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Chen P, Li Y, Long Q, Zuo T, Zhang Z, Guo J, Xu D, Li K, Liu S, Li S, Yin J, Chang L, Kukic P, Liddell M, Tulum L, Carmichael P, Peng S, Li J, Zhang Q, Xu P. The phosphoproteome is a first responder in tiered cellular adaptation to chemical stress followed by proteomics and transcriptomics alteration. Chemosphere 2023; 344:140329. [PMID: 37783352 DOI: 10.1016/j.chemosphere.2023.140329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 09/20/2023] [Accepted: 09/28/2023] [Indexed: 10/04/2023]
Abstract
Next-generation risk assessment (NGRA) for environmental chemicals involves a weight of evidence (WoE) framework integrating a suite of new approach methodologies (NAMs) based on points of departure (PoD) obtained from in vitro assays. Among existing NAMs, the omic-based technologies are of particular importance based on the premise that any apical endpoint change indicative of impaired health must be underpinned by some alterations at the omics level, such as transcriptome, proteome, metabolome, epigenome and genome. Transcriptomic assay plays a leading role in providing relatively conservative PoDs compared with apical endpoints. However, it is unclear whether and how parameters measured with other omics techniques predict the cellular response to chemical perturbations, especially at exposure levels below the transcriptomically defined PoD. Multi-omics coverage may provide additional sensitive or confirmative biomarkers to complement and reduce the uncertainty in safety decisions made using targeted and transcriptomics assays. In the present study, we conducted multi-omics studies of transcriptomics, proteomics and phosphoproteomics on two prototype compounds, coumarin and 2,4-dichlorophenoxyacetic acid (2,4-D), with multiple chemical concentrations and time points, to understand the sensitivity of the three omics techniques in response to chemically-induced changes in HepG2. We demonstrated that, phosphoproteomics alterations occur not only earlier in time, but also more sensitive to lower concentrations than proteomics and transcriptomics when the HepG2 cells were exposed to various chemical treatments. The phosphoproteomics changes appear to approach maximum when the transcriptomics alterations begin to initiate. Therefore, it is proximal to the very early effects induced by chemical exposure. We concluded that phosphoproteomics can be utilized to provide a more complete coverage of chemical-induced cellular alteration and supplement transcriptomics-based health safety decision making.
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Affiliation(s)
- Peiru Chen
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China; Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, 071002, China
| | - Yuan Li
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China; Department of Biomedicine, Medical College, Guizhou University, Guiyang, 550025, China; Guizhou Provincial People's Hospital, Affiliated Hospital of Guizhou University, Guiyang, 550002, China
| | - Qi Long
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China; School of Basic Medicine, Anhui Medical University, Hefei, 230032, China
| | - Tao Zuo
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China
| | - Zhenpeng Zhang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China
| | - Jiabin Guo
- Evaluation and Research Centre for Toxicology, Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Danyang Xu
- Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Kaixuan Li
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China; Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, 071002, China
| | - Shu Liu
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China
| | - Suzhen Li
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China; School of Basic Medicine, Anhui Medical University, Hefei, 230032, China
| | - Jian Yin
- Evaluation and Research Centre for Toxicology, Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Lei Chang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China
| | - Predrag Kukic
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Mark Liddell
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Liz Tulum
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Paul Carmichael
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Shuangqing Peng
- Evaluation and Research Centre for Toxicology, Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Jin Li
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK.
| | - Qiang Zhang
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, USA, GA, 30322.
| | - Ping Xu
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China; Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, 071002, China; Department of Biomedicine, Medical College, Guizhou University, Guiyang, 550025, China; School of Basic Medicine, Anhui Medical University, Hefei, 230032, China; Program of Environmental Toxicology, School of Public Health, China Medical University, Shenyang, 110122, China.
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Li Y, Zhang Z, Jiang S, Xu F, Tulum L, Li K, Liu S, Li S, Chang L, Liddell M, Tu F, Gu X, Carmichael PL, White A, Peng S, Zhang Q, Li J, Zuo T, Kukic P, Xu P. Using transcriptomics, proteomics and phosphoproteomics as new approach methodology (NAM) to define biological responses for chemical safety assessment. Chemosphere 2023; 313:137359. [PMID: 36427571 DOI: 10.1016/j.chemosphere.2022.137359] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/19/2022] [Accepted: 11/21/2022] [Indexed: 06/16/2023]
Abstract
Omic-based technologies are of particular interest and importance for hazard identification and health risk characterization of chemicals. Their application in the new approach methodologies (NAMs) anchored on cellular toxicity pathways is based on the premise that any apical health endpoint change must be underpinned by some alterations at the omic levels. In the present study we examined the cellular responses to two chemicals, caffeine and coumarin, by generating and integrating multi-omic data from multi-dose and multi-time point transcriptomic, proteomic and phosphoproteomic experiments. We showed that the methodology presented here was able to capture the complete chain of events from the first chemical-induced changes at the phosphoproteome level, to changes in gene expression, and lastly to changes in protein abundance, each with vastly different points of departure (PODs). In HepG2 cells we found that the metabolism of lipids and general cellular stress response to be the dominant biological processes in response to caffeine and coumarin exposure, respectively. The phosphoproteomic changes were detected early in time, at very low doses and provided a fast, adaptive cellular response to chemical exposure with 7-37-fold lower points of departure comparing to the transcriptomics. Changes in protein abundance were found much less frequently than transcriptomic changes. While challenges remain, our study provides strong and novel evidence supporting the notion that these three omic technologies can be used in an integrated manner to facilitate a more complete understanding of pathway perturbations and POD determinations for risk assessment of chemical exposures.
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Affiliation(s)
- Yuan Li
- Department of Biomedicine, Medical College, Guizhou University, Guiyang, 550025, China; State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China
| | - Zhenpeng Zhang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China
| | - Songhao Jiang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China; Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, 071002, China
| | - Feng Xu
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China
| | - Liz Tulum
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Kaixuan Li
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China
| | - Shu Liu
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China
| | - Suzhen Li
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China
| | - Lei Chang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China
| | - Mark Liddell
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Fengjuan Tu
- Unilever Research & Development Centre Shanghai, Shanghai, 200335, China
| | - Xuelan Gu
- Unilever Research & Development Centre Shanghai, Shanghai, 200335, China
| | - Paul Lawford Carmichael
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Andrew White
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Shuangqing Peng
- Evaluation and Research Centre for Toxicology, Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing, 100071, China
| | - Qiang Zhang
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA
| | - Jin Li
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK
| | - Tao Zuo
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China.
| | - Predrag Kukic
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK.
| | - Ping Xu
- Department of Biomedicine, Medical College, Guizhou University, Guiyang, 550025, China; State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, Beijing, 102206, China; Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, 071002, China; Program of Environmental Toxicology, School of Public Health, China Medical University, Shenyang, 110122, China.
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Tulum L, Deag Z, Brown M, Furniss A, Meech L, Lalljie A, Cochrane S. Airborne protein concentration: a key metric for type 1 allergy risk assessment-in home measurement challenges and considerations. Clin Transl Allergy 2018; 8:10. [PMID: 29599965 PMCID: PMC5868064 DOI: 10.1186/s13601-018-0196-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 02/28/2018] [Indexed: 11/15/2022] Open
Abstract
Background Exposure to airborne proteins can be associated with the development of immediate, IgE-mediated respiratory allergies, with genetic, epigenetic and environmental factors also playing a role in determining the likelihood that sensitisation will be induced. The main objective of this study was to determine whether airborne concentrations of selected common aeroallergens could be quantified in the air of homes using easily deployable, commercially available equipment and analytical methods, at low levels relevant to risk assessment of the potential to develop respiratory allergies. Additionally, air and dust sampling were compared and the influence of factors such as different filter types on allergen quantification explored. Methods Low volume air sampling pumps and DUSTREAM® dust samplers were used to sample 20 homes and allergen levels were quantified using a MARIA® immunoassay. Results It proved possible to detect a range of common aeroallergens in the home with sufficient sensitivity to quantify airborne concentrations in ranges relevant to risk assessment (Limits of Detection of 0.005–0.03 ng/m3). The methodology discriminates between homes related to pet ownership and there were clear advantages to sampling air over dust which are described in this paper. Furthermore, in an adsorption–extraction study, PTFE (polytetrafluoroethylene) filters gave higher and more consistent recovery values than glass fibre (grade A) filters for the range of aeroallergens studied. Conclusions Very low airborne concentrations of allergenic proteins in home settings can be successfully quantified using commercially available pumps and immunoassays. Considering the greater relevance of air sampling to human exposure of the respiratory tract and its other advantages, wider use of standardised, sensitive techniques to measure low airborne protein concentrations and how they influence development of allergic sensitisation and symptoms could accelerate our understanding of human dose–response relationships and refine our knowledge of thresholds of allergic sensitisation and elicitation via the respiratory tract.
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Affiliation(s)
- Liz Tulum
- SEAC Unilever Colworth, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ UK
| | - Zoë Deag
- SEAC Unilever Colworth, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ UK
| | - Matthew Brown
- SEAC Unilever Colworth, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ UK
| | - Annette Furniss
- SEAC Unilever Colworth, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ UK
| | - Lynn Meech
- SEAC Unilever Colworth, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ UK
| | - Anja Lalljie
- SEAC Unilever Colworth, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ UK
| | - Stella Cochrane
- SEAC Unilever Colworth, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ UK
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