1
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Thibault E, Brandizzi F. Post-translational modifications: emerging directors of cell-fate decisions during endoplasmic reticulum stress in Arabidopsis thaliana. Biochem Soc Trans 2024; 52:831-848. [PMID: 38600022 PMCID: PMC11088923 DOI: 10.1042/bst20231025] [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: 01/19/2024] [Revised: 03/23/2024] [Accepted: 04/02/2024] [Indexed: 04/12/2024]
Abstract
Homeostasis of the endoplasmic reticulum (ER) is critical for growth, development, and stress responses. Perturbations causing an imbalance in ER proteostasis lead to a potentially lethal condition known as ER stress. In ER stress situations, cell-fate decisions either activate pro-life pathways that reestablish homeostasis or initiate pro-death pathways to prevent further damage to the organism. Understanding the mechanisms underpinning cell-fate decisions in ER stress is critical for crop development and has the potential to enable translation of conserved components to ER stress-related diseases in metazoans. Post-translational modifications (PTMs) of proteins are emerging as key players in cell-fate decisions in situations of imbalanced ER proteostasis. In this review, we address PTMs orchestrating cell-fate decisions in ER stress in plants and provide evidence-based perspectives for where future studies may focus to identify additional PTMs involved in ER stress management.
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Affiliation(s)
- Ethan Thibault
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, U.S.A
- Department of Plant Biology, Michigan State University, East Lansing, MI, U.S.A
| | - Federica Brandizzi
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, U.S.A
- Department of Plant Biology, Michigan State University, East Lansing, MI, U.S.A
- Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI, U.S.A
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2
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Zbieralski K, Staszewski J, Konczak J, Lazarewicz N, Nowicka-Kazmierczak M, Wawrzycka D, Maciaszczyk-Dziubinska E. Multilevel Regulation of Membrane Proteins in Response to Metal and Metalloid Stress: A Lesson from Yeast. Int J Mol Sci 2024; 25:4450. [PMID: 38674035 PMCID: PMC11050377 DOI: 10.3390/ijms25084450] [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: 03/07/2024] [Revised: 04/06/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
In the face of flourishing industrialization and global trade, heavy metal and metalloid contamination of the environment is a growing concern throughout the world. The widespread presence of highly toxic compounds of arsenic, antimony, and cadmium in nature poses a particular threat to human health. Prolonged exposure to these toxins has been associated with severe human diseases, including cancer, diabetes, and neurodegenerative disorders. These toxins are known to induce analogous cellular stresses, such as DNA damage, disturbance of redox homeostasis, and proteotoxicity. To overcome these threats and improve or devise treatment methods, it is crucial to understand the mechanisms of cellular detoxification in metal and metalloid stress. Membrane proteins are key cellular components involved in the uptake, vacuolar/lysosomal sequestration, and efflux of these compounds; thus, deciphering the multilevel regulation of these proteins is of the utmost importance. In this review, we summarize data on the mechanisms of arsenic, antimony, and cadmium detoxification in the context of membrane proteome. We used yeast Saccharomyces cerevisiae as a eukaryotic model to elucidate the complex mechanisms of the production, regulation, and degradation of selected membrane transporters under metal(loid)-induced stress conditions. Additionally, we present data on orthologues membrane proteins involved in metal(loid)-associated diseases in humans.
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Affiliation(s)
| | | | | | | | | | | | - Ewa Maciaszczyk-Dziubinska
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland; (K.Z.); (J.S.); (J.K.); (N.L.); (M.N.-K.); (D.W.)
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3
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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] [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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4
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Long Q, Zhang Z, Li Y, Zhong Y, Liu H, Chang L, Ying Y, Zuo T, Wang Y, Xu P. Phosphoproteome reveals long-term potentiation deficit following treatment of ultra-low dose soman exposure in mice. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132211. [PMID: 37572605 DOI: 10.1016/j.jhazmat.2023.132211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/30/2023] [Accepted: 08/01/2023] [Indexed: 08/14/2023]
Abstract
Soman, a warfare nerve agent, poses a significant threat by inducing severe brain damage that often results in death. Nonetheless, our understanding of the biological changes underlying persistent neurocognitive dysfunction caused by low dosage of soman remains limited. This study used mice to examine the effects of different doses of soman over time. Phosphoproteomic analysis of the mouse brain is the first time to be used to detect toxic effects of soman at such low or ultra-low doses, which were undetectable based on measuring the activity of acetylcholinesterase at the whole-animal level. We also found that phosphoproteome alterations could accurately track the soman dose, irrespective of the sampling time. Moreover, phosphoproteome revealed a rapid and adaptive cellular response to soman exposure, with the points of departure 8-38 times lower than that of acetylcholinesterase activity. Impaired long-term potentiation was identified in phosphoproteomic studies, which was further validated by targeted quantitative proteomics, immunohistochemistry, and immunofluorescence analyses, with significantly increased levels of phosphorylation of protein phosphatase 1 in the hippocampus following soman exposure. This increase in phosphorylation inhibits long-term potentiation, ultimately leading to long-term memory dysfunction in mice.
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Affiliation(s)
- Qi Long
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China; School of Basic Medicine, Anhui Medical University, Hefei 230032, China
| | - Zhenpeng Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China
| | - Yuan Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China; Department of Biomedicine, Medical College, Guizhou University, Guiyang 550025, China
| | - Yuxu Zhong
- Toxicology and Medical Countermeasures, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences PLA China, Beijing 100850, China
| | - Hongyan Liu
- Toxicology and Medical Countermeasures, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences PLA China, Beijing 100850, China
| | - Lei Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China
| | - Ying Ying
- Toxicology and Medical Countermeasures, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences PLA China, Beijing 100850, China
| | - Tao Zuo
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China.
| | - Yong'an Wang
- Toxicology and Medical Countermeasures, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences PLA China, Beijing 100850, China.
| | - Ping Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China; School of Basic Medicine, Anhui Medical University, Hefei 230032, China; Department of Biomedicine, Medical College, Guizhou University, Guiyang 550025, China; Program of Environmental Toxicology, School of Public Health, China Medical University, Shenyang 110122, China.
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5
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Wang H, Zhang Q, Pi J. Advances in research strategies and approaches for toxicity testing of environmental exposures. Toxicol Appl Pharmacol 2023; 460:116363. [PMID: 36623737 DOI: 10.1016/j.taap.2023.116363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Huihui Wang
- Group of Chronic Disease and Environmental Genomics, School of Public Health, China Medical University, Shenyang 110122, China; The Key Laboratory of Liaoning Province on Toxic and Biological Effects of Arsenic, Shenyang 110122, China.
| | - Qiang Zhang
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA.
| | - Jingbo Pi
- The Key Laboratory of Liaoning Province on Toxic and Biological Effects of Arsenic, Shenyang 110122, China; Program of Environmental Toxicology, School of Public Health, China Medical University, Shenyang 110122, China..
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6
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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: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [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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Navarro C, Navarro MA, Leyva A. Arsenic perception and signaling: The yet unexplored world. FRONTIERS IN PLANT SCIENCE 2022; 13:993484. [PMID: 36119603 PMCID: PMC9479143 DOI: 10.3389/fpls.2022.993484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/15/2022] [Indexed: 06/15/2023]
Abstract
Arsenic is one of the most potent carcinogens in the biosphere, jeopardizing the health of millions of people due to its entrance into the human food chain through arsenic-contaminated waters and staple crops, particularly rice. Although the mechanisms of arsenic sensing are widely known in yeast and bacteria, scientific evidence concerning arsenic sensors or components of early arsenic signaling in plants is still in its infancy. However, in recent years, we have gained understanding of the mechanisms involved in arsenic uptake and detoxification in different plant species and started to get insights into arsenic perception and signaling, which allows us to glimpse the possibility to design effective strategies to prevent arsenic accumulation in edible crops or to increase plant arsenic extraction for phytoremediation purposes. In this context, it has been recently described a mechanism according to which arsenite, the reduced form of arsenic, regulates the arsenate/phosphate transporter, consistent with the idea that arsenite functions as a selective signal that coordinates arsenate uptake with detoxification mechanisms. Additionally, several transcriptional and post-translational regulators, miRNAs and phytohormones involved in arsenic signaling and tolerance have been identified. On the other hand, studies concerning the developmental programs triggered to adapt root architecture in order to cope with arsenic toxicity are just starting to be disclosed. In this review, we compile and analyze the latest advances toward understanding how plants perceive arsenic and coordinate its acquisition with detoxification mechanisms and root developmental programs.
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Liu S, Pi J, Zhang Q. Signal amplification in the KEAP1-NRF2-ARE antioxidant response pathway. Redox Biol 2022; 54:102389. [PMID: 35792437 PMCID: PMC9287733 DOI: 10.1016/j.redox.2022.102389] [Citation(s) in RCA: 119] [Impact Index Per Article: 59.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/26/2022] [Accepted: 06/27/2022] [Indexed: 12/19/2022] Open
Abstract
The KEAP1-NRF2-ARE signaling pathway plays a central role in mediating the adaptive cellular stress response to oxidative and electrophilic chemicals. This canonical pathway has been extensively studied and reviewed in the past two decades, but rarely was it looked at from a quantitative signaling perspective. Signal amplification, i.e., ultrasensitivity, is crucially important for robust induction of antioxidant genes to appropriate levels that can adequately counteract the stresses. In this review article, we examined a number of well-known molecular events in the KEAP1-NRF2-ARE pathway from a quantitative perspective with a focus on how signal amplification can be achieved. We illustrated, by using a series of mathematical models, that redox-regulated protein sequestration, stabilization, translation, nuclear trafficking, DNA promoter binding, and transcriptional induction - which are embedded in the molecular network comprising KEAP1, NRF2, sMaf, p62, and BACH1 - may generate highly ultrasensitive NRF2 activation and antioxidant gene induction. The emergence and degree of ultrasensitivity depend on the strengths of protein-protein and protein-DNA interaction and protein abundances. A unique, quantitative understanding of signal amplification in the KEAP1-NRF2-ARE pathway will help to identify sensitive targets for the prevention and therapeutics of oxidative stress-related diseases and develop quantitative adverse outcome pathway models to facilitate the health risk assessment of oxidative chemicals.
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Affiliation(s)
- Shengnan Liu
- Program of Environmental Toxicology, School of Public Health, China Medical University, Shenyang, 110122, China
| | - Jingbo Pi
- Program of Environmental Toxicology, School of Public Health, China Medical University, Shenyang, 110122, China.
| | - Qiang Zhang
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA.
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9
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Long Q, Feng L, Li Y, Zuo T, Chang L, Zhang Z, Xu P. Time-resolved quantitative phosphoproteomics reveals cellular responses induced by caffeine and coumarin. Toxicol Appl Pharmacol 2022; 449:116115. [PMID: 35691368 DOI: 10.1016/j.taap.2022.116115] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 05/27/2022] [Accepted: 06/06/2022] [Indexed: 11/30/2022]
Abstract
Protein phosphorylation is a critical way that cells respond to external signals and environmental stresses. However, the patterns of cellular response to chemicals at different times were largely unknown. Here, we used quantitative phosphoproteomics to analyze the cellular response of kinases and signaling pathways, as well as pattern change of phosphorylated substrates in HepG2 cells that were exposed to caffeine and coumarin for 10 min and 24 h. Comparing the 10 min and 24 h groups, 33 kinases were co-responded and 32 signaling pathways were co-enriched in caffeine treated samples, while 48 kinases and 34 signaling pathways were co-identified in coumarin treated samples. Instead, the percentage of co-identified phosphorylated substrates only accounted for 4.31% and 9.57% between 10 min and 24 h in caffeine and coumarin treated samples, respectively. The results showed that specific chemical exposure led to a bunch of the same kinases and signaling pathways changed in HepG2 cells, while the phosphorylated substrates were different. In addition, it was found that insulin signaling pathway was significantly enriched by both the caffeine and coumarin treatment. The pattern changes in phosphorylation of protein substrates, kinases and signaling pathways with varied chemicals and different time course shed light on the potential mechanism of cellular responses to endless chemical stimulation.
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Affiliation(s)
- Qi Long
- School of Basic Medicine, Anhui Medical University, Hefei 230032, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China
| | - Lijie Feng
- School of Basic Medicine, Anhui Medical University, Hefei 230032, China
| | - Yuan Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China; School of Medicine, Guizhou University, Guiyang 550025, China
| | - Tao Zuo
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China
| | - Lei Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China
| | - Zhenpeng Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China.
| | - Ping Xu
- School of Basic Medicine, Anhui Medical University, Hefei 230032, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Institute of Lifeomics, Beijing 102206, China; School of Medicine, Guizhou University, Guiyang 550025, China; School of Public Health, China Medical University, Shenyang 110122, China; Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding 071002, China.
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10
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Paten AM, Colin T, Coppin CW, Court LN, Barron AB, Oakeshott JG, Morgan MJ. Non-additive gene interactions underpin molecular and phenotypic responses in honey bee larvae exposed to imidacloprid and thymol. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 814:152614. [PMID: 34963587 DOI: 10.1016/j.scitotenv.2021.152614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/17/2021] [Accepted: 12/18/2021] [Indexed: 06/14/2023]
Abstract
Understanding the cumulative risk of chemical mixtures at environmentally realistic concentrations is a key challenge in honey bee ecotoxicology. Ecotoxicogenomics, including transcriptomics, measures responses in individual organisms at the molecular level which can provide insights into the mechanisms underlying phenotypic responses induced by one or more stressors and link impacts on individuals to populations. Here, fifth instar honey bee larvae were sampled from a previously reported field experiment exploring the phenotypic impacts of environmentally realistic chronic exposures of the pesticide imidacloprid (5 μg.kg-1 for six weeks) and the acaricide thymol (250 g.kg-1 applied via Apiguard gel in-hive for four weeks), both separately and in combination. RNA-seq was used to discover individual and interactive chemical effects on larval gene expression and to uncover molecular mechanisms linked to reported adult and colony phenotypes. The separate and combined treatments had distinct gene expression profiles which represented differentially affected signaling and metabolic pathways. The molecular signature of the mixture was characterised by additive interactions in canonical stress responses associated with oxidative stress and detoxification, and non-additive interactions in secondary responses including developmental, neurological, and immune pathways. Novel emergent impacts on eye development genes correlated with long-term defects in visual learning performance as adults. This is consistent with these chemicals working through independent modes of action that combine to impact common downstream pathways, and highlights the importance of establishing mechanistic links between molecular and phenotypic responses when predicting effects of chemical mixtures on ecologically relevant population outcomes.
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Affiliation(s)
- Amy M Paten
- Land and Water, CSIRO, Black Mountain, Canberra, ACT 2601, Australia.
| | - Théotime Colin
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Chris W Coppin
- Land and Water, CSIRO, Black Mountain, Canberra, ACT 2601, Australia.
| | - Leon N Court
- Land and Water, CSIRO, Black Mountain, Canberra, ACT 2601, Australia.
| | - Andrew B Barron
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia.
| | - John G Oakeshott
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia; Applied Biosciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Matthew J Morgan
- Land and Water, CSIRO, Black Mountain, Canberra, ACT 2601, Australia.
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11
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Bonilla DA, Moreno Y, Petro JL, Forero DA, Vargas-Molina S, Odriozola-Martínez A, Orozco CA, Stout JR, Rawson ES, Kreider RB. A Bioinformatics-Assisted Review on Iron Metabolism and Immune System to Identify Potential Biomarkers of Exercise Stress-Induced Immunosuppression. Biomedicines 2022; 10:724. [PMID: 35327526 PMCID: PMC8945881 DOI: 10.3390/biomedicines10030724] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 03/01/2022] [Accepted: 03/09/2022] [Indexed: 02/01/2023] Open
Abstract
The immune function is closely related to iron (Fe) homeostasis and allostasis. The aim of this bioinformatics-assisted review was twofold; (i) to update the current knowledge of Fe metabolism and its relationship to the immune system, and (ii) to perform a prediction analysis of regulatory network hubs that might serve as potential biomarkers during stress-induced immunosuppression. Several literature and bioinformatics databases/repositories were utilized to review Fe metabolism and complement the molecular description of prioritized proteins. The Search Tool for the Retrieval of Interacting Genes (STRING) was used to build a protein-protein interactions network for subsequent network topology analysis. Importantly, Fe is a sensitive double-edged sword where two extremes of its nutritional status may have harmful effects on innate and adaptive immunity. We identified clearly connected important hubs that belong to two clusters: (i) presentation of peptide antigens to the immune system with the involvement of redox reactions of Fe, heme, and Fe trafficking/transport; and (ii) ubiquitination, endocytosis, and degradation processes of proteins related to Fe metabolism in immune cells (e.g., macrophages). The identified potential biomarkers were in agreement with the current experimental evidence, are included in several immunological/biomarkers databases, and/or are emerging genetic markers for different stressful conditions. Although further validation is warranted, this hybrid method (human-machine collaboration) to extract meaningful biological applications using available data in literature and bioinformatics tools should be highlighted.
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Affiliation(s)
- Diego A. Bonilla
- Research Division, Dynamical Business & Science Society—DBSS International SAS, Bogota 110311, Colombia; (Y.M.); (J.L.P.)
- Research Group in Biochemistry and Molecular Biology, Faculty of Science and Education, Universidad Distrital Francisco José de Caldas, Bogota 110311, Colombia
- Research Group in Physical Activity, Sports and Health Sciences (GICAFS), Universidad de Córdoba, Montería 230002, Colombia
- Sport Genomics Research Group, Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain;
| | - Yurany Moreno
- Research Division, Dynamical Business & Science Society—DBSS International SAS, Bogota 110311, Colombia; (Y.M.); (J.L.P.)
- Research Group in Biochemistry and Molecular Biology, Faculty of Science and Education, Universidad Distrital Francisco José de Caldas, Bogota 110311, Colombia
| | - Jorge L. Petro
- Research Division, Dynamical Business & Science Society—DBSS International SAS, Bogota 110311, Colombia; (Y.M.); (J.L.P.)
- Research Group in Physical Activity, Sports and Health Sciences (GICAFS), Universidad de Córdoba, Montería 230002, Colombia
| | - Diego A. Forero
- Health and Sport Sciences Research Group, School of Health and Sport Sciences, Fundación Universitaria del Área Andina, Bogotá 111221, Colombia; (D.A.F.); (C.A.O.)
| | - Salvador Vargas-Molina
- Faculty of Sport Sciences, EADE-University of Wales Trinity Saint David, 29018 Málaga, Spain;
| | - Adrián Odriozola-Martínez
- Sport Genomics Research Group, Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain;
- kDNA Genomics, Joxe Mari Korta Research Center, University of the Basque Country UPV/EHU, 20018 Donostia, Spain
| | - Carlos A. Orozco
- Health and Sport Sciences Research Group, School of Health and Sport Sciences, Fundación Universitaria del Área Andina, Bogotá 111221, Colombia; (D.A.F.); (C.A.O.)
| | - Jeffrey R. Stout
- Physiology of Work and Exercise Response (POWER) Laboratory, Institute of Exercise Physiology and Rehabilitation Science, University of Central Florida, Orlando, FL 32816, USA;
| | - Eric S. Rawson
- Department of Health, Nutrition and Exercise Science, Messiah University, Mechanicsburg, PA 17055, USA;
| | - Richard B. Kreider
- Exercise & Sport Nutrition Laboratory, Human Clinical Research Facility, Department of Health & Kinesiology, Texas A&M University, College Station, TX 77843, USA;
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12
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Synthetic Protein Circuits and Devices Based on Reversible Protein-Protein Interactions: An Overview. Life (Basel) 2021; 11:life11111171. [PMID: 34833047 PMCID: PMC8623019 DOI: 10.3390/life11111171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 12/30/2022] Open
Abstract
Protein-protein interactions (PPIs) contribute to regulate many aspects of cell physiology and metabolism. Protein domains involved in PPIs are important building blocks for engineering genetic circuits through synthetic biology. These domains can be obtained from known proteins and rationally engineered to produce orthogonal scaffolds, or computationally designed de novo thanks to recent advances in structural biology and molecular dynamics prediction. Such circuits based on PPIs (or protein circuits) appear of particular interest, as they can directly affect transcriptional outputs, as well as induce behavioral/adaptational changes in cell metabolism, without the need for further protein synthesis. This last example was highlighted in recent works to enable the production of fast-responding circuits which can be exploited for biosensing and diagnostics. Notably, PPIs can also be engineered to develop new drugs able to bind specific intra- and extra-cellular targets. In this review, we summarize recent findings in the field of protein circuit design, with particular focus on the use of peptides as scaffolds to engineer these circuits.
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13
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Liu S, Pi J, Zhang Q. Mathematical modeling reveals quantitative properties of KEAP1-NRF2 signaling. Redox Biol 2021; 47:102139. [PMID: 34600335 PMCID: PMC8531862 DOI: 10.1016/j.redox.2021.102139] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/12/2021] [Accepted: 09/16/2021] [Indexed: 12/14/2022] Open
Abstract
Under oxidative and electrophilic stresses, cells launch an NRF2-mediated transcriptional antioxidant program. The activation of NRF2 depends on a redox sensor, KEAP1, which promotes the ubiquitination and degradation of NRF2. While a great deal has been learned about this duo, its quantitative signaling properties are largely unexplored. Here we examined these properties, including half-life, maximal activation, and response steepness (ultrasensitivity) of NRF2, through mathematical modeling. The models describe the binding of KEAP1 and NRF2 via ETGE and DLG motifs, NRF2 production, KEAP1-dependent and independent NRF2 degradation, and perturbations by different classes of NRF2 activators. Simulations revealed at the basal condition, NRF2 is sequestered by KEAP1 and the KEAP1-NRF2 complex is distributed comparably in an ETGE-bound (open) state and an ETGE and DLG dual-bound (closed) state. When two-step ETGE binding is considered, class I–V, electrophilic NRF2 activators shift the balance to a closed state incompetent to degrade NRF2, while the open and closed KEAP1-NRF2 complexes transition from operating in cycle mode to equilibrium mode. Ultrasensitive NRF2 activation (a steep rise of free NRF2) can occur when NRF2 nearly saturates KEAP1. The ultrasensitivity results from zero-order degradation through DLG binding and protein sequestration through ETGE binding. Optimal abundances of cytosolic and nuclear KEAP1 exist to maximize ultrasensitivity. These response characteristics do not require disruption of DLG binding as suggested by the hinge-latch hypothesis. In comparison, class VI NRF2 activators cause a shift to the open KEAP1-NRF2 complex and ultimately its complete dissociation, resulting in a fast release of NRF2 followed by stabilization. However, ultrasensitivity is lost due to decreasing free KEAP1 abundance. In summary, by simulating the dual role of KEAP1, i.e., sequestering and promoting degradation of NRF2, our modeling provides novel quantitative insights into NRF2 activation, which may help design novel NRF2 modulators and understand the oxidative actions of environmental stressors. Steep (ultrasensitive) NRF2 activation can occur when it rises to saturate KEAP1. Ultrasensitivity results from zero-order degradation and protein sequestration. Optimal cytosolic and nuclear KEAP1 abundances exist for maximal ultrasensitivity. Open and closed KEAP1-NRF2 complexes transition in cycle and equilibrium mode. NRF2 activation by KEAP1-NRF2 interaction inhibitors is more gradual.
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Affiliation(s)
- Shengnan Liu
- Program of Environmental Toxicology, School of Public Health, China Medical University, Shenyang, 110122, China; Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA
| | - Jingbo Pi
- Program of Environmental Toxicology, School of Public Health, China Medical University, Shenyang, 110122, China.
| | - Qiang Zhang
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA.
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14
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Park HJ, Jung HM, Lee A, Jo SH, Lee HJ, Kim HS, Jung CK, Min SR, Cho HS. SUMO Modification of OsFKBP20-1b Is Integral to Proper Pre-mRNA Splicing upon Heat Stress in Rice. Int J Mol Sci 2021; 22:ijms22169049. [PMID: 34445755 PMCID: PMC8396655 DOI: 10.3390/ijms22169049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 08/19/2021] [Indexed: 11/18/2022] Open
Abstract
OsFKBP20-1b, a plant-specific cyclophilin protein, has been implicated to regulate pre-mRNA splicing under stress conditions in rice. Here, we demonstrated that OsFKBP20-1b is SUMOylated in a reconstituted SUMOylation system in E.coli and in planta, and that the SUMOylation-coupled regulation was associated with enhanced protein stability using a less SUMOylated OsFKBP20-1b mutant (5KR_OsFKBP20-1b). Furthermore, OsFKBP20-1b directly interacted with OsSUMO1 and OsSUMO2 in the nucleus and cytoplasm, whereas the less SUMOylated 5KR_OsFKBP20-1b mutant had an impaired interaction with OsSUMO1 and 2 in the cytoplasm but not in the nucleus. Under heat stress, the abundance of an OsFKBP20-1b-GFP fusion protein was substantially increased in the nuclear speckles and cytoplasmic foci, whereas the heat-responsiveness was remarkably diminished in the presence of the less SUMOylated 5KR_OsFKBP20-1b-GFP mutant. The accumulation of endogenous SUMOylated OsFKBP20-1b was enhanced by heat stress in planta. Moreover, 5KR_OsFKBP20-1b was not sufficiently associated with the U snRNAs in the nucleus as a spliceosome component. A protoplast transfection assay indicated that the low SUMOylation level of 5KR_OsFKBP20-1b led to inaccurate alternative splicing and transcription under heat stress. Thus, our results suggest that OsFKBP20-1b is post-translationally regulated by SUMOylation, and the modification is crucial for proper RNA processing in response to heat stress in rice.
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Affiliation(s)
- Hyun-Ji Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (H.-J.P.); (H.-M.J.); (A.L.); (S.-H.J.); (H.-J.L.); (H.-S.K.)
| | - Hae-Myeong Jung
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (H.-J.P.); (H.-M.J.); (A.L.); (S.-H.J.); (H.-J.L.); (H.-S.K.)
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology, Daejeon 34113, Korea
| | - Areum Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (H.-J.P.); (H.-M.J.); (A.L.); (S.-H.J.); (H.-J.L.); (H.-S.K.)
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology, Daejeon 34113, Korea
| | - Seung-Hee Jo
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (H.-J.P.); (H.-M.J.); (A.L.); (S.-H.J.); (H.-J.L.); (H.-S.K.)
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology, Daejeon 34113, Korea
| | - Hyo-Jun Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (H.-J.P.); (H.-M.J.); (A.L.); (S.-H.J.); (H.-J.L.); (H.-S.K.)
- Department of Functional Genomics, KRIBB School of Biotechnology, Korea University of Science and Technology, Daejeon 34113, Korea
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (H.-J.P.); (H.-M.J.); (A.L.); (S.-H.J.); (H.-J.L.); (H.-S.K.)
| | - Choon-Kyun Jung
- Department of International Agricultural Technology and Crop Biotechnology Institute/Green Bio Science and Technology, Seoul National University, Pyeongchang 25354, Korea;
- Department of Agriculture, Forestry, and Bioresources and Integrated Major in Global Smart Farm, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Sung-Ran Min
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (H.-J.P.); (H.-M.J.); (A.L.); (S.-H.J.); (H.-J.L.); (H.-S.K.)
- Correspondence: (S.-R.M.); (H.-S.C.); Tel.: +82-42-860-4463 (S.-R.M.); +82-42-860-4469 (H.-S.C.)
| | - Hye-Sun Cho
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea; (H.-J.P.); (H.-M.J.); (A.L.); (S.-H.J.); (H.-J.L.); (H.-S.K.)
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology, Daejeon 34113, Korea
- Correspondence: (S.-R.M.); (H.-S.C.); Tel.: +82-42-860-4463 (S.-R.M.); +82-42-860-4469 (H.-S.C.)
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15
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Vega A, Fredes I, O'Brien J, Shen Z, Ötvös K, Abualia R, Benkova E, Briggs SP, Gutiérrez RA. Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture. EMBO Rep 2021; 22:e51813. [PMID: 34357701 PMCID: PMC8447600 DOI: 10.15252/embr.202051813] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 05/13/2021] [Accepted: 06/23/2021] [Indexed: 01/04/2023] Open
Abstract
Nitrate commands genome‐wide gene expression changes that impact metabolism, physiology, plant growth, and development. In an effort to identify new components involved in nitrate responses in plants, we analyze the Arabidopsis thaliana root phosphoproteome in response to nitrate treatments via liquid chromatography coupled to tandem mass spectrometry. 176 phosphoproteins show significant changes at 5 or 20 min after nitrate treatments. Proteins identified by 5 min include signaling components such as kinases or transcription factors. In contrast, by 20 min, proteins identified were associated with transporter activity or hormone metabolism functions, among others. The phosphorylation profile of NITRATE TRANSPORTER 1.1 (NRT1.1) mutant plants was significantly altered as compared to wild‐type plants, confirming its key role in nitrate signaling pathways that involves phosphorylation changes. Integrative bioinformatics analysis highlights auxin transport as an important mechanism modulated by nitrate signaling at the post‐translational level. We validated a new phosphorylation site in PIN2 and provide evidence that it functions in primary and lateral root growth responses to nitrate.
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Affiliation(s)
- Andrea Vega
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile.,FONDAP Center for Genome Regulation, ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Isabel Fredes
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile.,FONDAP Center for Genome Regulation, ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - José O'Brien
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile.,FONDAP Center for Genome Regulation, ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile.,Departamento de Fruticultura y Enología, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Zhouxin Shen
- Cell and Developmental Biology, University of California San Diego. San Diego, CA, USA
| | - Krisztina Ötvös
- Institute of Science and Technology (IST) Austria, Klosterneuburg, Austria.,Bioresources Unit, Center for Health & Bioresources, AIT Austrian Institute of Technology GmbH, Tulln, Austria
| | - Rashed Abualia
- Institute of Science and Technology (IST) Austria, Klosterneuburg, Austria
| | - Eva Benkova
- Institute of Science and Technology (IST) Austria, Klosterneuburg, Austria
| | - Steven P Briggs
- Cell and Developmental Biology, University of California San Diego. San Diego, CA, USA
| | - Rodrigo A Gutiérrez
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile.,FONDAP Center for Genome Regulation, ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago, Chile
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16
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Effective exposure of chemicals in in vitro cell systems: A review of chemical distribution models. Toxicol In Vitro 2021; 73:105133. [DOI: 10.1016/j.tiv.2021.105133] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 02/11/2021] [Accepted: 02/25/2021] [Indexed: 12/23/2022]
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17
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Sueiro-Olivares M, Scott J, Gago S, Petrovic D, Kouroussis E, Zivanovic J, Yu Y, Strobel M, Cunha C, Thomson D, Fortune-Grant R, Thusek S, Bowyer P, Beilhack A, Carvalho A, Bignell E, Filipovic MR, Amich J. Fungal and host protein persulfidation are functionally correlated and modulate both virulence and antifungal response. PLoS Biol 2021; 19:e3001247. [PMID: 34061822 PMCID: PMC8168846 DOI: 10.1371/journal.pbio.3001247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 04/27/2021] [Indexed: 02/07/2023] Open
Abstract
Aspergillus fumigatus is a human fungal pathogen that can cause devastating pulmonary infections, termed "aspergilloses," in individuals suffering immune imbalances or underlying lung conditions. As rapid adaptation to stress is crucial for the outcome of the host-pathogen interplay, here we investigated the role of the versatile posttranslational modification (PTM) persulfidation for both fungal virulence and antifungal host defense. We show that an A. fumigatus mutant with low persulfidation levels is more susceptible to host-mediated killing and displays reduced virulence in murine models of infection. Additionally, we found that a single nucleotide polymorphism (SNP) in the human gene encoding cystathionine γ-lyase (CTH) causes a reduction in cellular persulfidation and correlates with a predisposition of hematopoietic stem cell transplant recipients to invasive pulmonary aspergillosis (IPA), as correct levels of persulfidation are required for optimal antifungal activity of recipients' lung resident host cells. Importantly, the levels of host persulfidation determine the levels of fungal persulfidation, ultimately reflecting a host-pathogen functional correlation and highlighting a potential new therapeutic target for the treatment of aspergillosis.
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Affiliation(s)
- Monica Sueiro-Olivares
- Manchester Fungal Infection Group (MFIG), School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Jennifer Scott
- Manchester Fungal Infection Group (MFIG), School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Sara Gago
- Manchester Fungal Infection Group (MFIG), School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Dunja Petrovic
- Centre National de la Recherche Scientifique (CNRS), Institut de Biochimie et Genetique Cellulaires (IBGC), Bordeaux, France
- Université de Bordeaux, Institut de Biochimie et Genetique Cellulaires (IBGC), Bordeaux, France
| | - Emilia Kouroussis
- Centre National de la Recherche Scientifique (CNRS), Institut de Biochimie et Genetique Cellulaires (IBGC), Bordeaux, France
- Université de Bordeaux, Institut de Biochimie et Genetique Cellulaires (IBGC), Bordeaux, France
| | - Jasmina Zivanovic
- Centre National de la Recherche Scientifique (CNRS), Institut de Biochimie et Genetique Cellulaires (IBGC), Bordeaux, France
- Université de Bordeaux, Institut de Biochimie et Genetique Cellulaires (IBGC), Bordeaux, France
| | - Yidong Yu
- Interdisciplinary Center for Clinical Research (IZKF) Laboratory for Experimental Stem Cell Transplantation, Department of Internal Medicine II, University Hospital, Würzburg, Germany
| | - Marlene Strobel
- Interdisciplinary Center for Clinical Research (IZKF) Laboratory for Experimental Stem Cell Transplantation, Department of Internal Medicine II, University Hospital, Würzburg, Germany
| | - Cristina Cunha
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- Life and Health Sciences Research Institute (ICVS)/Biomaterials, Biodegradables and Biomimetics (3B’s)—PT Government Associate Laboratory, Guimarães, Braga, Portugal
| | - Darren Thomson
- Manchester Fungal Infection Group (MFIG), School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Rachael Fortune-Grant
- Manchester Fungal Infection Group (MFIG), School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Sina Thusek
- Interdisciplinary Center for Clinical Research (IZKF) Laboratory for Experimental Stem Cell Transplantation, Department of Internal Medicine II, University Hospital, Würzburg, Germany
| | - Paul Bowyer
- Manchester Fungal Infection Group (MFIG), School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Andreas Beilhack
- Interdisciplinary Center for Clinical Research (IZKF) Laboratory for Experimental Stem Cell Transplantation, Department of Internal Medicine II, University Hospital, Würzburg, Germany
| | - Agostinho Carvalho
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- Life and Health Sciences Research Institute (ICVS)/Biomaterials, Biodegradables and Biomimetics (3B’s)—PT Government Associate Laboratory, Guimarães, Braga, Portugal
| | - Elaine Bignell
- Manchester Fungal Infection Group (MFIG), School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | | | - Jorge Amich
- Manchester Fungal Infection Group (MFIG), School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
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18
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Li H, Yuan H, Middleton A, Li J, Nicol B, Carmichael P, Guo J, Peng S, Zhang Q. Next generation risk assessment (NGRA): Bridging in vitro points-of-departure to human safety assessment using physiologically-based kinetic (PBK) modelling - A case study of doxorubicin with dose metrics considerations. Toxicol In Vitro 2021; 74:105171. [PMID: 33848589 DOI: 10.1016/j.tiv.2021.105171] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/17/2021] [Accepted: 04/08/2021] [Indexed: 11/16/2022]
Abstract
Using the chemical doxorubicin (DOX), the objective of the present study was to evaluate the impact of dose metrics selection in the new approach method of integrating physiologically-based kinetic (PBK) modelling and relevant human cell-based assays to inform a priori the point of departure for human health risk. We reviewed the literature on the clinical consequences of DOX treatment to identify dosing scenarios with no or mild cardiotoxicity observed. Key concentrations of DOX that induced cardiomyocyte toxicity in vitro were derived from studies of our own and others. A human population-based PBK model of DOX was developed and verified against pharmacokinetic data. The model was then used to predict plasma and extracellular and intracellular heart concentrations of DOX under selected clinical settings and compared with in vitro outcomes, based on several dose metrics: Cmax (maximum concentration) or AUC (area under concentration-time curve) in free or total form of DOX. We found when using in vitro assays to predict cardiotoxicity for DOX, AUC is a better indicator. Our study illustrates that when appropriate dose metrics are used, it is possible to combine PBK modelling with in vitro-derived toxicity information to define margins of safety and predict low-risk human exposure levels.
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Affiliation(s)
- Hequn Li
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK
| | - Haitao Yuan
- Evaluation and Research Centre for Toxicology, Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, China
| | - Alistair Middleton
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK
| | - Jin Li
- Unilever Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK
| | - Beate Nicol
- 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
| | - Jiabin Guo
- Evaluation and Research Centre for Toxicology, Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, China
| | - Shuangqing Peng
- Evaluation and Research Centre for Toxicology, Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, China.
| | - Qiang Zhang
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA.
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19
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Liu X, Zhang H, Xue Q, Pan W, Zhang A. In silico health effect prioritization of environmental chemicals through transcriptomics data exploration from a chemo-centric view. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 762:143082. [PMID: 33143927 DOI: 10.1016/j.scitotenv.2020.143082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 10/11/2020] [Accepted: 10/11/2020] [Indexed: 06/11/2023]
Abstract
With the explosive growth of synthetic compounds, the health effects caused by exogenous chemical exposure have attracted more and more public attention. The prediction of health effect is a never-ending story. Collective resource of transcriptomics data offers an opportunity to understand and identify the multiple health effects of small molecule. Inspired by the fact that environmental chemicals of high health risk frequently share both similar gene expression profile and common structural feature of certain drugs, we here propose a novel computational effect prioritization method for environmental chemicals through transcriptomics data exploration from a chemo-centric view. Specifically, non-negative matrix factorization (NMF) method has been adopted to get the association network linking structural features with transcriptomics characteristics of drugs with specific effects. The model yields 13 pivotal types of effects, so-called components, that represent drug categories with common chemo- and geno- type features. Moreover, the established model effectively prioritizes potential toxic effects for the external chemicals from the endocrine disruptor screening program (EDSP) for their potential estrogenicity and other verified risks. Even if only the highest priority is set for the estrogenic effect, the precision and recall can reach 0.76 and 0.77 respectively for these chemicals. Our effort provides a successful endeavor as to profile potential toxic effects simultaneously for environmental chemicals using both chemical and omics data.
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Affiliation(s)
- Xian Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, PR China.
| | - Huazhou Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, PR China.
| | - Qiao Xue
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China.
| | - Wenxiao Pan
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China.
| | - Aiqian Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, PR China; Institute of Environment and Health, Jianghan University, Wuhan 430056, PR China.
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20
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Glucan Unmasking Identifies Regulators of Temperature-Induced Translatome Reprogramming in C. neoformans. mSphere 2021; 6:6/1/e01281-20. [PMID: 33568457 PMCID: PMC8544899 DOI: 10.1128/msphere.01281-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The cell walls of fungi are critical for cellular structure and rigidity but also serve as a major communicator to alert the cell to the changing environment. In response to stresses encountered in human hosts, pathogenic fungi remodel their cell walls. Masking the β-1,3-glucan component of the cell wall is critical to escape detection by innate immune cells. We previously demonstrated that β-1,3-glucan is unmasked in response to host temperature stress when translatome reprogramming is defective in Cryptococcus neoformans Here, we used β-1,3-glucan unmasking as an output to identify signaling modules involved both in masking and in translatome reprogramming in response to host temperature stress. We reveal that the high-osmolarity glycerol (HOG) mitogen-activated protein kinase (MAPK) pathway is involved in translatome reprogramming and that mutants in this pathway display moderate unmasking when grown at 37°C. Additionally, we show that mutants of the cell wall integrity (CWI)/Mpk1 MAPK pathway extensively unmask β-1,3-glucan. While the CWI pathway does not impact translatome reprogramming, our data suggest that it may play a role in the posttranslational regulation of transcription factors that govern masking.IMPORTANCE Cryptococcus neoformans is a fungal pathogen that causes devastating morbidity and mortality in immunocompromised individuals. It possesses several virulence factors that aid in its evasion from the host immune system, including a large polysaccharide capsule that cloaks the antigenic cell wall. Studies investigating how the cell wall is remodeled to keep this pathogen disguised in response to stress have been limited. We previously found that host temperature stress results in translatome reprogramming that is necessary for keeping the highly antigenic β-(1, 3)-glucan component masked. Our data reveal signaling modules that trigger these responses and suggest the points of regulation at which these pathways act in achieving masking. Understanding these mechanisms may allow for therapeutic manipulation that may promote the immune recognition and clearance of this fungal pathogen.
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21
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Gbotsyo YA, Rowarth NM, Weir LK, MacRae TH. Short-term cold stress and heat shock proteins in the crustacean Artemia franciscana. Cell Stress Chaperones 2020; 25:1083-1097. [PMID: 32794096 PMCID: PMC7591681 DOI: 10.1007/s12192-020-01147-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 07/02/2020] [Accepted: 07/28/2020] [Indexed: 01/09/2023] Open
Abstract
In their role as molecular chaperones, heat shock proteins (Hsps) mediate protein folding thereby mitigating cellular damage caused by physiological and environmental stress. Nauplii of the crustacean Artemia franciscana respond to heat shock by producing Hsps; however, the effects of cold shock on Hsp levels in A. franciscana have not been investigated previously. The effect of cold shock at 1 °C followed by recovery at 27 °C on the amounts of ArHsp90, Hsp70, ArHsp40, and ArHsp40-2 mRNA and their respective proteins in A. franciscana nauplii was examined by quantitative PCR (qPCR) and immunoprobing of western blots. The same Hsp mRNAs and proteins were also quantified during incubation of nauplii at their optimal growth temperature of 27 °C. qPCR analyses indicated that the abundance of ArHsp90, Hsp70, and ArHsp40 mRNA remained relatively constant during both cold shock and recovery and was not significantly different compared with levels at optimal temperature. Western blotting revealed that ArHsp90, ArHsp40, and ArHsp40-2 were generally below baseline, but at detectable levels during the 6 h of cold shock, and persisted in early recovery stages before declining. Hsp70 was the only protein that remained constant in quantity throughout cold shock and recovery. By contrast, all Hsps declined rapidly during 6 h when nauplii were incubated continuously at 27 °C optimal temperature. Generally, the amounts of ArHsp90, ArHsp40, and ArHsp40-2 were higher during cold shock/recovery than those during continuous incubation at 27 °C. Our data support the conclusion that low temperature preserves Hsp levels, making them available to assist in protein repair and recovery after cold shock.
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Affiliation(s)
- Yayra A Gbotsyo
- Department of Biology, Dalhousie University, Halifax, N. S., B3H 4R2, Canada
| | - Nathan M Rowarth
- Department of Biology, Dalhousie University, Halifax, N. S., B3H 4R2, Canada
| | - Laura K Weir
- Biology Department, Saint Mary's University Halifax, Halifax, N. S., B3H 3C3, Canada.
| | - Thomas H MacRae
- Department of Biology, Dalhousie University, Halifax, N. S., B3H 4R2, Canada
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22
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Zhou H, Zhang L, Li Y, Wu G, Zhu H, Zhang H, Su JK, Guo L, Zhou Q, Xiong F, Yu Q, Yang P, Zhang S, Cai J, Wang CY. Cigarette smoke extract stimulates bronchial epithelial cells to undergo a SUMOylation turnover. BMC Pulm Med 2020; 20:276. [PMID: 33097022 PMCID: PMC7584069 DOI: 10.1186/s12890-020-01300-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 09/21/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chronic obstructive pulmonary disease (COPD) characterized by the airway and lung inflammation, is a leading cause of morbidity and mortality worldwide, especially among smokers over 40 years of age and individuals exposed to biomass smoke. Although the detailed mechanisms of this disease remain elusive, there is feasible evidence that protein posttranslational modifications (PTMs) may play a role in its pathoetiology. We thus conducted studies to dissect the effect of cigarette smoke extracts (CSE) on the change of SUMOylated substrates in human bronchial epithelial cells (HBEs). METHODS Samples were collected in HBEs with or without 24 h of CSE insult and then subjected to Western-blot and LC-MS/MS analysis. Subsequently, bioinformatic tools were used to analyze the data. The effect of SUMOylation on cytochrome P450 1A1 (CYP1A1) was evaluated by flow cytometry. RESULTS It was noted that CSE stimulated HBEs to undergo a SUMOylation turnover as evidenced by the changes of SUMOylated substrates and SUMOylation levels for a particular substrate. The SUMOylated proteins are relevant to the regulation of biological processes, molecular function and cellular components. Particularly, CSE stimulated a significant increase of SUMOylated CYP1A1, a critical enzyme involved in the induction of oxidative stress. CONCLUSIONS Our data provide a protein SUMOylation profile for better understanding of the mechanisms underlying COPD and support that smoking induces oxidative stress in HBEs, which may predispose to the development of COPD in clinical settings.
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Affiliation(s)
- Haifeng Zhou
- The Center for Biomedical Research, Tongji Hospital Research Building, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Caidian, 431000, China
| | - Lei Zhang
- The Center for Biomedical Research, Tongji Hospital Research Building, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Caidian, 431000, China
- Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Li
- The Center for Biomedical Research, Tongji Hospital Research Building, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Caidian, 431000, China
| | - Guorao Wu
- The Center for Biomedical Research, Tongji Hospital Research Building, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Caidian, 431000, China
- Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - He Zhu
- The Center for Biomedical Research, Tongji Hospital Research Building, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Caidian, 431000, China
| | - Huilan Zhang
- The Center for Biomedical Research, Tongji Hospital Research Building, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Caidian, 431000, China
- Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jia-Kun Su
- The Technology Center, China Tobacco Jiangxi Industrial Co., Ltd., Nanchang High Technology Development Valley, Nanchang, 330096, China
| | - Lei Guo
- The Technology Center, China Tobacco Jiangxi Industrial Co., Ltd., Nanchang High Technology Development Valley, Nanchang, 330096, China
| | - Qing Zhou
- The Center for Biomedical Research, Tongji Hospital Research Building, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Caidian, 431000, China
| | - Fei Xiong
- The Center for Biomedical Research, Tongji Hospital Research Building, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Caidian, 431000, China
| | - Qilin Yu
- The Center for Biomedical Research, Tongji Hospital Research Building, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Caidian, 431000, China
| | - Ping Yang
- The Center for Biomedical Research, Tongji Hospital Research Building, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Caidian, 431000, China
| | - Shu Zhang
- The Center for Biomedical Research, Tongji Hospital Research Building, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Caidian, 431000, China
| | - Jibao Cai
- The Technology Center, China Tobacco Jiangxi Industrial Co., Ltd., Nanchang High Technology Development Valley, Nanchang, 330096, China.
| | - Cong-Yi Wang
- The Center for Biomedical Research, Tongji Hospital Research Building, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Caidian, 431000, China.
- Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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23
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Schneider K, Venn B, Mühlhaus T. TMEA: A Thermodynamically Motivated Framework for Functional Characterization of Biological Responses to System Acclimation. ENTROPY 2020; 22:e22091030. [PMID: 33286800 PMCID: PMC7597090 DOI: 10.3390/e22091030] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 09/07/2020] [Accepted: 09/11/2020] [Indexed: 12/16/2022]
Abstract
The objective of gene set enrichment analysis (GSEA) in modern biological studies is to identify functional profiles in huge sets of biomolecules generated by high-throughput measurements of genes, transcripts, metabolites, and proteins. GSEA is based on a two-stage process using classical statistical analysis to score the input data and subsequent testing for overrepresentation of the enrichment score within a given functional coherent set. However, enrichment scores computed by different methods are merely statistically motivated and often elusive to direct biological interpretation. Here, we propose a novel approach, called Thermodynamically Motivated Enrichment Analysis (TMEA), to account for the energy investment in biological relevant processes. Therefore, TMEA is based on surprisal analysis, which offers a thermodynamic-free energy-based representation of the biological steady state and of the biological change. The contribution of each biomolecule underlying the changes in free energy is used in a Monte Carlo resampling procedure resulting in a functional characterization directly coupled to the thermodynamic characterization of biological responses to system perturbations. To illustrate the utility of our method on real experimental data, we benchmark our approach on plant acclimation to high light and compare the performance of TMEA with the most frequently used method for GSEA.
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24
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Hernández RB, Carrascal M, Abian J, Michalke B, Farina M, Gonzalez YR, Iyirhiaro GO, Moteshareie H, Burnside D, Golshani A, Suñol C. Manganese-induced neurotoxicity in cerebellar granule neurons due to perturbation of cell network pathways with potential implications for neurodegenerative disorders. Metallomics 2020; 12:1656-1678. [PMID: 33206086 DOI: 10.1039/d0mt00085j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Manganese (Mn) is essential for living organisms, playing an important role in nervous system function. Nevertheless, chronic and/or acute exposure to this metal, especially during early life stages, can lead to neurotoxicity and dementia by unclear mechanisms. Thus, based on previous works of our group with yeast and zebrafish, we hypothesized that the mechanisms mediating manganese-induced neurotoxicity can be associated with the alteration of protein metabolism. These mechanisms may also depend on the chemical speciation of manganese. Therefore, the current study aimed at investigating the mechanisms mediating the toxic effects of manganese in primary cultures of cerebellar granule neurons (CGNs). By exposing cultured CGNs to different chemical species of manganese ([[2-[(dithiocarboxy)amino]ethyl]carbamodithioato]](2-)-kS,kS']manganese, named maneb (MB), and [[1,2-ethanediylbis[carbamodithioato]](2-)]manganese mixture with [[1,2-ethanediylbis[carbamodithioato]](2-)]zinc, named mancozeb (MZ), and manganese chloride (MnCl2)), and using the MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay, we observed that both MB and MZ induced similar cytotoxicity (LC50∼ 7-9 μM), which was higher than that of MnCl2 (LC50∼ 27 μM). Subsequently, we applied systems biology approaches, including metallomics, proteomics, gene expression and bioinformatics, and revealed that independent of chemical speciation, for non-cytotoxic concentrations (0.3-3 μM), Mn-induced neurotoxicity in CGNs is associated with metal dyshomeostasis and impaired protein metabolism. In this way, we verified that MB induced more post-translational alterations than MnCl2, which can be a plausible explanation for cytotoxic differences between both chemical species. The metabolism of proteins is one of the most energy consuming cellular processes and its impairment appears to be a key event of some cellular stress processes reported separately in other studies such as cell cycle arrest, energy impairment, cell signaling, excitotoxicity, immune response, potential protein accumulation and apoptosis. Interestingly, we verified that Mn-induced neurotoxicity shares pathways associated with the development of Alzheimer's disease, Amyotrophic Lateral Sclerosis, Huntington's disease, and Parkinson's disease. This has been observed in baker's yeast and zebrafish suggesting that the mode of action of Mn may be evolutionarily conserved.
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Affiliation(s)
- Raúl Bonne Hernández
- Laboratory of Bioinorganic and Environmental Toxicology - LABITA, Department of Exact and Earth Sciences, Federal University of São Paulo, Rua Prof. Artur Riedel, 275, CEP 09972-270, Diadema, SP, Brazil.
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25
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Suresh S, Crease TJ, Cristescu ME, Chain FJJ. Alternative splicing is highly variable among Daphnia pulex lineages in response to acute copper exposure. BMC Genomics 2020; 21:433. [PMID: 32586292 PMCID: PMC7318467 DOI: 10.1186/s12864-020-06831-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 06/15/2020] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Despite being one of the primary mechanisms of gene expression regulation in eukaryotes, alternative splicing is often overlooked in ecotoxicogenomic studies. The process of alternative splicing facilitates the production of multiple mRNA isoforms from a single gene thereby greatly increasing the diversity of the transcriptome and proteome. This process can be important in enabling the organism to cope with stressful conditions. Accurate identification of splice sites using RNA sequencing requires alignment to independent exonic positions within the genome, presenting bioinformatic challenges, particularly when using short read data. Although technological advances allow for the detection of splicing patterns on a genome-wide scale, very little is known about the extent of intraspecies variation in splicing patterns, particularly in response to environmental stressors. In this study, we used RNA-sequencing to study the molecular responses to acute copper exposure in three lineages of Daphnia pulex by focusing on the contribution of alternative splicing in addition to gene expression responses. RESULTS By comparing the overall gene expression and splicing patterns among all 15 copper-exposed samples and 6 controls, we identified 588 differentially expressed (DE) genes and 16 differentially spliced (DS) genes. Most of the DS genes (13) were not found to be DE, suggesting unique transcriptional regulation in response to copper that went unnoticed with conventional DE analysis. To understand the influence of genetic background on gene expression and alternative splicing responses to Cu, each of the three lineages was analyzed separately. In contrast to the overall analysis, each lineage had a higher proportion of unique DS genes than DE genes suggesting that genetic background has a larger influence on DS than on DE. Gene Ontology analysis revealed that some pathways involved in stress response were jointly regulated by DS and DE genes while others were regulated by only transcription or only splicing. CONCLUSIONS Our findings suggest an important role for alternative splicing in shaping transcriptome diversity in response to metal exposure in Daphnia, highlighting the importance of integrating splicing analyses with gene expression surveys to characterize molecular pathways in evolutionary and environmental studies.
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Affiliation(s)
- Sneha Suresh
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, 01854, USA
- Present address: The Swire Institute of Marine Science and School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Pok Fu Lam, Hong Kong SAR
| | - Teresa J Crease
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Melania E Cristescu
- Department of Biology, McGill University, 1205 Docteur Penfield, Montreal, QC, H3A 1B1, Canada
| | - Frédéric J J Chain
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, 01854, USA.
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Guo P, Chen S, Li D, Zhang J, Luo J, Zhang A, Yu D, Bloom MS, Chen L, Chen W. SFPQ is involved in regulating arsenic-induced oxidative stress by interacting with the miRNA-induced silencing complexes. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 261:114160. [PMID: 32066060 DOI: 10.1016/j.envpol.2020.114160] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 02/06/2020] [Accepted: 02/09/2020] [Indexed: 06/10/2023]
Abstract
Arsenic exposure contributed to the development of human diseases. Arsenic exerted multiple organ toxicities mainly by triggering oxidative stress. However, the signaling pathway underlying oxidative stress is unclear. We previously found that the expression of SFPQ, a splicing factor, was positively associated with urinary arsenic concentration in an arsenic-exposed population, suggesting an oxidative stress regulatory role for SFPQ. To test this hypothesis, we established cell models of oxidative stress in human hepatocyte cells (L02) treated with NaAsO2. Reactive oxygen species (ROS) synthesis displayed a time- and dose-dependent increase with NaAsO2 treatment. SFPQ suppression resulted in a 36%-53% decrease in ROS generation, leading to enhanced cellular damage determined by 8-OHdG, comet tail moment, and micronucleus analysis. Particularly, SFPQ deficiency attenuated expression of the oxidase genes DUOX1, DUOX2, NCF2, and NOX2. A fluorescent-based RNA electrophoretic mobility shift assay (FREMSA) and dual-luciferase reporter system revealed that miR-92b-5p targeted DUOX2 mRNA degradation. An RNA immunoprecipitation assay showed an interaction between SFPQ and miR-92b-5p of the miRNA-induced silencing complex (miRISC). Notably, NaAsO2 treatment diminished the interaction between SFPQ and miR92b-5p, accompanied by decreased binding between miR-92b-5p and 3'-UTR of DUOX2. However, SFPQ deficiency suppressed the dissociation of miR-92b-5p from 3'-UTR of DUOX2, indicating that miR-92b-5p regulated the SFPQ-dependent DUOX2 expression. Taken together, we reveal that SFPQ responds to arsenic-induced oxidative stress by interacting with the miRISC. These findings offer new insight into the potential role of SFPQ in regulating cellular stress response.
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Affiliation(s)
- Ping Guo
- The Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Shen Chen
- The Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Daochuan Li
- The Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Jinmiao Zhang
- The Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Jiao Luo
- School of Public Health, Qingdao University, Qingdao 266071, China
| | - Aihua Zhang
- Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Department of Toxicology, School of Public Health, Guizhou Medical University, Guiyang, Guizhou, China
| | - Dianke Yu
- School of Public Health, Qingdao University, Qingdao 266071, China
| | - Michael S Bloom
- Departments of Environmental Health Sciences & Epidemiology and Biostatistics, University at Albany, State University of New York, Rensselaer, NY 12144, USA
| | - Liping Chen
- The Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China.
| | - Wen Chen
- The Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, China
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27
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Lakshmi PK, Kumar S, Pawar S, Kuriakose BB, Sudheesh MS, Pawar RS. Targeting metabolic syndrome with phytochemicals: Focus on the role of molecular chaperones and hormesis in drug discovery. Pharmacol Res 2020; 159:104925. [PMID: 32492491 DOI: 10.1016/j.phrs.2020.104925] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 05/10/2020] [Accepted: 05/10/2020] [Indexed: 12/21/2022]
Abstract
Adaptive cellular stress response confers stress tolerance against inflammatory and metabolic disorders. In response to metabolic stress, the key mediator of cellular adaptation and tolerance is a class of molecules called the molecular chaperones (MCs). MCs are highly conserved molecules that play critical role in maintaining protein stability and functionality. Hormesis in this context is a unique adaptation mechanism where a low dose of a stressor (which is toxic at high dose) confers a stress-resistant adaptive cellular phenotype. Hormesis can be observed at different level of biological organization at various measurable endpoints. The MCs are believed to play a key role in adaptation during hormesis. Several phytochemicals are known for their hormetic response and are called phytochemical hormetins. The role of phytochemical-mediated hormesis on the adaptive cellular processes is proposed as a potential therapeutic approach to target inflammation associated with metabolic syndrome. However, the screening of phytochemical hormetins would require a paradigm shift in the methods currently used in drug discovery.
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Affiliation(s)
- P K Lakshmi
- Pharmacognosy and Phytochemistry Laboratory, Faculty of Pharmacy, VNS Group of Institutions, VNS Campus, Vidya Vihar, Neelbad-462044, Bhopal, MP, India
| | - Shweta Kumar
- Pharmacognosy and Phytochemistry Laboratory, Faculty of Pharmacy, VNS Group of Institutions, VNS Campus, Vidya Vihar, Neelbad-462044, Bhopal, MP, India
| | - Sulakshhna Pawar
- Ravi Shankar College of Pharmacy, Bypass Road, Bhanpur Square, Bhopal, MP 462010, India
| | - Beena Briget Kuriakose
- Department of Basic Medical Sciences, College of Applied Medical Sciences, King Khalid University, Khamis, Mushayt, Saudi Arabia
| | - M S Sudheesh
- Department of Pharmaceutics, Amrita School of Pharmacy, Amrita Health Science Campus, Amrita Vishwa Vidyapeetham, Ponekkara, Kochi 682041, India
| | - Rajesh Singh Pawar
- Truba Institute of Pharmacy, Karond-Gandhi Nagar, By Pass Road, Bhopal, 462038, India.
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Post-translational modifications and stress adaptation: the paradigm of FKBP51. Biochem Soc Trans 2020; 48:441-449. [PMID: 32318709 PMCID: PMC7200631 DOI: 10.1042/bst20190332] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/21/2020] [Accepted: 03/24/2020] [Indexed: 01/22/2023]
Abstract
Adaptation to stress is a fundamental requirement to cope with changing environmental conditions that pose a threat to the homeostasis of cells and organisms. Post-translational modifications (PTMs) of proteins represent a possibility to quickly produce proteins with new features demanding relatively little cellular resources. FK506 binding protein (FKBP) 51 is a pivotal stress protein that is involved in the regulation of several executers of PTMs. This mini-review discusses the role of FKBP51 in the function of proteins responsible for setting the phosphorylation, ubiquitination and lipidation of other proteins. Examples include the kinases Akt1, CDK5 and GSK3β, the phosphatases calcineurin, PP2A and PHLPP, and the ubiquitin E3-ligase SKP2. The impact of FKBP51 on PTMs of signal transduction proteins significantly extends the functional versatility of this protein. As a stress-induced protein, FKBP51 uses re-setting of PTMs to relay the effect of stress on various signaling pathways.
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Klapacz J, Gollapudi BB. Considerations for the Use of Mutation as a Regulatory Endpoint in Risk Assessment. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:84-93. [PMID: 31301246 DOI: 10.1002/em.22318] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/08/2019] [Accepted: 07/10/2019] [Indexed: 06/10/2023]
Abstract
Assessment of a chemical's potential to cause permanent changes in the genetic code has been a common practice in the industry and regulatory settings for decades. Furthermore, the genetic toxicity battery of tests has typically been employed during the earliest stages of the research and development programs of new product development. A positive outcome from such battery has a major impact on the chemical's utility, industrial hygiene, product stewardship practices, and product life cycle analysis, among many other decisions that need to be taken by the industry, even before the registration of a chemical is undertaken. Under the prevailing regulatory paradigm, the dichotomous (yes/no) evaluation of the chemical's genotoxic potential leads to a conservative, linear no-threshold (LNT) risk assessment, unless compelling and undeniable data to the contrary can be provided to satisfy regulators, typically in a number of different global jurisdictions. With the current advent of predictive methods, new testing paradigms, mode-of-action/adverse outcome pathways, and quantitative risk assessment approaches, various stakeholders are starting to employ these state-of-the-science methodologies to further the conversation on decision making and advance the regulatory paradigm beyond the dominant LNT status quo. This commentary describes these novel methodologies, relevant biological responses, and how these can affect internal and regulatory risk assessment approaches. Environ. Mol. Mutagen. 61:84-93, 2020. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Joanna Klapacz
- Toxicology and Environmental Research and Consulting, The Dow Chemical Company, Midland, Michigan
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Samimi F, Baazm M, Eftekhar E, Rajabi S, Goodarzi MT, Jalali Mashayekhi F. Possible antioxidant mechanism of coenzyme Q10 in diabetes: impact on Sirt1/Nrf2 signaling pathways. Res Pharm Sci 2019; 14:524-533. [PMID: 32038732 PMCID: PMC6937743 DOI: 10.4103/1735-5362.272561] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Oxidative stress is a major complication in diabetes mellitus. The aim of this study was to investigate potential antioxidant activity of coenzyme Q10 (Co Q10) against hyperglycemia-induced oxidative stress in diabetic rat and unraveling its mechanism of action by focusing on silent information regulator 1 (Sirt1) and nuclear factor E2-related factor 2 (Nrf2) mRNA expression level. Furthermore, the activity of two Nrf2-dependent antioxidant enzymes (superoxide dismutase and catalase) in the liver of diabetic rats was studied. After induction of diabetes in rats using streptozotocin (55 mg/kg), rats were divided into five groups of six each. Groups 1 and 2 (healthy control groups) were injected with isotonic saline or sesame oil; group 3 received Co Q10 (10 mg /Kg /day), group 4, as a diabetic control, received sesame oil; and group 5 was diabetic rats treated with Co Q10. Afterwards, serum and liver samples were collected, and oxidative stress markers, lipid profile, as well as the expression of Sirt1 and Nrf2 genes were measured. Diabetes induction significantly reduced expression level of Sirt1 and Nrf2 mRNAs and also declined catalase, superoxide dismutase activities, and total thiol groups levels in diabetic group in comparison to healthy controls, while a significant increase was found in the levels of malondialdehyde and lipid profile. Co Q10 treatment significantly up-regulated Sirt1 and Nrf2 mRNA levels along with an increase in catalase activity in diabetic group as compared with untreated diabetic rats. Furthermore, Co Q10 caused a marked decrease in malondialdehyde levels and significantly improved lipid profile. Our data demonstrated that Co Q10 may exert its antioxidant activity in diabetes through the induction of Sirt1/Nrf2 gene expression.
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Affiliation(s)
- Fatemeh Samimi
- Department of Biochemistry and Genetics, School of Medicine, Arak University of Medical Sciences, Arak, I.R. Iran
| | - Maryam Baazm
- Department of Anatomy, School of Medicine, Arak University of Medical Sciences, Arak, I.R. Iran
| | - Ebrahim Eftekhar
- Endocrinology and Metabolism Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, I.R. Iran
| | - Sadegh Rajabi
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, I.R. Iran
| | - Mohammad Taghi Goodarzi
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, I.R. Iran
| | - Farideh Jalali Mashayekhi
- Department of Biochemistry and Genetics, School of Medicine, Arak University of Medical Sciences, Arak, I.R. Iran.,Research Center and Molecular Medicine, Arak University of Medical Sciences, Arak, I.R. Iran
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Schittenhelm D, Neuss-Radu M, Verma N, Pink M, Schmitz-Spanke S. ROS and pentose phosphate pathway: mathematical modelling of the metabolic regulation in response to xenobiotic-induced oxidative stress and the proposed Impact of the gluconate shunt. Free Radic Res 2019; 53:979-992. [PMID: 31476923 DOI: 10.1080/10715762.2019.1660777] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Elevated intracellular levels of reactive oxygen species (ROS), e.g. resulting from exposure to xenobiotics, can cause severe damages. Antioxidant defence mechanisms, which involve regulation of enzyme activities, protect cells to a certain extent. Nevertheless, continuous or increased exposure can overwhelm this system resulting in an adverse cellular state. To simulate exposure scenarios and to investigate the transition to an adverse cellular state, a mathematical model for the dynamics of ROS in response to xenobiotic-induced oxidative stress has been developed. It is based on exposure experiments of human urothelial cells (RT4) to the nitrated polycyclic aromatic hydrocarbon 3-nitrobenzanthrone (3-NBA), a component of diesel engine exhaust, and takes into account the following metabolic pathways of the antioxidant defence system: glutathione redox cycle scavenging directly ROS, the pentose phosphate pathway and the gluconate shunt as NADPH supplier and the beginning of glycolysis. In addition, ROS generation due to the bioactivation of 3-NBA has been implemented. The regulation of enzyme activities plays an important role in the presented mathematical model. The in silico model consists of ordinary differential equations on the basis of enzyme kinetics and mass action for the metabolism of 3-NBA. Parameters are either estimated from performed in vitro experiments via least-squares fitting or obtained from the literature. The results underline the importance of the pentose phosphate pathway to cope with oxidative stress and suggest an important role of the gluconate shunt during low-dose exposure.
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Affiliation(s)
- Doris Schittenhelm
- Department of Mathematics, Friedrich-Alexander-Universität Erlangen-Nürnberg , Erlangen , Germany
| | - Maria Neuss-Radu
- Department of Mathematics, Friedrich-Alexander-Universität Erlangen-Nürnberg , Erlangen , Germany
| | - Nisha Verma
- Institute and Outpatient Clinic of Occupational, Social and Environmental Medicine, Friedrich-Alexander-Universität Erlangen-Nürnberg , Erlangen , Germany
| | - Mario Pink
- Institute and Outpatient Clinic of Occupational, Social and Environmental Medicine, Friedrich-Alexander-Universität Erlangen-Nürnberg , Erlangen , Germany
| | - Simone Schmitz-Spanke
- Institute and Outpatient Clinic of Occupational, Social and Environmental Medicine, Friedrich-Alexander-Universität Erlangen-Nürnberg , Erlangen , Germany
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Effects of Post-translational Modifications on Membrane Localization and Signaling of Prostanoid GPCR-G Protein Complexes and the Role of Hypoxia. J Membr Biol 2019; 252:509-526. [PMID: 31485700 DOI: 10.1007/s00232-019-00091-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 08/17/2019] [Indexed: 02/07/2023]
Abstract
G protein-coupled receptors (GPCRs) play a pivotal role in the adaptive responses to cellular stresses such as hypoxia. In addition to influencing cellular gene expression profiles, hypoxic microenvironments can perturb membrane protein localization, altering GPCR effector scaffolding and altering downstream signaling. Studies using proteomics approaches have revealed significant regulation of GPCR and G proteins by their state of post-translational modification. The aim of this review is to examine the effects of post-translational modifications on membrane localization and signaling of GPCR-G protein complexes, with an emphasis on vascular prostanoid receptors, and to highlight what is known about the effect of cellular hypoxia on these mechanisms. Understanding post-translational modifications of protein targets will help to define GPCR targets in treatment of disease, and to inform research into mechanisms of hypoxic cellular responses.
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Zhang Q, Caudle WM, Pi J, Bhattacharya S, Andersen ME, Kaminski NE, Conolly RB. Embracing Systems Toxicology at Single-Cell Resolution. CURRENT OPINION IN TOXICOLOGY 2019; 16:49-57. [PMID: 31768481 PMCID: PMC6876623 DOI: 10.1016/j.cotox.2019.04.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
As systems biology expands its multi-omic spectrum to increasing resolutions, distinguishing cells based on single-cell profiles becomes feasible. Unlike traditional bulk assays that average cellular responses and blur the distinct identities of responsive cells, single-cell technologies enable sensitive detection of small cellular changes and precise identification of those cells perturbed by toxicants. Among the suite of omic technologies that continue to expand and become affordable, single-cell RNA sequencing (scRNA-seq) is at the cutting edge and leading the way to transform systems toxicology. Single-cell systems toxicology can provide a wealth of information to elucidate cell-specific alterations and response trajectories, detect points-of-departure, map and develop dynamical models of toxicity pathways.
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Affiliation(s)
- Qiang Zhang
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - W. Michael Caudle
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Jingbo Pi
- Program of Environmental Toxicology, School of Public Health, China Medical University, Shenyang, China
| | - Sudin Bhattacharya
- Department of Biomedical Engineering, Department of Pharmacology and Toxicology, Center for Research on Ingredient Safety, Institute for Quantitative Health Science and Engineering, and Institute for Integrative Toxicology, Michigan State University, East Lansing, Michigan, USA
| | | | - Norbert E. Kaminski
- Departments of Pharmacology and Toxicology and Institute for Integrative Toxicology, Michigan State University, East Lansing, Michigan, USA
| | - Rory B. Conolly
- Integrated Systems Toxicology Division, National Health and Environmental Effects Research Laboratory, United States Environmental Protection Agency, Durham, North Carolina, USA
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Gagnaire B, Bonnet M, Tchamitchian S, Cavalié I, Della-Vedova C, Dubourg N, Adam-Guillermin C, Brunet JL, Belzunces LP. Physiological effects of gamma irradiation in the honeybee, Apis mellifera. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 174:153-163. [PMID: 30825738 DOI: 10.1016/j.ecoenv.2019.02.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/17/2019] [Accepted: 02/11/2019] [Indexed: 06/09/2023]
Abstract
Terrestrial ecosystems are exposed to various kinds of pollutants, including radionuclides. The honeybee, Apis mellifera, is commonly used in ecotoxicology as a model species for evaluating the effects of pollutants. In the present study, honeybees were irradiated right after birth for 14 days with gamma rays at dose rates ranging between 4.38 × 10-3 and 588 mGy/d. Biological tissues (head, intestine and abdomen) were sampled at D3, D10 and D14. Ten different physiological markers involved in nervous (acetylcholinesterase (AChE)), antioxidative (catalase (CAT), superoxide dismutase (SOD), glutathione peroxidase (GPx) and glutathione-S-transferase (GST)), immune system (phenoloxidase (PO)) and metabolism (carboxylesterases (CaEs) and alkaline phosphatase (ALP)) were measured. Univariate analyses were conducted to determine whether each individual biomarker response was positively or negatively correlated with the dose rate. Then, multivariate analyses were applied to investigate the relationships between all the biomarker responses. Although no mortality occurred during the experiment, several biomarkers varied significantly in relation to the dose rate. Globally, the biomarkers of antioxidant and immune systems decreased as the dose rate increased. Reversible effects on the indicator of the neural system were found. Concerning indicators of metabolism (carboxylesterases), variations occurred but no clear pattern was found. Taken altogether, these results help better understand the effects of ionizing radiation on bees by identifying relevant physiological markers of effects. These results could improve the assessment of the environmental risk due to ionizing radiation in terrestrial ecosystems.
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Affiliation(s)
- B Gagnaire
- Institut de Radioprotection et de Sureté Nucléaire (IRSN), PSE-ENV/SRTE/LECO, Cadarache, Saint-Paul-lez-Durance 13115, France.
| | - M Bonnet
- INRA, Institut National de la Recherche Agronomique, Laboratoire de Toxicologie Environnementale, UR 406 A&E, CS 40509, 84914 Avignon Cedex 9, France
| | - S Tchamitchian
- INRA, Institut National de la Recherche Agronomique, Laboratoire de Toxicologie Environnementale, UR 406 A&E, CS 40509, 84914 Avignon Cedex 9, France
| | - I Cavalié
- Institut de Radioprotection et de Sureté Nucléaire (IRSN), PSE-ENV/SRTE/LECO, Cadarache, Saint-Paul-lez-Durance 13115, France
| | - C Della-Vedova
- Institut de Radioprotection et de Sureté Nucléaire (IRSN), PSE-ENV/SRTE/LRTA, Cadarache, Saint-Paul-lez-Durance 13115, France
| | - N Dubourg
- Institut de Radioprotection et de Sureté Nucléaire (IRSN), PSE-ENV/SRTE/LECO, Cadarache, Saint-Paul-lez-Durance 13115, France
| | - C Adam-Guillermin
- Institut de Radioprotection et de Sureté Nucléaire (IRSN), PSE-ENV/SRTE/LECO, Cadarache, Saint-Paul-lez-Durance 13115, France
| | - J-L Brunet
- INRA, Institut National de la Recherche Agronomique, Laboratoire de Toxicologie Environnementale, UR 406 A&E, CS 40509, 84914 Avignon Cedex 9, France
| | - L P Belzunces
- INRA, Institut National de la Recherche Agronomique, Laboratoire de Toxicologie Environnementale, UR 406 A&E, CS 40509, 84914 Avignon Cedex 9, France.
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Liu X, Zhang H, Pan W, Xue Q, Fu J, Liu G, Zheng M, Zhang A. A novel computational solution to the health risk assessment of air pollution via joint toxicity prediction: A case study on selected PAH binary mixtures in particulate matters. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 170:427-435. [PMID: 30553920 DOI: 10.1016/j.ecoenv.2018.12.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 11/28/2018] [Accepted: 12/04/2018] [Indexed: 06/09/2023]
Abstract
Regional haze episode has already caused overwhelming public concern. Unraveling the health effects of the representative composition mixtures of atmospheric fine particulate matters (PM2.5) becomes a top priority. In this study, a novel computational solution integrating chemical-induced genomic residual effect prediction with in vitro-based risk assessment is proposed to obtain the cumulative health risk of typical chemical mixtures of particulate matters (PM). The joint toxicity of binary mixtures is estimated by analyzing both genomic similarity and dose-response curve of relevant pollutants for the chemical-induced genomic residual effect. Specifically, the modified relative potency factor (mRPF) of mixtures is introduced for this purpose, and the ratio of activation (RA) value is defined to assess the corresponding health risks of the mixtures. As a methodology demonstration, the health risk of typical binary polycyclic aromatic hydrocarbon (PAH) mixtures in PM, containing Benzo[a]pyrene (BaP) as a component, is assessed using the proposed solution. Our results indicate that the combined effect of pairwise PAHs of BaP with Benzo[b]fluoranthene (BbF) and Benz[a]anthracene (BaA) is synergistic on p53 pathway, and that the health risk of the such mixtures increases compared to that of the individual ones. Obviously, the cumulative health risk of environmental mixtures will be underestimated when the synergistic effect is wrongly assumed to be additive. To our knowledge, this is the first study ever report on a computational solution to the health risk assessment of environmental pollution via joint toxicity prediction. The novel methodology proposed here makes full use of the open-access in vitro assay data and transcriptomic information in literatures and provides a successful demonstration of the concept of systems biology and translational science.
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Affiliation(s)
- Xian Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, PR China
| | - Huazhou Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, PR China
| | - Wenxiao Pan
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Qiao Xue
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Jianjie Fu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Guorui Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Minghui Zheng
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, PR China; Institute of Environment and Health, Jianghan University, Wuhan 430056, PR China
| | - Aiqian Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, PR China; Institute of Environment and Health, Jianghan University, Wuhan 430056, PR China.
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Madeira D, Mendonça V, Madeira C, Gaiteiro C, Vinagre C, Diniz MS. Molecular assessment of wild populations in the marine realm: Importance of taxonomic, seasonal and habitat patterns in environmental monitoring. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 654:250-263. [PMID: 30447573 DOI: 10.1016/j.scitotenv.2018.11.064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 11/01/2018] [Accepted: 11/05/2018] [Indexed: 06/09/2023]
Abstract
Scientists are currently faced with the challenge of assessing the effects of anthropogenic stressors on aquatic ecosystems. Cellular stress response (CSR) biomarkers are ubiquitous and phylogenetically conserved among metazoans and have been successfully applied in environmental monitoring but they can also vary according to natural biotic and abiotic factors. The reported variability may thus limit the wide application of biomarkers in monitoring, imposing the need to identify variability levels in the field. Our aim was to carry out a comprehensive in situ assessment of the CSR (heat shock protein 70 kDa, ubiquitin, antioxidant enzymes) and oxidative damage (lipid peroxidation) in wild populations across marine taxa by collecting fish, crustaceans, mollusks and cnidarians during two different seasons (spring and summer) and two habitat types (coast and estuary). CSR end-point patterns were different between taxa with mollusks having higher biomarker levels, followed by the cnidarians, while fish and crustaceans showed lower biomarker levels. The PCA showed clear clusters related to mobility/sessile traits with sessile organisms showing greater levels (>2-fold) of CSR proteins and oxidative damage. Mean intraspecific variability in the CSR measured by the coefficient of variation (% CV) (including data from all seasons and sites) was elevated (35-94%). Overall, there was a seasonal differentiation in biomarker patterns across taxonomic groups, especially evident in fish and cnidarians. A differentiation in biomarker patterns between habitat types was also observed and associated with phenotypic plasticity or local adaptation. Overall, specimens collected in the estuary had lower biomarker levels when compared to specimens collected in the coast. This work highlights the importance of assessing baseline biomarker levels across taxa, seasons and habitats prior to applying biomarker analyses in environmental monitoring. Selecting bioindicator species, defining sampling strategies, and identifying confounding factors are crucial preliminary steps that ensure the success of biomarkers as powerful tools in biomonitoring.
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Affiliation(s)
- Diana Madeira
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Quinta da Torre, 2829-516 Caparica, Portugal; Departamento de Biologia & CESAM & ECOMARE, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal.
| | - Vanessa Mendonça
- MARE - Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Carolina Madeira
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Quinta da Torre, 2829-516 Caparica, Portugal; MARE - Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Cristiana Gaiteiro
- Experimental Pathology and Therapeutics Group, Portuguese Institute of Oncology of Porto (CI-IPOP), 4200-072 Porto, Portugal
| | - Catarina Vinagre
- MARE - Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Mário S Diniz
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Quinta da Torre, 2829-516 Caparica, Portugal.
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37
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Dose-dependence of chemical carcinogenicity: Biological mechanisms for thresholds and implications for risk assessment. Chem Biol Interact 2019; 301:112-127. [DOI: 10.1016/j.cbi.2019.01.025] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 01/11/2019] [Accepted: 01/25/2019] [Indexed: 12/19/2022]
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Guimera AM, Shanley DP, Proctor CJ. Modelling the role of redox-related mechanisms in musculoskeletal ageing. Free Radic Biol Med 2019; 132:11-18. [PMID: 30219703 DOI: 10.1016/j.freeradbiomed.2018.09.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 09/07/2018] [Accepted: 09/12/2018] [Indexed: 02/06/2023]
Abstract
The decline in the musculoskeletal system with age is driven at the cellular level by random molecular damage. Cells possess mechanisms to repair or remove damage and many of the pathways involved in this response are regulated by redox signals. However, with ageing there is an increase in oxidative stress which can lead to chronic inflammation and disruption of redox signalling pathways. The complexity of the processes involved has led to the use of computational modelling to help increase our understanding of the system, test hypotheses and make testable predictions. This paper will give a brief background of the biological systems that have been modelled, an introduction to computational modelling, a review of models that involve redox-related mechanisms that are applicable to musculoskeletal ageing, and finally a discussion of the future potential for modelling in this field.
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Affiliation(s)
- Alvaro Martinez Guimera
- Institute for Cell and Molecular Biosciences, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne NE4 5PL, UK
| | - Daryl P Shanley
- Institute for Cell and Molecular Biosciences, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne NE4 5PL, UK
| | - Carole J Proctor
- Institute of Cellular Medicine, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne NE4 5PL, UK.
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Dingemans MML, Baken KA, van der Oost R, Schriks M, van Wezel AP. Risk-based approach in the revised European Union drinking water legislation: Opportunities for bioanalytical tools. INTEGRATED ENVIRONMENTAL ASSESSMENT AND MANAGEMENT 2019; 15:126-134. [PMID: 30144268 PMCID: PMC7379647 DOI: 10.1002/ieam.4096] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 07/06/2018] [Accepted: 08/21/2018] [Indexed: 05/28/2023]
Abstract
A plethora of in vitro bioassays are developed in the context of chemical risk assessment and clinical diagnostics to test effects on different biological processes. Such assays can also be implemented in effect-based monitoring (EBM) of (drinking) water quality alongside chemical analyses. Effects-based monitoring can provide insight into risks for the environment and human health associated with exposure to (unknown) complex, low-level mixtures of micropollutants, which fits in the risk-based approach that was recently introduced in the European Drinking Water Directive. Some challenges remain, in particular those related to selection and interpretation of bioassays. For water quality assessment, carcinogenesis, adverse effects on reproduction and development, effects on xenobiotic metabolism, modulation of hormone systems, DNA reactivity, and adaptive stress responses are considered the most relevant toxicological endpoints. An evaluation procedure of the applicability and performance of in vitro bioassays for water quality monitoring, based on existing information, has been developed, which can be expanded with guidelines for experimental evaluations. In addition, a methodology for the interpretation of in vitro monitoring data is required, because the sensitivity of specific in vitro bioassays in combination with sample concentration may lead to responses of chemicals (far) below exposure concentrations that are relevant for human health effects. Different approaches are proposed to derive effect-based trigger values (EBTs), including EBTs based on (1) relative ecotoxicity potency, (2) health-based threshold values for chronic exposure in humans and kinetics of reference chemicals, and (3) read-across from (drinking) water guideline values. Effects-based trigger values need to be chosen carefully in order to be sufficiently but not overly conservative to indicate potential health effects. Consensus on the crucial steps in the selection and interpretation of in vitro bioassay data will facilitate implementation and legal embedding in the context of water quality monitoring of such assays in EBM strategies. Integr Environ Assess Manag 2019;15:126-134. © 2018 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals, Inc. on behalf of Society of Environmental Toxicology & Chemistry (SETAC).
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Affiliation(s)
| | | | - Ron van der Oost
- Waternet Institute for the Urban Water CycleAmsterdamThe Netherlands
| | | | - Annemarie P van Wezel
- KWR Watercycle Research InstituteNieuwegeinThe Netherlands
- Copernicus Institute of Sustainable DevelopmentUtrecht UniversityUtrechtThe Netherlands
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Ke T, Gonçalves FM, Gonçalves CL, Dos Santos AA, Rocha JBT, Farina M, Skalny A, Tsatsakis A, Bowman AB, Aschner M. Post-translational modifications in MeHg-induced neurotoxicity. Biochim Biophys Acta Mol Basis Dis 2018; 1865:2068-2081. [PMID: 30385410 DOI: 10.1016/j.bbadis.2018.10.024] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 10/16/2018] [Accepted: 10/19/2018] [Indexed: 12/29/2022]
Abstract
Mercury (Hg) exposure remains a major public health concern due to its widespread distribution in the environment. Organic mercurials, such as MeHg, have been extensively investigated especially because of their congenital effects. In this context, studies on the molecular mechanism of MeHg-induced neurotoxicity are pivotal to the understanding of its toxic effects and the development of preventive measures. Post-translational modifications (PTMs) of proteins, such as phosphorylation, ubiquitination, and acetylation are essential for the proper function of proteins and play important roles in the regulation of cellular homeostasis. The rapid and transient nature of many PTMs allows efficient signal transduction in response to stress. This review summarizes the current knowledge of PTMs in MeHg-induced neurotoxicity, including the most commonly PTMs, as well as PTMs induced by oxidative stress and PTMs of antioxidant proteins. Though PTMs represent an important molecular mechanism for maintaining cellular homeostasis and are involved in the neurotoxic effects of MeHg, we are far from understanding the complete picture on their role, and further research is warranted to increase our knowledge of PTMs in MeHg-induced neurotoxicity.
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Affiliation(s)
- Tao Ke
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, United States.
| | - Filipe Marques Gonçalves
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, United States
| | - Cinara Ludvig Gonçalves
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, United States
| | | | - João B T Rocha
- Departamento de Bioquímica e Biologia Molecular, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, 97105900 Santa Maria, RS, Brazil
| | - Marcelo Farina
- Departamento de Bioquímica, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina, 88040900 Florianópolis, SC, Brazil
| | - Anatoly Skalny
- Yaroslavl State University, Sovetskaya St., 14, Yaroslavl 150000, Russia; Peoples' Friendship University of Russia (RUDN University), Miklukho-Maklaya St., 6, Moscow 105064, Russia; Orenburg State University, Pobedy Ave., 13, Orenburg 460352, Russia
| | - Aristidis Tsatsakis
- Center of Toxicology Science & Research, Medical School, University of Crete, Heraklion, Crete, Greece
| | - Aaron B Bowman
- School of Health Sciences, Purdue University, West Lafayette, IN, United States.
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, United States.
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Zhang Q, Li J, Middleton A, Bhattacharya S, Conolly RB. Bridging the Data Gap From in vitro Toxicity Testing to Chemical Safety Assessment Through Computational Modeling. Front Public Health 2018; 6:261. [PMID: 30255008 PMCID: PMC6141783 DOI: 10.3389/fpubh.2018.00261] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 08/21/2018] [Indexed: 12/18/2022] Open
Abstract
Chemical toxicity testing is moving steadily toward a human cell and organoid-based in vitro approach for reasons including scientific relevancy, efficiency, cost, and ethical rightfulness. Inferring human health risk from chemical exposure based on in vitro testing data is a challenging task, facing various data gaps along the way. This review identifies these gaps and makes a case for the in silico approach of computational dose-response and extrapolation modeling to address many of the challenges. Mathematical models that can mechanistically describe chemical toxicokinetics (TK) and toxicodynamics (TD), for both in vitro and in vivo conditions, are the founding pieces in this regard. Identifying toxicity pathways and in vitro point of departure (PoD) associated with adverse health outcomes requires an understanding of the molecular key events in the interacting transcriptome, proteome, and metabolome. Such an understanding will in turn help determine the sets of sensitive biomarkers to be measured in vitro and the scope of toxicity pathways to be modeled in silico. In vitro data reporting both pathway perturbation and chemical biokinetics in the culture medium serve to calibrate the toxicity pathway and virtual tissue models, which can then help predict PoDs in response to chemical dosimetry experienced by cells in vivo. Two types of in vitro to in vivo extrapolation (IVIVE) are needed. (1) For toxic effects involving systemic regulations, such as endocrine disruption, organism-level adverse outcome pathway (AOP) models are needed to extrapolate in vitro toxicity pathway perturbation to in vivo PoD. (2) Physiologically-based toxicokinetic (PBTK) modeling is needed to extrapolate in vitro PoD dose metrics into external doses for expected exposure scenarios. Linked PBTK and TD models can explore the parameter space to recapitulate human population variability in response to chemical insults. While challenges remain for applying these modeling tools to support in vitro toxicity testing, they open the door toward population-stratified and personalized risk assessment.
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Affiliation(s)
- Qiang Zhang
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Jin Li
- Unilever, Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, United Kingdom
| | - Alistair Middleton
- Unilever, Safety and Environmental Assurance Centre, Colworth Science Park, Sharnbrook, United Kingdom
| | - Sudin Bhattacharya
- Biomedical Engineering, Michigan State University, East Lansing, MI, United States
| | - Rory B Conolly
- Integrated Systems Toxicology Division, National Health and Environmental Effects Research Laboratory, United States Environmental Protection Agency, Durham, NC, United States
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Smith KA, Schumacker PT. Sensors and signals: the role of reactive oxygen species in hypoxic pulmonary vasoconstriction. J Physiol 2018; 597:1033-1043. [PMID: 30091476 DOI: 10.1113/jp275852] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 07/20/2018] [Indexed: 12/12/2022] Open
Abstract
When lung cells experience hypoxia, the functional response, termed hypoxic pulmonary vasoconstriction, activates a multitude of pathways with the goal of optimizing gas exchange. While previously controversial, overwhelming evidence now suggests that increased reactive oxygen species - produced at complex III of the mitochondrial electron transport chain and released into the intermembrane space - is the cellular oxygen signal responsible for triggering hypoxic pulmonary vasoconstriction. The increased reactive oxygen species (ROS) activate many downstream targets that ultimately lead to increased intracellular ionized calcium concentration and contraction of pulmonary arterial smooth muscle cells. While the specific targets of ROS signals are not completely understood, it is clear that this signalling pathway is critical for development and for normal lung function in newborns and adults.
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Affiliation(s)
- Kimberly A Smith
- Department of Pediatrics, Division of Neonatology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Paul T Schumacker
- Department of Pediatrics, Division of Neonatology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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43
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Bogen KT. Biphasic hCAR Inhibition-Activation by Two Aminoazo Liver Carcinogens. NUCLEAR RECEPTOR RESEARCH 2018. [DOI: 10.11131/2018/101321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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Poellmann MJ, Lee RC. Repair and Regeneration of the Wounded Cell Membrane. REGENERATIVE ENGINEERING AND TRANSLATIONAL MEDICINE 2017. [DOI: 10.1007/s40883-017-0031-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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45
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Abstract
Kelch-like ECH-associated protein 1 (Keap1), nuclear factor erythroid 2-like factor 2-related factor 2 (Nrf2), and the antioxidant response element (ARE) are interacting components of a master regulatory signaling pathway that coordinates redox homeostasis, cytoprotective responses, and shifts in stem cell state. This study reexamined detailed dose–response (DR) data reported for in vitro Nrf2-ARE activation in human hepatoblastoma HepG2 cell lines containing either a ARE-bla or ARE-luc reporter at 12 different concentrations of each of 15 chemicals. The normalized study data were combined among chemicals exhibiting a positive response, yielding n = 531 (179) DR data for 9 (7) chemicals using the ARE-bla (ARE-luc) assay. Three-parameter linear/kth-power regression fits obtained to each combined set of ARE-bla- or ARE-luc-assay response data provided good fits (R2 = .99 or .91, respectively, Pfit > .99) that each incorporate a highly significant negative initial linear slope (P = 4 × 10−5 or .00025) and an overall J-shaped DR pattern. Results from this reanalysis of high-resolution ARE response data support the hypothesis that nonlinear ARE-mediated adaptive cellular responses to oxidative stress are governed by an ultrasensitive molecular switch.
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McMullen PD, Pendse S, Adeleye Y, Carmichael PL, Andersen ME, Clewell RA. Using Transcriptomics to Evaluate Thresholds in Genotoxicity Dose–Response. TOXICOGENOMICS IN PREDICTIVE CARCINOGENICITY 2016. [DOI: 10.1039/9781782624059-00185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Several genotoxic chemicals have been reported to produce threshold-shaped dose–response curves for mutation and genotoxicity assays, both in vivo and in vitro, challenging the current default practice for risk assessment of genotoxic chemicals, which assumes a linear dose–response below the lowest tested dose. Statistical methods cannot determine whether a biological threshold exists with sufficient confidence to overturn this assumption of linearity. Indeed, to truly define the shape of the dose–response curves, we must look to the underlying biology and develop targeted experiments to identify and measure the key processes governing the response of the cell to DNA damage. This chapter describes a series of studies aimed at defining the key transcriptional responses. Two approaches were taken to evaluate transcriptional responses preventing micronucleus induction: (1) comparison of gene signatures for several prototype compounds at a single chemical dose that led to a similar activation of the p53-DNA damage pathway (i.e. 1.5-fold increase in total p53); and (2) evaluation of a subset of chemicals with in-depth dose–response studies. The goal of these efforts was to determine the transcriptional pathways responsible for maintaining homeostasis at low levels of DNA damage, i.e., the biological underpinning of threshold-shaped dose–response curves for mutagenicity.
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Affiliation(s)
| | - Salil Pendse
- The Hamner Institutes for Health Sciences Research Triangle Park NC USA
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Lutein acts via multiple antioxidant pathways in the photo-stressed retina. Sci Rep 2016; 6:30226. [PMID: 27444056 PMCID: PMC4957151 DOI: 10.1038/srep30226] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 07/01/2016] [Indexed: 11/08/2022] Open
Abstract
Lutein slows the progression of age-related macular degeneration (AMD), a leading cause of blindness in ageing societies. However, the underlying mechanisms remain elusive. Here, we evaluated lutein's effects on light-induced AMD-related pathological events. Balb/c mice exposed to light (2000 lux, 3 h) showed tight junction disruption in the retinal pigment epithelium (RPE) at 12 h, as detected by zona occludens-1 immunostaining. Substantial disruption remained 48 h after light exposure in the vehicle-treated group; however, this was ameliorated in the mice treated with intraperitoneal lutein at 12 h, suggesting that lutein promoted tight junction repair. In the photo-stressed RPE and the neighbouring choroid tissue, lutein suppressed reactive oxygen species and increased superoxide dismutase (SOD) activity at 24 h, and produced sustained increases in sod1 and sod2 mRNA levels at 48 h. SOD activity was induced by lutein in an RPE cell line, ARPE19. We also found that lutein suppressed upregulation of macrophage-related markers, f4/80 and mcp-1, in the RPE-choroid tissue at 18 h. In ARPE19, lutein reduced mcp-1 mRNA levels. These findings indicated that lutein promoted tight junction repair and suppressed inflammation in photo-stressed mice, reducing local oxidative stress by direct scavenging and most likely by induction of endogenous antioxidant enzymes.
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48
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Clewell RA, Andersen ME. Approaches for characterizing threshold dose-response relationships for DNA-damage pathways involved in carcinogenicity in vivo and micronuclei formation in vitro. Mutagenesis 2016; 31:333-40. [PMID: 26846943 DOI: 10.1093/mutage/gev078] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Assessing the shape of dose-response curves for DNA-damage in cellular systems and for the consequences of DNA damage in intact animals remains a controversial topic. This overview looks at aspects of the pharmacokinetics (PK) and pharmacodynamics (PD) of cellular DNA-damage/repair and their role in defining the shape of dose-response curves using an in vivo example with formaldehyde and in vitro examples for micronuclei (MN) formation with several test compounds. Formaldehyde is both strongly mutagenic and an endogenous metabolite in cells. With increasing inhaled concentrations, there were transitions in gene changes, from activation of selective stress pathway genes at low concentrations, to activation of pathways for cell-cycle control, p53-DNA damage, and stem cell niche pathways at higher exposures. These gene expression changes were more consistent with dose-dependent transitions in the PD responses to formaldehyde in epithelial cells in the intact rat rather than the low-dose linear extrapolation methods currently used for carcinogens. However, more complete PD explanations of non-linear dose response for creation of fixed damage in cells require detailed examination of cellular responses in vitro using measures of DNA damage and repair that are not easily accessible in the intact animal. In the second section of the article, we illustrate an approach from our laboratory that develops fit-for-purpose, in vitro assays and evaluates the PD of DNA damage and repair through studies using prototypical DNA-damaging agents. Examination of a broad range of responses in these cells showed that transcriptional upregulation of cell cycle control and DNA repair pathways only occurred at doses higher than those causing overt damage fixed damage-measured as MN formation. Lower levels of damage appear to be handled by post-translational repair process using pre-existing proteins. In depth evaluation of the PD properties of one such post-translational process (formation of DNA repair centers; DRCs) has indicated that the formation of DRCs and their ability to complete repair before replication are consistent with threshold behaviours for mutagenesis and, by extension, with chemical carcinogenesis.
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Affiliation(s)
- Rebecca A Clewell
- The Hamner Institutes for Health Sciences, Research Triangle Park, NC 27709-2137 , USA
| | - Melvin E Andersen
- The Hamner Institutes for Health Sciences, Research Triangle Park, NC 27709-2137 , USA
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49
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Yuan H, Zhang Q, Guo J, Zhang T, Zhao J, Li J, White A, Carmichael PL, Westmoreland C, Peng S. A PGC-1α-Mediated Transcriptional Network Maintains Mitochondrial Redox and Bioenergetic Homeostasis against Doxorubicin-Induced Toxicity in Human Cardiomyocytes: Implementation of TT21C. Toxicol Sci 2016; 150:400-17. [PMID: 26781513 DOI: 10.1093/toxsci/kfw006] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Chemical toxicity testing is fast moving in a direction that relies increasingly on cell-basedin vitroassays anchored on toxicity pathways according to the toxicity testing in the 21st century vision. Identifying points of departure (POD) via these assays and revealing their mechanistic underpinnings via computational modeling of the relevant pathways are critical and challenging steps. Here we used doxorubicin (DOX) as a prototype chemical to study mitochondrial toxicity in human AC16 cells. Mitochondrial toxicity has been linked to cardiovascular risk of DOX, which has limited its clinical use as an antitumor drug. Ourin vitrostudy revealed a well-defined POD concentration of DOX below which adaptive induction of proliferator-activated receptor-γ coactivator-1α (PGC-1α) -mediated mitochondrial genes, including NRF-1, MnSOD, UCP2, and COX1, concurred with negligible changes in mitochondrial superoxide and cytotoxicity. At higher DOX concentrations adversity became significant with elevated superoxide and suppressed ATP levels. A computational model was formulated to simulate the PGC-1α-mediated transcriptional network comprising multiple negative feedback loops that underlie redox and bioenergetics homeostasis in the mitochondrion. The model recapitulated the transition phase from adaptive to adverse responses, supporting the notion that saturated induction of PGC-1α-mediated gene network underpins POD. The model further predicts (follow-up experiments verified) that silencing PGC-1α compromises the adaptive function of the transcriptional network, leading to disruption of mitochondria and cytotoxicity at lower DOX concentrations. In summary, our study demonstrates that combining pathway-focusedin vitroassays and computational simulation of relevant biochemical network is synergistic for understanding dose-response behaviors in the low-dose region and identifying POD.
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Affiliation(s)
- Haitao Yuan
- *Evaluation and Research Centre for Toxicology, Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, China;
| | - Qiang Zhang
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA; and
| | - Jiabin Guo
- *Evaluation and Research Centre for Toxicology, Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, China
| | - Tingfen Zhang
- *Evaluation and Research Centre for Toxicology, Institute of Disease Control and Prevention, Academy of Military Medical Sciences, Beijing 100071, China
| | - Jun Zhao
- *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 Center, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK
| | - Andrew White
- Unilever Safety and Environmental Assurance Center, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK
| | - Paul L Carmichael
- Unilever Safety and Environmental Assurance Center, Colworth Science Park, Sharnbrook, Bedfordshire MK44 1LQ, UK
| | - Carl Westmoreland
- Unilever Safety and Environmental Assurance Center, 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;
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50
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Clewell RA, McMullen PD, Adeleye Y, Carmichael PL, Andersen ME. Pathway Based Toxicology and Fit-for-Purpose Assays. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 856:205-230. [DOI: 10.1007/978-3-319-33826-2_8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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