 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
| | - Julia Hoeng
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
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16
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Martins C, Dreij K, Costa PM. The State-of-the Art of Environmental Toxicogenomics: Challenges and Perspectives of "Omics" Approaches Directed to Toxicant Mixtures. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16234718. [PMID: 31779274 PMCID: PMC6926496 DOI: 10.3390/ijerph16234718] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/23/2019] [Accepted: 11/25/2019] [Indexed: 12/17/2022]
Abstract
The last decade witnessed extraordinary advances in “omics” methods, particularly transcriptomics, proteomics and metabolomics, enabling toxicologists to integrate toxicokinetics and toxicodynamics with mechanistic insights on the mode-of-action of noxious chemicals, single or combined. The toxicology of mixtures is, nonetheless, a most challenging enterprise, especially for environmental toxicologists and ecotoxicologists, who invariably deal with chemical mixtures, many of which contain unknowns. Despite costs and demanding computations, the systems toxicology framework, of which “omics” is a major component, endeavors extracting adverse outcome pathways for complex mixtures. Still, the interplay between the multiple components of gene expression and cell metabolism tends to be overlooked. As an example, the proteome allocates DNA methyltransferases whose altered transcription or loss of function by action of chemicals can have a global impact on gene expression in the cell. On the other hand, chemical insult can produce reactive metabolites and radicals that can intercalate or bind to DNA as well as to enzymes and structural proteins, compromising their activity. These examples illustrate the importance of exploring multiple “omes” and the purpose of “omics” and multi-“omics” for building truly predictive models of hazard and risk. Here we will review the state-of-the-art of toxicogenomics highlighting successes, shortcomings and perspectives for next-generation environmental toxicologists.
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Affiliation(s)
- Carla Martins
- UCIBIO—Applied Molecular Biosciences Unit, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
- Unit of Biochemical Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Box 210, SE-171 77 Stockholm, Sweden;
- Correspondence: (C.M.); (P.M.C.); Tel.: +351-212-948-300 (ext. 11103) (P.M.C.)
| | - Kristian Dreij
- Unit of Biochemical Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Box 210, SE-171 77 Stockholm, Sweden;
| | - Pedro M. Costa
- UCIBIO—Applied Molecular Biosciences Unit, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
- Correspondence: (C.M.); (P.M.C.); Tel.: +351-212-948-300 (ext. 11103) (P.M.C.)
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17
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Wang X, Shen S, Rasam SS, Qu J. MS1 ion current-based quantitative proteomics: A promising solution for reliable analysis of large biological cohorts. MASS SPECTROMETRY REVIEWS 2019; 38:461-482. [PMID: 30920002 PMCID: PMC6849792 DOI: 10.1002/mas.21595] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 02/28/2019] [Indexed: 05/04/2023]
Abstract
The rapidly-advancing field of pharmaceutical and clinical research calls for systematic, molecular-level characterization of complex biological systems. To this end, quantitative proteomics represents a powerful tool but an optimal solution for reliable large-cohort proteomics analysis, as frequently involved in pharmaceutical/clinical investigations, is urgently needed. Large-cohort analysis remains challenging owing to the deteriorating quantitative quality and snowballing missing data and false-positive discovery of altered proteins when sample size increases. MS1 ion current-based methods, which have become an important class of label-free quantification techniques during the past decade, show considerable potential to achieve reproducible protein measurements in large cohorts with high quantitative accuracy/precision. Nonetheless, in order to fully unleash this potential, several critical prerequisites should be met. Here we provide an overview of the rationale of MS1-based strategies and then important considerations for experimental and data processing techniques, with the emphasis on (i) efficient and reproducible sample preparation and LC separation; (ii) sensitive, selective and high-resolution MS detection; iii)accurate chromatographic alignment; (iv) sensitive and selective generation of quantitative features; and (v) optimal post-feature-generation data quality control. Prominent technical developments in these aspects are discussed. Finally, we reviewed applications of MS1-based strategy in disease mechanism studies, biomarker discovery, and pharmaceutical investigations.
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Affiliation(s)
- Xue Wang
- Department of Cell Stress BiologyRoswell Park Cancer InstituteBuffaloNew York
| | - Shichen Shen
- Department of Pharmaceutical SciencesUniversity at BuffaloState University of New YorkNew YorkNew York
| | - Sailee Suryakant Rasam
- Department of Biochemistry, University at BuffaloState University of New YorkNew YorkNew York
| | - Jun Qu
- Department of Cell Stress BiologyRoswell Park Cancer InstituteBuffaloNew York
- Department of Pharmaceutical SciencesUniversity at BuffaloState University of New YorkNew YorkNew York
- Department of Biochemistry, University at BuffaloState University of New YorkNew YorkNew York
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18
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Ishikawa S, Matsumura K, Kitamura N, Takanami Y, Ito S. Multi-omics analysis: Repeated exposure of a 3D bronchial tissue culture to whole-cigarette smoke. Toxicol In Vitro 2019; 54:251-262. [PMID: 30291989 DOI: 10.1016/j.tiv.2018.10.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 08/09/2018] [Accepted: 10/01/2018] [Indexed: 02/02/2023]
Abstract
Cigarette smoke (CS) is a major risk factor in the development of chronic inflammatory lung diseases such as chronic obstructive pulmonary disease. A comprehensive investigation of the biological impacts of chronic CS exposure on lung tissue is therefore important for understanding the pathogenesis of lung disease. We used three-dimensional (3D) organotypic human bronchial tissue cultures and metabolomics, transcriptomics, and proteomics to investigate changes in biological processes affected by repeated whole-CS exposure. We found that CS perturbed central carbon metabolism in relation with oxidative stress responses. Epidermal growth factor receptor, which is involved in the early-stage pathogenesis of airway diseases, was identified as a key regulator of the perturbed processes. Proteomic analysis of proteins in the apical surface liquid of the 3D bronchial tissue cultures indicated that repeated whole-CS exposure induced alterations in the secretion of several known biomarkers of airway diseases, including mucins and matrix metalloproteinases. These findings are consistent with observations from lung disease patients. Overall, our results suggest that 3D bronchial tissue cultures can provide valuable information on tissue-specific alterations in biological processes induced by chronic exposure to CS.
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Affiliation(s)
- Shinkichi Ishikawa
- Scientific Product Assessment Center, R&D Group, Japan Tobacco Inc., 6-2 Umegaoka, Aoba-ku, Yokohama, Kanagawa 227-8512, Japan.
| | - Kazushi Matsumura
- Scientific Product Assessment Center, R&D Group, Japan Tobacco Inc., 6-2 Umegaoka, Aoba-ku, Yokohama, Kanagawa 227-8512, Japan.
| | - Nobumasa Kitamura
- Scientific Product Assessment Center, R&D Group, Japan Tobacco Inc., 6-2 Umegaoka, Aoba-ku, Yokohama, Kanagawa 227-8512, Japan.
| | - Yuichiro Takanami
- Scientific Product Assessment Center, R&D Group, Japan Tobacco Inc., 6-2 Umegaoka, Aoba-ku, Yokohama, Kanagawa 227-8512, Japan.
| | - Shigeaki Ito
- Scientific Product Assessment Center, R&D Group, Japan Tobacco Inc., 6-2 Umegaoka, Aoba-ku, Yokohama, Kanagawa 227-8512, Japan.
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19
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Titz B, Gadaleta RM, Lo Sasso G, Elamin A, Ekroos K, Ivanov NV, Peitsch MC, Hoeng J. Proteomics and Lipidomics in Inflammatory Bowel Disease Research: From Mechanistic Insights to Biomarker Identification. Int J Mol Sci 2018; 19:ijms19092775. [PMID: 30223557 PMCID: PMC6163330 DOI: 10.3390/ijms19092775] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 09/11/2018] [Accepted: 09/12/2018] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel disease (IBD) represents a group of progressive disorders characterized by recurrent chronic inflammation of the gut. Ulcerative colitis and Crohn's disease are the major manifestations of IBD. While our understanding of IBD has progressed in recent years, its etiology is far from being fully understood, resulting in suboptimal treatment options. Complementing other biological endpoints, bioanalytical "omics" methods that quantify many biomolecules simultaneously have great potential in the dissection of the complex pathogenesis of IBD. In this review, we focus on the rapidly evolving proteomics and lipidomics technologies and their broad applicability to IBD studies; these range from investigations of immune-regulatory mechanisms and biomarker discovery to studies dissecting host⁻microbiome interactions and the role of intestinal epithelial cells. Future studies can leverage recent advances, including improved analytical methodologies, additional relevant sample types, and integrative multi-omics analyses. Proteomics and lipidomics could effectively accelerate the development of novel targeted treatments and the discovery of complementary biomarkers, enabling continuous monitoring of the treatment response of individual patients; this may allow further refinement of treatment and, ultimately, facilitate a personalized medicine approach to IBD.
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Affiliation(s)
- Bjoern Titz
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
| | - Raffaella M Gadaleta
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
| | - Giuseppe Lo Sasso
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
| | - Ashraf Elamin
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
| | - Kim Ekroos
- Lipidomics Consulting Ltd., Irisviksvägen 31D, 02230 Esbo, Finland.
| | - Nikolai V Ivanov
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
| | - Manuel C Peitsch
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
| | - Julia Hoeng
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
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20
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Biological Activities, Health Benefits, and Therapeutic Properties of Avenanthramides: From Skin Protection to Prevention and Treatment of Cerebrovascular Diseases. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:6015351. [PMID: 30245775 PMCID: PMC6126071 DOI: 10.1155/2018/6015351] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 07/24/2018] [Indexed: 12/18/2022]
Abstract
Oat (Avena sativa) is a cereal known since antiquity as a useful grain with abundant nutritional and health benefits. It contains distinct molecular components with high antioxidant activity, such as tocopherols, tocotrienols, and flavanoids. In addition, it is a unique source of avenanthramides, phenolic amides containing anthranilic acid and hydroxycinnamic acid moieties, and endowed with major beneficial health properties because of their antioxidant, anti-inflammatory, and antiproliferative effects. In this review, we report on the biological activities of avenanthramides and their derivatives, including analogs produced in recombinant yeast, with a major focus on the therapeutic potential of these secondary metabolites in the treatment of aging-related human diseases. Moreover, we also present recent advances pointing to avenanthramides as interesting therapeutic candidates for the treatment of cerebral cavernous malformation (CCM) disease, a major cerebrovascular disorder affecting up to 0.5% of the human population. Finally, we highlight the potential of foodomics and redox proteomics approaches in outlining distinctive molecular pathways and redox protein modifications associated with avenanthramide bioactivities in promoting human health and contrasting the onset and progression of various pathologies. The paper is dedicated to the memory of Adelia Frison.
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Zhang Y, Zhan C, Chen G, Sun J. Label‑free quantitative proteomics and bioinformatics analyses of alcoholic liver disease in a chronic and binge mouse model. Mol Med Rep 2018; 18:2079-2087. [PMID: 29956796 PMCID: PMC6072164 DOI: 10.3892/mmr.2018.9225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 02/14/2018] [Indexed: 12/13/2022] Open
Abstract
As a significant cause of mortality and morbidity, alcoholic liver disease (ALD) has been widely investigated. However, little is known about the underlying metabolic mechanisms involved in the complicated pathological processes of ALD. The present study used label‑free quantitative proteomics and bioinformatics analyses to investigate the differentially expressed proteins (DEPs) and their functions in the livers of alcohol‑feed (AF) and control pair‑feed (PF) mice. As a result, 87 upregulated DEPs and 133 downregulated DEPs were identified in AF liver tissues compared with PF livers. Gene ontology and Kyoto encyclopedia of genes and genomes bioinformatics analyses demonstrated that the DEPs were significantly enriched in 'protein binding', 'metabolism', 'signal conduction' and 'immune response'. The expression of several core proteins including thyroid hormone receptor interactor 12 (TRIP12), NADH dehydrogenase (ubiquinone)1 α subcomplex, assembly factor 3 (NDUFAF3) and guanine monophosphate synthetase (GMPS) was validated by reverse transcription‑quantitative polymerase chain reaction (RT‑qPCR) in a larger series of samples. The RT‑qPCR results confirmed that TRIP12, NDUFAF3 and GMPS genes were significantly differentially expressed in between the AF and PF samples. These results extend our understanding of the molecular mechanisms underlying the occurrence and development of ALD. The present study indicated that the majority of DEPs serve vital roles in multiple metabolic pathways and this extends our knowledge of the molecular mechanisms involved in the occurrence and progression of ALD.
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Affiliation(s)
- Yu Zhang
- Department of Gastroenterology, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Cheng Zhan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Genwen Chen
- Department of Gastroenterology, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Jianyong Sun
- Department of Gastroenterology, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
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22
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Karri V, Ramos D, Martinez JB, Odena A, Oliveira E, Coort SL, Evelo CT, Mariman ECM, Schuhmacher M, Kumar V. Differential protein expression of hippocampal cells associated with heavy metals (Pb, As, and MeHg) neurotoxicity: Deepening into the molecular mechanism of neurodegenerative diseases. J Proteomics 2018; 187:106-125. [PMID: 30017948 DOI: 10.1016/j.jprot.2018.06.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 06/26/2018] [Accepted: 06/26/2018] [Indexed: 12/29/2022]
Abstract
Chronic exposure to heavy metals such as Pb, As, and MeHg can be associated with an increased risk of developing neurodegenerative diseases. Our in vitro bioassays results showed the potency of heavy metals in the order of Pb < As < MeHg on hippocampal cells. The main objective of this study was combining in vitro label free proteomics and systems biology approach for elucidating patterns of biological response, discovering underlying mechanisms of Pb, As, and MeHg toxicity in hippocampal cells. The omics data was refined by using different filters and normalization and multilevel analysis tools were employed to explore the data visualization. The functional and pathway visualization was performed by using Gene ontology and PathVisio tools. Using these all integrated approaches, we identified significant proteins across treatments within the mitochondrial dysfunction, oxidative stress, ubiquitin proteome dysfunction, and mRNA splicing related to neurodegenerative diseases. The systems biology analysis revealed significant alterations in proteins implicated in Parkinson's disease (PD) and Alzheimer's disease (AD). The current proteomics analysis of three metals support the insight into the proteins involved in neurodegeneration and the altered proteins can be useful for metal-specific biomarkers of exposure and its adverse effects. SIGNIFICANCE The proteomics techniques have been claimed to be more sensitive than the conventional toxicological assays, facilitating the measurement of responses to heavy metals (Pb, As, and MeHg) exposure before obvious harm has occurred demonstrating their predictive value. Also, proteomics allows for the comparison of responses between Pb, As, and MeHg metals, permitting the evaluation of potency differences hippocampal cells of the brain. Hereby, the molecular information provided by pathway and gene functional analysis can be used to develop a more thorough understanding of each metal mechanism at the protein level for different neurological adverse outcomes (e.g. Parkinson's disease, Alzheimer's diseases). Efforts are put into developing proteomics based toxicity testing methods using in vitro models for improving human risk assessment. Some of the key proteins identified can also potentially be used as biomarkers in epidemiologic studies. These heavy metal response patterns shed new light on the mechanisms of mRNA splicing, ubiquitin pathway role in neurodegeneration, and can be useful for the development of molecular biomarkers of heavy metals exposure.
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Affiliation(s)
- Venkatanaidu Karri
- Environmental Engineering Laboratory, Departament d'Enginyeria Quimica, Universitat Rovira i Virgili, Av. Països Catalans 26, 43007 Tarragona, Spain
| | - David Ramos
- Plataforma de Proteòmica, Parc Científic de Barcelona, C/Baldiri Reixac, 10-12, 08028 Barcelona, Spain
| | - Julia Bauzá Martinez
- Plataforma de Proteòmica, Parc Científic de Barcelona, C/Baldiri Reixac, 10-12, 08028 Barcelona, Spain
| | - Antonia Odena
- Plataforma de Proteòmica, Parc Científic de Barcelona, C/Baldiri Reixac, 10-12, 08028 Barcelona, Spain
| | - Eliandre Oliveira
- Unidad de Toxicologia, Parc Científic de Barcelona, C/Baldiri Reixac, 10-12, 08028 Barcelona, Spain
| | - Susan L Coort
- Department of Bioinformatics, BiGCaT, NUTRIM, Maastricht University, 6229, ER, Maastricht, the Netherlands
| | - Chris T Evelo
- Department of Bioinformatics, BiGCaT, NUTRIM, Maastricht University, 6229, ER, Maastricht, the Netherlands
| | - Edwin C M Mariman
- Department of Human Biology, NUTRIM School for Nutrition, Toxicology and Metabolism, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - Marta Schuhmacher
- Environmental Engineering Laboratory, Departament d'Enginyeria Quimica, Universitat Rovira i Virgili, Av. Països Catalans 26, 43007 Tarragona, Spain
| | - Vikas Kumar
- Environmental Engineering Laboratory, Departament d'Enginyeria Quimica, Universitat Rovira i Virgili, Av. Països Catalans 26, 43007 Tarragona, Spain; IISPV, Hospital Universitari Sant Joan de Reus, Universitat Rovira I Virgili, Reus, Spain.
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Titz B, Kogel U, Martin F, Schlage WK, Xiang Y, Nury C, Dijon S, Baumer K, Peric D, Bornand D, Dulize R, Phillips B, Leroy P, Vuillaume G, Lebrun S, Elamin A, Guedj E, Trivedi K, Ivanov NV, Vanscheeuwijck P, Peitsch MC, Hoeng J. A 90-day OECD TG 413 rat inhalation study with systems toxicology endpoints demonstrates reduced exposure effects of the aerosol from the carbon heated tobacco product version 1.2 (CHTP1.2) compared with cigarette smoke. II. Systems toxicology assessment. Food Chem Toxicol 2018; 115:284-301. [PMID: 29545142 DOI: 10.1016/j.fct.2018.02.058] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 02/27/2018] [Indexed: 12/11/2022]
Abstract
Modified risk tobacco products (MRTPs) have the potential to reduce smoking-related health risks. The Carbon Heated Tobacco Product 1.2 (CHTP1.2) is a potential MRTP that uses a pressed carbon heat source to generate an aerosol by heating tobacco. Here, we report the results from the systems toxicology arm of a 90-day rat inhalation study (OECD test guideline 413) to assess the effects of CHTP1.2 aerosol compared with cigarette smoke (CS). Transcriptomics, proteomics, and lipidomics analyses complemented the standard endpoints. In the respiratory nasal epithelium, CS induced an adaptive tissue and inflammatory response, which was much weaker after CHTP1.2 aerosol exposure, mostly limited to the highest CHTP1.2 concentration (at twice the 3R4F CS concentration: 50 vs. 23 μg nicotine/L), in female rats. In the lungs, the effects of CS exposure included inflammatory and cellular stress responses, which were absent or much lower after CHTP1.2 aerosol exposure. Outside of the respiratory tract, CS and CHTP1.2 aerosol induced effects that were previously associated with exposure to any nicotine-containing aerosol, e.g., lower lipid concentrations in serum. Overall, this systems toxicology analysis complements and confirms the results from classical toxicological endpoints and further suggests potentially reduced respiratory health risks of CHTP1.2.
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Affiliation(s)
- Bjoern Titz
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchatel, Switzerland(2)
| | - Ulrike Kogel
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchatel, Switzerland(2)
| | - Florian Martin
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchatel, Switzerland(2)
| | - Walter K Schlage
- Biology Consultant, Max-Baermann-Str. 21, 51429, Bergisch Gladbach, Germany
| | - Yang Xiang
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchatel, Switzerland(2)
| | - Catherine Nury
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchatel, Switzerland(2)
| | - Sophie Dijon
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchatel, Switzerland(2)
| | - Karine Baumer
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchatel, Switzerland(2)
| | - Dariusz Peric
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchatel, Switzerland(2)
| | - David Bornand
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchatel, Switzerland(2)
| | - Remi Dulize
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchatel, Switzerland(2)
| | - Blaine Phillips
- PMI R&D, Philip Morris International Research Laboratories Pte. Ltd., Science Park II, Singapore(2)
| | - Patrice Leroy
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchatel, Switzerland(2)
| | - Gregory Vuillaume
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchatel, Switzerland(2)
| | - Stefan Lebrun
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchatel, Switzerland(2)
| | - Ashraf Elamin
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchatel, Switzerland(2)
| | - Emmanuel Guedj
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchatel, Switzerland(2)
| | - Keyur Trivedi
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchatel, Switzerland(2)
| | - Nikolai V Ivanov
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchatel, Switzerland(2)
| | - Patrick Vanscheeuwijck
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchatel, Switzerland(2)
| | - Manuel C Peitsch
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchatel, Switzerland(2)
| | - Julia Hoeng
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchatel, Switzerland(2).
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Horii I. The principle of safety evaluation in medicinal drug - how can toxicology contribute to drug discovery and development as a multidisciplinary science? J Toxicol Sci 2017; 41:SP49-SP67. [PMID: 28250284 DOI: 10.2131/jts.41.sp49] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Pharmaceutical (drug) safety assessment covers a diverse science-field in the drug discovery and development including the post-approval and post-marketing phases in order to evaluate safety and risk management. The principle in toxicological science is to be placed on both of pure and applied sciences that are derived from past/present scientific knowledge and coming new science and technology. In general, adverse drug reactions are presented as "biological responses to foreign substances." This is the basic concept of thinking about the manifestation of adverse drug reactions. Whether or not toxic expressions are extensions of the pharmacological effect, adverse drug reactions as seen from molecular targets are captured in the category of "on-target" or "off-target", and are normally expressed as a biological defense reaction. Accordingly, reactions induced by pharmaceuticals can be broadly said to be defensive reactions. Recent molecular biological conception is in line with the new, remarkable scientific and technological developments in the medical and pharmaceutical areas, and the viewpoints in the field of toxicology have shown that they are approaching toward the same direction as well. This paper refers to the basic concept of pharmaceutical toxicology, the differences for safety assessment in each stage of drug discovery and development, regulatory submission, and the concept of scientific considerations for risk assessment and management from the viewpoint of "how can multidisciplinary toxicology contribute to innovative drug discovery and development?" And also realistic translational research from preclinical to clinical application is required to have a significant risk management in post market by utilizing whole scientific data derived from basic and applied scientific research works. In addition, the significance for employing the systems toxicology based on AOP (Adverse Outcome Pathway) analysis is introduced, and coming challenges on precision medicine are to be addressed for the new aspect of efficacy and safety evaluation.
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Affiliation(s)
- Ikuo Horii
- Global Drug Safety Research & Development, Pfizer
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25
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Guo DD, Hu B, Tang HY, Sun YY, Liu B, Tian QM, Bi HS. Proteomic Profiling Analysis Reveals a Link between Experimental Autoimmune Uveitis and Complement Activation in Rats. Scand J Immunol 2017; 85:331-342. [DOI: 10.1111/sji.12539] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 02/08/2017] [Indexed: 01/01/2023]
Affiliation(s)
- D. D. Guo
- Shandong Provincial Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Therapy of Ocular Diseases; Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Therapy of Ocular Diseases in Universities of Shandong; Eye Institute of Shandong University of Traditional Chinese Medicine; Jinan China
| | - B. Hu
- Affiliated Eye Hospital of Shandong University of Traditional Chinese Medicine; Jinan China
| | - H. Y. Tang
- The Second Clinical Medical College; Shandong University of Traditional Chinese Medicine; Jinan China
| | - Y. Y. Sun
- The Second Clinical Medical College; Shandong University of Traditional Chinese Medicine; Jinan China
| | - B. Liu
- The Second Clinical Medical College; Shandong University of Traditional Chinese Medicine; Jinan China
| | - Q. M. Tian
- Affiliated Eye Hospital of Shandong University of Traditional Chinese Medicine; Jinan China
| | - H. S. Bi
- Shandong Provincial Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Therapy of Ocular Diseases; Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Therapy of Ocular Diseases in Universities of Shandong; Eye Institute of Shandong University of Traditional Chinese Medicine; Jinan China
- Affiliated Eye Hospital of Shandong University of Traditional Chinese Medicine; Jinan China
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26
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Kreutz D, Bileck A, Plessl K, Wolrab D, Groessl M, Keppler BK, Meier SM, Gerner C. Response Profiling Using Shotgun Proteomics Enables Global Metallodrug Mechanisms of Action To Be Established. Chemistry 2017; 23:1881-1890. [PMID: 28071820 DOI: 10.1002/chem.201604516] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Indexed: 12/23/2022]
Abstract
Response profiling using shotgun proteomics for establishing global metallodrug mechanisms of action in two colon carcinoma cell lines, HCT116 and SW480, has been applied and evaluated with the clinically approved arsenic trioxide. Surprisingly, the complete established mechanism of action of arsenic trioxide was observed by protein regulations in SW480, but not HCT116 cells. Comparing the basal protein expression in the two cell lines revealed an 80 % convergence of protein identification, but with significant expression differences, which in turn seem to affect the extent of protein regulation. A clear-cut redox response was observed in SW480 cells upon treatment with arsenic, but hardly in HCT116 cells. Response profiling was then used to investigate four anti-cancer metallodrugs (KP46, KP772, KP1339 and KP1537). Proteome alterations were mapped to selected functional groups, including DNA repair, endocytosis, protection from oxidative stress, protection from endoplasmatic reticulum (ER) stress, cell adhesion and mitochondrial function. The present data suggest that knowledge of the mechanism of action of anti-cancer metallodrugs and improved patient stratification strategies are imperative for the design of clinical studies.
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Affiliation(s)
- Dominique Kreutz
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Strasse 38, 1090, Vienna, Austria
| | - Andrea Bileck
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Strasse 38, 1090, Vienna, Austria
| | - Kerstin Plessl
- Department of Obstetrics and Fetal-Maternal Medicine, Reproductive Biology Unit, Medical University of Vienna, Waehringer Guertel 18-20, 5Q, 1090, Vienna, Austria
| | - Denise Wolrab
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Strasse 38, 1090, Vienna, Austria
| | - Michael Groessl
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Strasse 38, 1090, Vienna, Austria
| | - Bernhard K Keppler
- Department of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Strasse 42, 1090, Vienna, Austria
| | - Samuel M Meier
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Strasse 38, 1090, Vienna, Austria
| | - Christopher Gerner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Strasse 38, 1090, Vienna, Austria
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Oviedo A, Lebrun S, Kogel U, Ho J, Tan WT, Titz B, Leroy P, Vuillaume G, Bera M, Martin F, Rodrigo G, Esposito M, Dempsey R, Ivanov NV, Hoeng J, Peitsch MC, Vanscheeuwijck P. Evaluation of the Tobacco Heating System 2.2. Part 6: 90-day OECD 413 rat inhalation study with systems toxicology endpoints demonstrates reduced exposure effects of a mentholated version compared with mentholated and non-mentholated cigarette smoke. Regul Toxicol Pharmacol 2016; 81 Suppl 2:S93-S122. [DOI: 10.1016/j.yrtph.2016.11.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 10/28/2016] [Accepted: 11/01/2016] [Indexed: 10/20/2022]
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28
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Evaluation of the Tobacco Heating System 2.2. Part 7: Systems toxicological assessment of a mentholated version revealed reduced cellular and molecular exposure effects compared with mentholated and non-mentholated cigarette smoke. Regul Toxicol Pharmacol 2016; 81 Suppl 2:S123-S138. [DOI: 10.1016/j.yrtph.2016.11.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 10/31/2016] [Accepted: 11/01/2016] [Indexed: 12/29/2022]
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29
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Nath Roy D, Goswami R, Pal A. Nanomaterial and toxicity: what can proteomics tell us about the nanotoxicology? Xenobiotica 2016; 47:632-643. [PMID: 27414072 DOI: 10.1080/00498254.2016.1205762] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
1. In the last few years, a substantial scientific work is focused to identify the potential toxicity of nanomaterials by studying the cellular pathways under in vitro and in vivo conditions. Owing to high surface area to volume ratio nanoparticles (NPs) can pass through cell membranes which might be responsible for creating adverse interactions in biological systems. Simultaneously, researchers are also interested to assess the fate of NP inside the living system, which may lead to altered protein expression as well as protein corona formation. 2. According to published reports, NP-mediated toxicity involves altered cellular system including cell morphology, cell differentiation, cell metabolism, cell mobility, cellular immunity, which is derived from the side effects of nanoformulation and leading to apoptosis and necrosis. These results indicate the existence of potential toxic effect of these particles to human health. 3. The advent of proteomics with sophisticated technical improvement coupled with advanced bioinformatics has led to identify altered proteins due to nanomaterial exposure that could provide a new avenue to biomarker discovery. 4. This review aims to provide the current status of safe production and use of nanomaterials.
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Affiliation(s)
- Dijendra Nath Roy
- a Department of Bioengineering , National Institute of Technology , Agartala , Tripura , India
| | - Ritobrata Goswami
- b Division of Biological & Life Sciences , School of Arts & Sciences, Ahmedabad University , Ahmedabad , Gujarat , India , and
| | - Ayantika Pal
- c Department of Human Physiology , Tripura University , Suryamaninagar , Tripura , India
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30
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Elamin A, Titz B, Dijon S, Merg C, Geertz M, Schneider T, Martin F, Schlage WK, Frentzel S, Talamo F, Phillips B, Veljkovic E, Ivanov NV, Vanscheeuwijck P, Peitsch MC, Hoeng J. Quantitative proteomics analysis using 2D-PAGE to investigate the effects of cigarette smoke and aerosol of a prototypic modified risk tobacco product on the lung proteome in C57BL/6 mice. J Proteomics 2016; 145:237-245. [PMID: 27268958 DOI: 10.1016/j.jprot.2016.05.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 05/27/2016] [Accepted: 05/28/2016] [Indexed: 12/11/2022]
Abstract
UNLABELLED Smoking is associated with several serious diseases, such as lung cancer and chronic obstructive pulmonary disease (COPD). Within our systems toxicology framework, we are assessing whether potential modified risk tobacco products (MRTP) can reduce smoking-related health risks compared to conventional cigarettes. In this article, we evaluated to what extent 2D-PAGE/MALDI MS/MS (2D-PAGE) can complement the iTRAQ LC-MS/MS results from a previously reported mouse inhalation study, in which we assessed a prototypic MRTP (pMRTP). Selected differentially expressed proteins identified by both LC-MS/MS and 2D-PAGE approaches were further verified using reverse-phase protein microarrays. LC-MS/MS captured the effects of cigarette smoke (CS) on the lung proteome more comprehensively than 2D-PAGE. However, an integrated analysis of both proteomics data sets showed that 2D-PAGE data complement the LC-MS/MS results by supporting the overall trend of lower effects of pMRTP aerosol than CS on the lung proteome. Biological effects of CS exposure supported by both methods included increases in immune-related, surfactant metabolism, proteasome, and actin cytoskeleton protein clusters. Overall, while 2D-PAGE has its value, especially as a complementary method for the analysis of effects on intact proteins, LC-MS/MS approaches will likely be the method of choice for proteome analysis in systems toxicology investigations. SIGNIFICANCE Quantitative proteomics is anticipated to play a growing role within systems toxicology assessment frameworks in the future. To further understand how different proteomics technologies can contribute to toxicity assessment, we conducted a quantitative proteomics analysis using 2D-PAGE and isobaric tag-based LC-MS/MS approaches and compared the results produced from the 2 approaches. Using a prototypic modified risk tobacco product (pMRTP) as our test item, we show compared with cigarette smoke, how 2D-PAGE results can complement and support LC-MS/MS data, demonstrating the much lower effects of pMRTP aerosol than cigarette smoke on the mouse lung proteome. The combined analysis of 2D-PAGE and LC-MS/MS data identified an effect of cigarette smoke on the proteasome and actin cytoskeleton in the lung.
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Affiliation(s)
- Ashraf Elamin
- Philip Morris Research and Development, Philip Morris Products SA (part of Philip Morris International group of companies), Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Bjoern Titz
- Philip Morris Research and Development, Philip Morris Products SA (part of Philip Morris International group of companies), Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Sophie Dijon
- Philip Morris Research and Development, Philip Morris Products SA (part of Philip Morris International group of companies), Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Celine Merg
- Philip Morris Research and Development, Philip Morris Products SA (part of Philip Morris International group of companies), Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Marcel Geertz
- Philip Morris Research and Development, Philip Morris Products SA (part of Philip Morris International group of companies), Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland; Bayer Technology Services GmbH, 51368 Leverkusen, Germany
| | - Thomas Schneider
- Philip Morris Research and Development, Philip Morris Products SA (part of Philip Morris International group of companies), Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Florian Martin
- Philip Morris Research and Development, Philip Morris Products SA (part of Philip Morris International group of companies), Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Walter K Schlage
- Biology Consultant, Max-Baermann-Str. 21, 51429, Bergisch Gladbach, Germany
| | - Stefan Frentzel
- Philip Morris Research and Development, Philip Morris Products SA (part of Philip Morris International group of companies), Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Fabio Talamo
- Philip Morris Research and Development, Philip Morris Products SA (part of Philip Morris International group of companies), Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Blaine Phillips
- Philip Morris International Research Laboratories (part of Philip Morris International group of companies), 50 Science Park Road, 117406, Singapore
| | - Emilija Veljkovic
- Philip Morris International Research Laboratories (part of Philip Morris International group of companies), 50 Science Park Road, 117406, Singapore
| | - Nikolai V Ivanov
- Philip Morris Research and Development, Philip Morris Products SA (part of Philip Morris International group of companies), Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Patrick Vanscheeuwijck
- Philip Morris Research and Development, Philip Morris Products SA (part of Philip Morris International group of companies), Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Manuel C Peitsch
- Philip Morris Research and Development, Philip Morris Products SA (part of Philip Morris International group of companies), Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland
| | - Julia Hoeng
- Philip Morris Research and Development, Philip Morris Products SA (part of Philip Morris International group of companies), Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland.
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Fernando RN, Chaudhari U, Escher SE, Hengstler JG, Hescheler J, Jennings P, Keun HC, Kleinjans JCS, Kolde R, Kollipara L, Kopp-Schneider A, Limonciel A, Nemade H, Nguemo F, Peterson H, Prieto P, Rodrigues RM, Sachinidis A, Schäfer C, Sickmann A, Spitkovsky D, Stöber R, van Breda SGJ, van de Water B, Vivier M, Zahedi RP, Vinken M, Rogiers V. "Watching the Detectives" report of the general assembly of the EU project DETECTIVE Brussels, 24-25 November 2015. Arch Toxicol 2016; 90:1529-1539. [PMID: 27129694 DOI: 10.1007/s00204-016-1719-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 04/20/2016] [Indexed: 11/25/2022]
Abstract
SEURAT-1 is a joint research initiative between the European Commission and Cosmetics Europe aiming to develop in vitro- and in silico-based methods to replace the in vivo repeated dose systemic toxicity test used for the assessment of human safety. As one of the building blocks of SEURAT-1, the DETECTIVE project focused on a key element on which in vitro toxicity testing relies: the development of robust and reliable, sensitive and specific in vitro biomarkers and surrogate endpoints that can be used for safety assessments of chronically acting toxicants, relevant for humans. The work conducted by the DETECTIVE consortium partners has established a screening pipeline of functional and "-omics" technologies, including high-content and high-throughput screening platforms, to develop and investigate human biomarkers for repeated dose toxicity in cellular in vitro models. Identification and statistical selection of highly predictive biomarkers in a pathway- and evidence-based approach constitute a major step in an integrated approach towards the replacement of animal testing in human safety assessment. To discuss the final outcomes and achievements of the consortium, a meeting was organized in Brussels. This meeting brought together data-producing and supporting consortium partners. The presentations focused on the current state of ongoing and concluding projects and the strategies employed to identify new relevant biomarkers of toxicity. The outcomes and deliverables, including the dissemination of results in data-rich "-omics" databases, were discussed as were the future perspectives of the work completed under the DETECTIVE project. Although some projects were still in progress and required continued data analysis, this report summarizes the presentations, discussions and the outcomes of the project.
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Affiliation(s)
- Ruani N Fernando
- Department of In Vitro Toxicology and Dermato-Cosmetology, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Umesh Chaudhari
- Centre of Physiology and Pathophysiology, Institute of Neurophysiology and Centre for Molecular Medicine Cologne (CMMC), 50931 Cologne, Germany
| | - Sylvia E Escher
- Fraunhofer Institute for Toxicology and Experimental Medicine, Nikolai-Fuchs-Str. 1, 30625 Hannover, Germany
| | - Jan G Hengstler
- Leibniz Research Centre for Working Environment and Human Factors (IFADO), Technical University of Dortmund, 44139, Dortmund, Germany
| | - Jürgen Hescheler
- Centre of Physiology and Pathophysiology, Institute of Neurophysiology and Centre for Molecular Medicine Cologne (CMMC), 50931 Cologne, Germany
| | - Paul Jennings
- The Division of Physiology, Department of Physiology and Medical Physics, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Hector C Keun
- Biomolecular Medicine, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Jos C S Kleinjans
- Department of Toxicogenomics, Maastricht University , Universiteitssingel 40, 6229 ER Maastricht, The Netherlands
| | - Raivo Kolde
- QURE Ltd. Ülikooli 6a, 51003, Tartu, Estonia
| | - Laxmikanth Kollipara
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, 44227, Dortmund, Germany
| | - Annette Kopp-Schneider
- Division of Biostatistics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
| | - Alice Limonciel
- The Division of Physiology, Department of Physiology and Medical Physics, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Harshal Nemade
- Centre of Physiology and Pathophysiology, Institute of Neurophysiology and Centre for Molecular Medicine Cologne (CMMC), 50931 Cologne, Germany
| | - Filomain Nguemo
- Centre of Physiology and Pathophysiology, Institute of Neurophysiology and Centre for Molecular Medicine Cologne (CMMC), 50931 Cologne, Germany
| | | | - Pilar Prieto
- EURL ECVAM (The European Union Reference Laboratory for Alternatives to Animal Testing), Systems Toxicology Unit, Institute for Health and Consumer Protection, European Commission, Joint Research Centre, Ispra, Italy
| | - Robim M Rodrigues
- Department of In Vitro Toxicology and Dermato-Cosmetology, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Agapios Sachinidis
- Centre of Physiology and Pathophysiology, Institute of Neurophysiology and Centre for Molecular Medicine Cologne (CMMC), 50931 Cologne, Germany
| | - Christoph Schäfer
- Centre of Physiology and Pathophysiology, Institute of Neurophysiology and Centre for Molecular Medicine Cologne (CMMC), 50931 Cologne, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, 44227, Dortmund, Germany
- Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom
- Medizinische Fakultät, Medizinische Proteom-Center (MPC), Ruhr-Universität Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Dimitry Spitkovsky
- Centre of Physiology and Pathophysiology, Institute of Neurophysiology and Centre for Molecular Medicine Cologne (CMMC), 50931 Cologne, Germany
| | - Regina Stöber
- Leibniz Research Centre for Working Environment and Human Factors (IFADO), Technical University of Dortmund, 44139, Dortmund, Germany
| | - Simone G J van Breda
- Department of Toxicogenomics, Maastricht University , Universiteitssingel 40, 6229 ER Maastricht, The Netherlands
| | - Bob van de Water
- Division of Toxicology, Leiden/Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
| | - Manon Vivier
- Department of In Vitro Toxicology and Dermato-Cosmetology, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, 44227, Dortmund, Germany
| | - Mathieu Vinken
- Department of In Vitro Toxicology and Dermato-Cosmetology, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Vera Rogiers
- Department of In Vitro Toxicology and Dermato-Cosmetology, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium
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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] [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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33
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Thomas S, Hao L, Ricke WA, Li L. Biomarker discovery in mass spectrometry-based urinary proteomics. Proteomics Clin Appl 2016; 10:358-70. [PMID: 26703953 DOI: 10.1002/prca.201500102] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Revised: 12/05/2015] [Accepted: 12/21/2015] [Indexed: 01/03/2023]
Abstract
Urinary proteomics has become one of the most attractive topics in disease biomarker discovery. MS-based proteomic analysis has advanced continuously and emerged as a prominent tool in the field of clinical bioanalysis. However, only few protein biomarkers have made their way to validation and clinical practice. Biomarker discovery is challenged by many clinical and analytical factors including, but not limited to, the complexity of urine and the wide dynamic range of endogenous proteins in the sample. This article highlights promising technologies and strategies in the MS-based biomarker discovery process, including study design, sample preparation, protein quantification, instrumental platforms, and bioinformatics. Different proteomics approaches are discussed, and progresses in maximizing urinary proteome coverage and standardization are emphasized in this review. MS-based urinary proteomics has great potential in the development of noninvasive diagnostic assays in the future, which will require collaborative efforts between analytical scientists, systems biologists, and clinicians.
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Affiliation(s)
- Samuel Thomas
- Molecular and Environmental Toxicology Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Ling Hao
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA
| | - William A Ricke
- Molecular and Environmental Toxicology Center, University of Wisconsin-Madison, Madison, WI, USA.,Department of Urology, University of Wisconsin-Madison, Madison, WI, USA
| | - Lingjun Li
- Molecular and Environmental Toxicology Center, University of Wisconsin-Madison, Madison, WI, USA.,School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA.,Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
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34
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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] [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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Oldrati V, Arrell M, Violette A, Perret F, Sprüngli X, Wolfender JL, Stöcklin R. Advances in venomics. MOLECULAR BIOSYSTEMS 2016; 12:3530-3543. [DOI: 10.1039/c6mb00516k] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The term “venomics” was coined to describe the global study of venom and venom glands, targeting comprehensive characterization of the whole toxin profile of a venomous animal by means of proteomics, transcriptomics, genomics and bioinformatics studies.
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Affiliation(s)
- Vera Oldrati
- Atheris SA
- Geneva
- Switzerland
- School of Pharmaceutical Sciences
- EPGL
| | | | - Aude Violette
- Alphabiotoxine Laboratory Sprl
- Montroeul-au-Bois B-7911
- Belgium
| | | | | | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences
- EPGL
- University of Geneva
- University of Lausanne
- CMU
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36
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Wallace MAG, Kormos TM, Pleil JD. Blood-borne biomarkers and bioindicators for linking exposure to health effects in environmental health science. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART B, CRITICAL REVIEWS 2016; 19:380-409. [PMID: 27759495 PMCID: PMC6147038 DOI: 10.1080/10937404.2016.1215772] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Environmental health science aims to link environmental pollution sources to adverse health outcomes to develop effective exposure intervention strategies that reduce long-term disease risks. Over the past few decades, the public health community recognized that health risk is driven by interaction between the human genome and external environment. Now that the human genetic code has been sequenced, establishing this "G × E" (gene-environment) interaction requires a similar effort to decode the human exposome, which is the accumulation of an individual's environmental exposures and metabolic responses throughout the person's lifetime. The exposome is composed of endogenous and exogenous chemicals, many of which are measurable as biomarkers in blood, breath, and urine. Exposure to pollutants is assessed by analyzing biofluids for the pollutant itself or its metabolic products. New methods are being developed to use a subset of biomarkers, termed bioindicators, to demonstrate biological changes indicative of future adverse health effects. Typically, environmental biomarkers are assessed using noninvasive (excreted) media, such as breath and urine. Blood is often avoided for biomonitoring due to practical reasons such as medical personnel, infectious waste, or clinical setting, despite the fact that blood represents the central compartment that interacts with every living cell and is the most relevant biofluid for certain applications and analyses. The aims of this study were to (1) review the current use of blood samples in environmental health research, (2) briefly contrast blood with other biological media, and (3) propose additional applications for blood analysis in human exposure research.
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Affiliation(s)
- M Ariel Geer Wallace
- a Exposure Methods and Measurement Division, National Exposure Research Laboratory, Office of Research and Development , U.S. Environmental Protection Agency , Research Triangle Park , North Carolina , USA
| | | | - Joachim D Pleil
- a Exposure Methods and Measurement Division, National Exposure Research Laboratory, Office of Research and Development , U.S. Environmental Protection Agency , Research Triangle Park , North Carolina , USA
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37
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Golizeh M, LeBlanc A, Sleno L. Identification of Acetaminophen Adducts of Rat Liver Microsomal Proteins using 2D-LC-MS/MS. Chem Res Toxicol 2015; 28:2142-50. [DOI: 10.1021/acs.chemrestox.5b00317] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Makan Golizeh
- Chemistry
Department/Pharmaqam, Université du Québec à Montréal (UQÀM), Montréal, Québec H2X 2J6, Canada
| | - André LeBlanc
- Chemistry
Department/Pharmaqam, Université du Québec à Montréal (UQÀM), Montréal, Québec H2X 2J6, Canada
| | - Lekha Sleno
- Chemistry
Department/Pharmaqam, Université du Québec à Montréal (UQÀM), Montréal, Québec H2X 2J6, Canada
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38
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Li YH, Tai WCS, Xue JY, Wong WY, Lu C, Ruan JQ, Li N, Wan TF, Chan WY, Hsiao WLW, Lin G. Proteomic Study of Pyrrolizidine Alkaloid-Induced Hepatic Sinusoidal Obstruction Syndrome in Rats. Chem Res Toxicol 2015; 28:1715-27. [DOI: 10.1021/acs.chemrestox.5b00113] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yan-Hong Li
- School
of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - William Chi-Shing Tai
- Centre
of Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
- Institute of Integrated Bioinfomedicine & Translational Science, Hong Kong Baptist University Shenzhen Research Institute and Continuing Education, Shenzhen, China
| | - Jun-Yi Xue
- School
of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Wing-Yan Wong
- Centre
of Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Cheng Lu
- Centre
of Cancer and Inflammation Research, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
- Institute
of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jian-Qing Ruan
- School
of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Na Li
- School
of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Tai-Fung Wan
- School
of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Wood-Yee Chan
- School
of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Wen-Luan Wendy Hsiao
- State
Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Macau, China
| | - Ge Lin
- School
of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
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da Costa JP, Carvalhais V, Ferreira R, Amado F, Vilanova M, Cerca N, Vitorino R. Proteome signatures—how are they obtained and what do they teach us? Appl Microbiol Biotechnol 2015. [DOI: 10.1007/s00253-015-6795-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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40
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Butt AQ, McArdle A, Gibson DS, FitzGerald O, Pennington SR. Psoriatic Arthritis Under a Proteomic Spotlight: Application of Novel Technologies to Advance Diagnosis and Management. Curr Rheumatol Rep 2015; 17:35. [DOI: 10.1007/s11926-015-0509-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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41
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Lin L, Lin H, Zhang M, Dong X, Yin X, Qu C, Ni J. Types, principle, and characteristics of tandem high-resolution mass spectrometry and its applications. RSC Adv 2015. [DOI: 10.1039/c5ra22856e] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We review the principle and functional characteristics of different types or models for THRMS and provide a brief description of its applications in medical research, food safety, and environmental protection fields.
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Affiliation(s)
- Longfei Lin
- School of Chinese Materia Medica
- Beijing University of Chinese Medicine
- Beijing
- China
| | - Hongmei Lin
- School of Chinese Materia Medica
- Beijing University of Chinese Medicine
- Beijing
- China
| | - Miao Zhang
- School of Chinese Materia Medica
- Beijing University of Chinese Medicine
- Beijing
- China
| | - Xiaoxv Dong
- School of Chinese Materia Medica
- Beijing University of Chinese Medicine
- Beijing
- China
| | - Xingbin Yin
- School of Chinese Materia Medica
- Beijing University of Chinese Medicine
- Beijing
- China
| | - Changhai Qu
- Modern Research Center for TCM
- Beijing University of Chinese Medicine
- Beijing
- China
| | - Jian Ni
- School of Chinese Materia Medica
- Beijing University of Chinese Medicine
- Beijing
- China
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