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Nguyen NHA, Falagan-Lotsch P. Mechanistic Insights into the Biological Effects of Engineered Nanomaterials: A Focus on Gold Nanoparticles. Int J Mol Sci 2023; 24:ijms24044109. [PMID: 36835521 PMCID: PMC9963226 DOI: 10.3390/ijms24044109] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 02/10/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Nanotechnology has great potential to significantly advance the biomedical field for the benefit of human health. However, the limited understanding of nano-bio interactions leading to unknowns about the potential adverse health effects of engineered nanomaterials and to the poor efficacy of nanomedicines has hindered their use and commercialization. This is well evidenced considering gold nanoparticles, one of the most promising nanomaterials for biomedical applications. Thus, a fundamental understanding of nano-bio interactions is of interest to nanotoxicology and nanomedicine, enabling the development of safe-by-design nanomaterials and improving the efficacy of nanomedicines. In this review, we introduce the advanced approaches currently applied in nano-bio interaction studies-omics and systems toxicology-to provide insights into the biological effects of nanomaterials at the molecular level. We highlight the use of omics and systems toxicology studies focusing on the assessment of the mechanisms underlying the in vitro biological responses to gold nanoparticles. First, the great potential of gold-based nanoplatforms to improve healthcare along with the main challenges for their clinical translation are presented. We then discuss the current limitations in the translation of omics data to support risk assessment of engineered nanomaterials.
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Affiliation(s)
- Nhung H. A. Nguyen
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec (TUL), Studentsk. 2, 46117 Liberec, Czech Republic
| | - Priscila Falagan-Lotsch
- Department of Biological Sciences, College of Sciences and Mathematics, Auburn University, Auburn, AL 36849, USA
- Correspondence:
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2
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Han J, Tian Y, Wang M, Li Y, Yin J, Qu W, Yan C, Ding R, Guan Y, Wang Q. Proteomics unite traditional toxicological assessment methods to evaluate the toxicity of iron oxide nanoparticles. Front Pharmacol 2022; 13:1011065. [PMID: 36172182 PMCID: PMC9512491 DOI: 10.3389/fphar.2022.1011065] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 08/22/2022] [Indexed: 11/23/2022] Open
Abstract
Iron oxide nanoparticles (IONPs) are the first generation of nanomaterials approved by the Food and Drug Administration for use as imaging agents and for the treatment of iron deficiency in chronic kidney disease. However, several IONPs-based imaging agents have been withdrawn because of toxic effects and the poor understanding of the underlying mechanisms. This study aimed to evaluate IONPs toxicity and to elucidate the underlying mechanism after intravenous administration in rats. Seven-week-old rats were intravenously administered IONPs at doses of 0, 10, 30, and 90 mg/kg body weight for 14 consecutive days. Toxicity and molecular perturbations were evaluated using traditional toxicological assessment methods and proteomics approaches, respectively. The administration of 90 mg/kg IONPs induced mild toxic effects, including abnormal clinical signs, lower body weight gain, changes in serum biochemical and hematological parameters, and increased organ coefficients in the spleen, liver, heart, and kidneys. Toxicokinetics, tissue distribution, histopathological, and transmission electron microscopy analyses revealed that the spleen was the primary organ for IONPs elimination from the systemic circulation and that the macrophage lysosomes were the main organelles of IONPs accumulation after intravenous administration. We identified 197 upregulated and 75 downregulated proteins in the spleen following IONPs administration by proteomics. Mechanically, the AKT/mTOR/TFEB signaling pathway facilitated autophagy and lysosomal activation in splenic macrophages. This is the first study to elucidate the mechanism of IONPs toxicity by combining proteomics with traditional methods for toxicity assessment.
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Analysis of Nanotoxicity with Integrated Omics and Mechanobiology. NANOMATERIALS 2021; 11:nano11092385. [PMID: 34578701 PMCID: PMC8470953 DOI: 10.3390/nano11092385] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/06/2021] [Accepted: 09/09/2021] [Indexed: 12/13/2022]
Abstract
Nanoparticles (NPs) in biomedical applications have benefits owing to their small size. However, their intricate and sensitive nature makes an evaluation of the adverse effects of NPs on health necessary and challenging. Since there are limitations to conventional toxicological methods and omics analyses provide a more comprehensive molecular profiling of multifactorial biological systems, omics approaches are necessary to evaluate nanotoxicity. Compared to a single omics layer, integrated omics across multiple omics layers provides more sensitive and comprehensive details on NP-induced toxicity based on network integration analysis. As multi-omics data are heterogeneous and massive, computational methods such as machine learning (ML) have been applied for investigating correlation among each omics. This integration of omics and ML approaches will be helpful for analyzing nanotoxicity. To that end, mechanobiology has been applied for evaluating the biophysical changes in NPs by measuring the traction force and rigidity sensing in NP-treated cells using a sub-elastomeric pillar. Therefore, integrated omics approaches are suitable for elucidating mechanobiological effects exerted by NPs. These technologies will be valuable for expanding the safety evaluations of NPs. Here, we review the integration of omics, ML, and mechanobiology for evaluating nanotoxicity.
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Chen Y, Alba M, Tieu T, Tong Z, Minhas RS, Rudd D, Voelcker NH, Cifuentes-Rius A, Elnathan R. Engineering Micro–Nanomaterials for Biomedical Translation. ADVANCED NANOBIOMED RESEARCH 2021. [DOI: 10.1002/anbr.202100002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Yaping Chen
- Monash Institute of Pharmaceutical Sciences Monash University 381 Royal Parade Parkville VIC 3052 Australia
- Melbourne Centre for Nanofabrication Victorian Node of the Australian National Fabrication Facility 151 Wellington Road Clayton VIC 3168 Australia
| | - Maria Alba
- Monash Institute of Pharmaceutical Sciences Monash University 381 Royal Parade Parkville VIC 3052 Australia
- Melbourne Centre for Nanofabrication Victorian Node of the Australian National Fabrication Facility 151 Wellington Road Clayton VIC 3168 Australia
| | - Terence Tieu
- Monash Institute of Pharmaceutical Sciences Monash University 381 Royal Parade Parkville VIC 3052 Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Manufacturing Commonwealth Scientific and Industrial Research Organisation (CSIRO) Clayton VIC 3168 Australia
| | - Ziqiu Tong
- Monash Institute of Pharmaceutical Sciences Monash University 381 Royal Parade Parkville VIC 3052 Australia
| | - Rajpreet Singh Minhas
- Monash Institute of Pharmaceutical Sciences Monash University 381 Royal Parade Parkville VIC 3052 Australia
- Melbourne Centre for Nanofabrication Victorian Node of the Australian National Fabrication Facility 151 Wellington Road Clayton VIC 3168 Australia
| | - David Rudd
- Monash Institute of Pharmaceutical Sciences Monash University 381 Royal Parade Parkville VIC 3052 Australia
- Melbourne Centre for Nanofabrication Victorian Node of the Australian National Fabrication Facility 151 Wellington Road Clayton VIC 3168 Australia
| | - Nicolas H. Voelcker
- Monash Institute of Pharmaceutical Sciences Monash University 381 Royal Parade Parkville VIC 3052 Australia
- Melbourne Centre for Nanofabrication Victorian Node of the Australian National Fabrication Facility 151 Wellington Road Clayton VIC 3168 Australia
- Department of Materials Science and Engineering Monash University 22 Alliance Lane Clayton VIC 3168 Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Manufacturing Commonwealth Scientific and Industrial Research Organisation (CSIRO) Clayton VIC 3168 Australia
- INM-Leibniz Institute for New Materials Campus D2 2 Saarbrücken 66123 Germany
| | - Anna Cifuentes-Rius
- Monash Institute of Pharmaceutical Sciences Monash University 381 Royal Parade Parkville VIC 3052 Australia
| | - Roey Elnathan
- Monash Institute of Pharmaceutical Sciences Monash University 381 Royal Parade Parkville VIC 3052 Australia
- Melbourne Centre for Nanofabrication Victorian Node of the Australian National Fabrication Facility 151 Wellington Road Clayton VIC 3168 Australia
- Department of Materials Science and Engineering Monash University 22 Alliance Lane Clayton VIC 3168 Australia
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5
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Holmila R, Wu H, Lee J, Tsang AW, Singh R, Furdui CM. Integrated Redox Proteomic Analysis Highlights New Mechanisms of Sensitivity to Silver Nanoparticles. Mol Cell Proteomics 2021; 20:100073. [PMID: 33757833 PMCID: PMC8724861 DOI: 10.1016/j.mcpro.2021.100073] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 03/17/2021] [Indexed: 02/07/2023] Open
Abstract
Silver nanoparticles (AgNPs) are widely used nanomaterials in both commercial and clinical biomedical applications, but the molecular mechanisms underlying their activity remain elusive. In this study we profiled proteomics and redox proteomics changes induced by AgNPs in two lung cancer cell lines: AgNPs-sensitive Calu-1 and AgNPs-resistant NCI-H358. We show that AgNPs induce changes in protein abundance and reversible oxidation in a time and cell-line-dependent manner impacting critical cellular processes such as protein translation and modification, lipid metabolism, bioenergetics, and mitochondrial dynamics. Supporting confocal microscopy and transmission electron microscopy (TEM) data further emphasize mitochondria as a target of AgNPs toxicity differentially impacting mitochondrial networks and morphology in Calu-1 and NCI-H358 lung cells. Proteomics data are available via ProteomeXchange with identifier PXD021493. AgNP-sensitive cells experience broader changes in protein abundance. Redox proteomics reveals increased reversible oxidation in AgNP-sensitive cells. AgNPs alter protein translation, lipid metabolism, and bioenergetics. Mitochondria is identified as key target underlying AgNP toxicity.
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Affiliation(s)
- Reetta Holmila
- Section on Molecular Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Hanzhi Wu
- Section on Molecular Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA; Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, North Carolina, USA
| | - Jingyun Lee
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, North Carolina, USA
| | - Allen W Tsang
- Section on Molecular Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA; Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, North Carolina, USA; Center for Redox Biology and Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Ravi Singh
- Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, North Carolina, USA; Center for Redox Biology and Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA; Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Cristina M Furdui
- Section on Molecular Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA; Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, North Carolina, USA; Center for Redox Biology and Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA.
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Karkossa I, Raps S, von Bergen M, Schubert K. Systematic Review of Multi-Omics Approaches to Investigate Toxicological Effects in Macrophages. Int J Mol Sci 2020; 21:E9371. [PMID: 33317022 PMCID: PMC7764599 DOI: 10.3390/ijms21249371] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/26/2020] [Accepted: 12/04/2020] [Indexed: 12/19/2022] Open
Abstract
Insights into the modes of action (MoAs) of xenobiotics are of utmost importance for the definition of adverse outcome pathways (AOPs), which are essential for a mechanism-based risk assessment. A well-established strategy to reveal MoAs of xenobiotics is the use of omics. However, often an even more comprehensive approach is needed, which can be achieved using multi-omics. Since the immune system plays a central role in the defense against foreign substances and pathogens, with the innate immune system building a first barrier, we systematically reviewed multi-omics studies investigating the effects of xenobiotics on macrophages. Surprisingly, only nine publications were identified, combining proteomics with transcriptomics or metabolomics. We summarized pathways and single proteins, transcripts, or metabolites, which were described to be affected upon treatment with xenobiotics in the reviewed studies, thus revealing a broad range of effects. In summary, we show that macrophages are a relevant model system to investigate the toxicological effects induced by xenobiotics. Furthermore, the multi-omics approaches led to a more comprehensive overview compared to only one omics layer with slight advantages for combinations that complement each other directly, e.g., proteome and metabolome.
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Affiliation(s)
- Isabel Karkossa
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research—UFZ, 04318 Leipzig, Germany; (I.K.); (S.R.); (M.v.B.)
| | - Stefanie Raps
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research—UFZ, 04318 Leipzig, Germany; (I.K.); (S.R.); (M.v.B.)
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research—UFZ, 04318 Leipzig, Germany; (I.K.); (S.R.); (M.v.B.)
- Institute of Biochemistry, Leipzig University, 04103 Leipzig, Germany
| | - Kristin Schubert
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research—UFZ, 04318 Leipzig, Germany; (I.K.); (S.R.); (M.v.B.)
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7
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Zhang T, Gaffrey MJ, Li X, Qian WJ. Characterization of cellular oxidative stress response by stoichiometric redox proteomics. Am J Physiol Cell Physiol 2020; 320:C182-C194. [PMID: 33264075 DOI: 10.1152/ajpcell.00040.2020] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The thiol redox proteome refers to all proteins whose cysteine thiols are subjected to various redox-dependent posttranslational modifications (PTMs) including S-glutathionylation (SSG), S-nitrosylation (SNO), S-sulfenylation (SOH), and S-sulfhydration (SSH). These modifications can impact various aspects of protein function such as activity, binding, conformation, localization, and interactions with other molecules. To identify novel redox proteins in signaling and regulation, it is highly desirable to have robust redox proteomics methods that can provide global, site-specific, and stoichiometric quantification of redox PTMs. Mass spectrometry (MS)-based redox proteomics has emerged as the primary platform for broad characterization of thiol PTMs in cells and tissues. Herein, we review recent advances in MS-based redox proteomics approaches for quantitative profiling of redox PTMs at physiological or oxidative stress conditions and highlight some recent applications. Considering the relative maturity of available methods, emphasis will be on two types of modifications: 1) total oxidation (i.e., all reversible thiol modifications), the level of which represents the overall redox state, and 2) S-glutathionylation, a major form of reversible thiol oxidation. We also discuss the significance of stoichiometric measurements of thiol PTMs as well as future perspectives toward a better understanding of cellular redox regulatory networks in cells and tissues.
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Affiliation(s)
- Tong Zhang
- Integrative Omics, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Matthew J Gaffrey
- Integrative Omics, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
| | - Xiaolu Li
- Integrative Omics, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington.,Bioproducts Sciences and Engineering Laboratory, Department of Biological Systems Engineering, Washington State University, Richland, Washington
| | - Wei-Jun Qian
- Integrative Omics, Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington
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8
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Xiang QQ, Gao Y, Li QQ, Ling J, Chen LQ. Proteomic profiling reveals the differential toxic responses of gills of common carp exposed to nanosilver and silver nitrate. JOURNAL OF HAZARDOUS MATERIALS 2020; 394:122562. [PMID: 32213387 DOI: 10.1016/j.jhazmat.2020.122562] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 03/13/2020] [Accepted: 03/16/2020] [Indexed: 06/10/2023]
Abstract
Although the toxic effects of silver nanoparticles (AgNPs) on fish gills have been reported, the underlying mechanism of toxicity remains unclear. The present study aimed to elucidate the mechanism of toxicity in the gills of common carp following exposure to AgNPs and silver nitrate (AgNO3) using histopathology and proteomics. Histopathological findings revealed that both AgNPs and AgNO3 caused telangiectasia and epithelial cell hyperplasia in fish gills; however, the pathological features and location of lesions caused by the two forms of silver were markedly different. Proteomics revealed that AgNPs and AgNO3 induced 139 and 185 differential expression proteins (DEPs) in gills, respectively, and the two forms of silver induced only 42 shared proteins. AgNPs specifically induced 87 DEPs which mainly involved signaling mechanisms, cytoskeleton, and the arachidonic acid metabolism processes. AgNO3 specifically induced 125 DEPs that were mainly clustered in the glutathione metabolism and protease processes. These results suggested that the toxic effects of AgNPs and AgNO3 were dramatically different in terms of protein expression in fish gills, which may provide novel perspectives for understanding the toxicity mechanism of silver nanoparticles in fish gills.
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Affiliation(s)
- Qian-Qian Xiang
- Instititue of International Rivers and Eco-security, Yunnan Key Laboratory of International Rivers and Trans-Boundary Eco-security, Yunnan University, Kunming, 650091, People's Republic of China; Yunnan International Joint Research Center for Hydro-Ecology Science & Engineering, Yunnan University, Kunming, 650091, People's Republic of China
| | - Ying Gao
- Instititue of International Rivers and Eco-security, Yunnan Key Laboratory of International Rivers and Trans-Boundary Eco-security, Yunnan University, Kunming, 650091, People's Republic of China; Yunnan International Joint Research Center for Hydro-Ecology Science & Engineering, Yunnan University, Kunming, 650091, People's Republic of China
| | - Qin-Qin Li
- Instititue of International Rivers and Eco-security, Yunnan Key Laboratory of International Rivers and Trans-Boundary Eco-security, Yunnan University, Kunming, 650091, People's Republic of China; Yunnan International Joint Research Center for Hydro-Ecology Science & Engineering, Yunnan University, Kunming, 650091, People's Republic of China
| | - Jian Ling
- College of Chemical Science and Technology, Yunnan University, Kunming, 650091, People's Republic of China
| | - Li-Qiang Chen
- Instititue of International Rivers and Eco-security, Yunnan Key Laboratory of International Rivers and Trans-Boundary Eco-security, Yunnan University, Kunming, 650091, People's Republic of China; Yunnan International Joint Research Center for Hydro-Ecology Science & Engineering, Yunnan University, Kunming, 650091, People's Republic of China.
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9
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Zheng F, Gonçalves FM, Abiko Y, Li H, Kumagai Y, Aschner M. Redox toxicology of environmental chemicals causing oxidative stress. Redox Biol 2020; 34:101475. [PMID: 32336668 PMCID: PMC7327986 DOI: 10.1016/j.redox.2020.101475] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/18/2020] [Accepted: 02/20/2020] [Indexed: 12/17/2022] Open
Abstract
Living organisms are surrounded with heavy metals such as methylmercury, manganese, cobalt, cadmium, arsenic, as well as pesticides such as deltamethrin and paraquat, or atmospheric pollutants such as quinone. Extensive studies have demonstrated a strong link between environmental pollutants and human health. Redox toxicity is proposed as one of the main mechanisms of chemical-induced pathology in humans. Acting as both a sensor of oxidative stress and a positive regulator of antioxidants, the nuclear factor erythroid 2-related factor 2 (NRF2) has attracted recent attention. However, the role NRF2 plays in environmental pollutant-induced toxicity has not been systematically addressed. Here, we characterize NRF2 function in response to various pollutants, such as metals, pesticides and atmospheric quinones. NRF2 related signaling pathways and epigenetic regulations are also reviewed.
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Affiliation(s)
- Fuli Zheng
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, Fujian, 350122, China; Department of Molecular Pharmacology, Albert Einstein College of Medicine, Forchheimer 209, 1300 Morris Park Avenue, Bronx, NY, 10461, United States.
| | - Filipe Marques Gonçalves
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Forchheimer 209, 1300 Morris Park Avenue, Bronx, NY, 10461, United States
| | - Yumi Abiko
- Environmental Biology Laboratory, Faculty of Medicine, University of Tsukuba, Tsukuba, 305-8575, Japan
| | - Huangyuan Li
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou, Fujian, 350122, China.
| | - Yoshito Kumagai
- Environmental Biology Laboratory, Faculty of Medicine, University of Tsukuba, Tsukuba, 305-8575, Japan.
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Forchheimer 209, 1300 Morris Park Avenue, Bronx, NY, 10461, United States.
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Gallo V, Srivastava V, Bulone V, Zappettini A, Villani M, Marmiroli N, Marmiroli M. Proteomic Analysis Identifies Markers of Exposure to Cadmium Sulphide Quantum Dots (CdS QDs). NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E1214. [PMID: 32580447 PMCID: PMC7353101 DOI: 10.3390/nano10061214] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/10/2020] [Accepted: 06/17/2020] [Indexed: 12/11/2022]
Abstract
The use of cadmium sulphide quantum dot (CdS QD)-enabled products has become increasingly widespread. The prospect of their release in the environment is raising concerns. Here we have used the yeast model Saccharomyces cerevisiae to determine the potential impact of CdS QD nanoparticles on living organisms. Proteomic analyses and cell viability assays performed after 9 h exposure revealed expression of proteins involved in oxidative stress and reduced lethality, respectively, whereas oxidative stress declined, and lethality increased after 24 h incubation in the presence of CdS QDs. Quantitative proteomics using the iTRAQ approach (isobaric tags for relative and absolute quantitation) revealed that key proteins involved in essential biological pathways were differentially regulated over the time course of the experiment. At 9 h, most of the glycolytic functions increased, and the abundance of the number of heat shock proteins increased. This contrasts with the situation at 24 h where glycolytic functions, some heat shock proteins as well as oxidative phosphorylation and ATP synthesis were down-regulated. It can be concluded from our data that cell exposure to CdS QDs provokes a metabolic shift from respiration to fermentation, comparable to the situation reported in some cancer cell lines.
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Affiliation(s)
- Valentina Gallo
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43123 Parma, Italy; (V.G.); (N.M.)
| | - Vaibhav Srivastava
- Royal Institute of Technology (KTH), Department of Chemistry, Division of Glycoscience, School of Engineering Sciences in Chemistry, Biotechnology and Health, AlbaNova University Center, SE-106 91 Stockholm, Sweden; (V.S.); (V.B.)
| | - Vincent Bulone
- Royal Institute of Technology (KTH), Department of Chemistry, Division of Glycoscience, School of Engineering Sciences in Chemistry, Biotechnology and Health, AlbaNova University Center, SE-106 91 Stockholm, Sweden; (V.S.); (V.B.)
- ARC Centre of Excellence in Plant Cell Walls and School of Agriculture, Food and Wine, The University of Adelaide, Urbrae, SA 5064, Australia
| | - Andrea Zappettini
- Department of Nanomaterials, Institute of Materials for Electronics and Magnetism (IMEM)Department of Nanomaterials, National Research Council (CNR), 43124 Parma, Italy; (A.Z.); (M.V.)
| | - Marco Villani
- Department of Nanomaterials, Institute of Materials for Electronics and Magnetism (IMEM)Department of Nanomaterials, National Research Council (CNR), 43124 Parma, Italy; (A.Z.); (M.V.)
| | - Nelson Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43123 Parma, Italy; (V.G.); (N.M.)
- The Italian National Interuniversity Consortium for Environmental Sciences (CINSA), 43124 Parma, Italy
| | - Marta Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43123 Parma, Italy; (V.G.); (N.M.)
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11
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Zhang T, Gaffrey MJ, Monroe ME, Thomas DG, Weitz KK, Piehowski PD, Petyuk VA, Moore RJ, Thrall BD, Qian WJ. Block Design with Common Reference Samples Enables Robust Large-Scale Label-Free Quantitative Proteome Profiling. J Proteome Res 2020; 19:2863-2872. [PMID: 32407631 DOI: 10.1021/acs.jproteome.0c00310] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Label-free quantitative proteomics has become an increasingly popular tool for profiling global protein abundances. However, one major limitation is the potential performance drift of the LC-MS platform over time, which, in turn, limits its utility for analyzing large-scale sample sets. To address this, we introduce an experimental and data analysis scheme based on a block design with common references within each block for enabling large-scale label-free quantification. In this scheme, a large number of samples (e.g., >100 samples) are analyzed in smaller and more manageable blocks, minimizing instrument drift and variability within individual blocks. Each designated block also contains common reference samples (e.g., controls) for normalization across all blocks. We demonstrated the robustness of this approach by profiling the proteome response of human macrophage THP-1 cells to 11 engineered nanomaterials at two different doses. A total of 116 samples were analyzed in six blocks, yielding an average coverage of 4500 proteins per sample. Following a common reference-based correction, 2537 proteins were quantified with high reproducibility without any imputation of missing values from 116 data sets. The data revealed the consistent quantification of proteins across all six blocks, as illustrated by the highly consistent abundances of house-keeping proteins in all samples and the high levels of correlation among samples from different blocks. The data also demonstrated that label-free quantification is robust and accurate enough to quantify even very subtle abundance changes as well as large fold-changes. Our streamlined workflow is easy to implement and can be readily adapted to other large cohort studies for reproducible label-free proteome quantification.
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Affiliation(s)
- Tong Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Matthew J Gaffrey
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Matthew E Monroe
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Dennis G Thomas
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Karl K Weitz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Paul D Piehowski
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Brian D Thrall
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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12
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13
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Zhang T, Gaffrey MJ, Thomas DG, Weber TJ, Hess BM, Weitz KK, Piehowski PD, Petyuk VA, Moore RJ, Qian WJ, Thrall BD. A proteome-wide assessment of the oxidative stress paradigm for metal and metal-oxide nanomaterials in human macrophages. NANOIMPACT 2020; 17:100194. [PMID: 32133426 PMCID: PMC7055704 DOI: 10.1016/j.impact.2019.100194] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Responsible implementation of engineered nanomaterials (ENMs) into commercial applications is an important societal issue, driving demand for new approaches for rapid and comprehensive evaluation of their bioactivity and safety. An essential part of any research focused on identifying potential hazards of ENMs is the appropriate selection of biological endpoints to evaluate. Herein, we use a tiered strategy employing both targeted biological assays and untargeted quantitative proteomics to elucidate the biological responses of human THP-1 derived macrophages across a library of metal/metal oxide ENMs, raised as priority ENMs for investigation by NIEHS's Nanomaterial Health Implications Research (NHIR) program. Our results show that quantitative cellular proteome profiles readily distinguish ENM types based on their cytotoxic potential according to induction of biological processes and pathways involved in the cellular antioxidant response, TCA cycle, oxidative stress, endoplasmic reticulum stress, and immune responses as major processes impacted. Interestingly, bioinformatics analysis of differentially expressed proteins also revealed new biological processes that were influenced by all ENMs independent of their cytotoxic potential. These included biological processes that were previously implicated as mechanisms cells employ as adaptive responses to low levels of oxidative stress, including cell adhesion, protein translation and protein targeting. Unsupervised clustering revealed the most striking proteome changes that differentiated ENM classes highlight a small subset of proteins involved in the oxidative stress response (HMOX1), protein chaperone functions (HS71B, DNJB1), and autophagy (SQSTM), providing a potential new panel of markers of ENM-induced cellular stress. To our knowledge, the results represent the most comprehensive profiling of the biological responses to a library of ENMs conducted using quantitative mass spectrometry-based proteomics. The results provide a basis to identify the patterns of a diverse set of cellular pathways and biological processes impacted by ENM exposure in an important immune cell type, laying the foundation for multivariate, pathway-level structure activity assessments of ENMs in the future.
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Affiliation(s)
- Tong Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA 99352
| | - Matthew J Gaffrey
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA 99352
| | - Dennis G Thomas
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA 99352
| | - Thomas J Weber
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA 99352
| | - Becky M Hess
- Signatures Sciences and Technology Division, Pacific Northwest National Laboratory, Richland, WA 99352
| | - Karl K Weitz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA 99352
| | - Paul D Piehowski
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA 99352
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA 99352
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA 99352
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA 99352
| | - Brian D Thrall
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland WA 99352
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Cao X, Zhang T, DeLoid GM, Gaffrey MJ, Weitz KK, Thrall BD, Qian WJ, Demokritou P. Evaluation of the cytotoxic and cellular proteome impacts of food-grade TiO 2 (E171) using simulated gastrointestinal digestions and a tri-culture small intestinal epithelial model. NANOIMPACT 2020; 17:10.1016/j.impact.2019.100202. [PMID: 32133427 PMCID: PMC7055729 DOI: 10.1016/j.impact.2019.100202] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Engineered nanomaterials (ENMs) are widely used in the food industry; however, regulations for ENMs in food are still in the early stages of development due to insufficient health data. This study investigated the cytotoxicity and changes to the proteomic profile in an in vitro small intestinal epithelium model after exposure to digested food models containing the ubiquitous engineered particulate food additive, TiO2 (E171) with an average size around 110 nm. TiO2 at 0.75% or 1.5% (w/w) concentrations in either a fasting food model (FFM) or a standardized food model (SFM) based on American diet were digested using an in vitro oral-gastric-small intestinal simulator, and the resulting digestas were applied to a small intestinal epithelium tri-culture cellular model. Effects on cell layer integrity, cytotoxicity, and oxidative stress were assessed. In order to explore the impact on cellular processes beyond basic cytotoxicity, mass spectrometry-based quantitative proteomic analyses of control and exposed tri-culture cells was performed. TiO2 in FFM, but not in SFM, produced significant, dose-dependent cytotoxicity (24%, p<0.001), and at the higher dose caused significant oxidative stress (1.24-fold, p<0.01), indicative of a food matrix effect. No significant perturbations of the cellular proteome were observed with TiO2 in either FFM or SFM food models. However, proteins involved in energy metabolism and protein synthesis were up-regulated by digestas from SFM compared to those from FFM, indicative of a food matrix effect on the cellular proteome. Interestingly, the differences in profiles between the two food models was more pronounced in the presence of TiO2. Together, these results indicate that TiO2 in a fasting diet may be slightly cytotoxic, and that ingested TiO2 does not significantly alter the epithelial proteome, whereas the food matrix alone can have a dramatic effect on the proteome.
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Affiliation(s)
- Xiaoqiong Cao
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Tong Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Glen M. DeLoid
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Matthew J Gaffrey
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Karl K. Weitz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Brian D. Thrall
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
- corresponding authors Philip Demokritou, , Wei-Jun Qian,
| | - Philip Demokritou
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
- corresponding authors Philip Demokritou, , Wei-Jun Qian,
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15
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Cui L, Wang X, Sun B, Xia T, Hu S. Predictive Metabolomic Signatures for Safety Assessment of Metal Oxide Nanoparticles. ACS NANO 2019; 13:13065-13082. [PMID: 31682760 DOI: 10.1021/acsnano.9b05793] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The widespread use of metal oxide nanoparticles (MOx NPs) poses a risk of exposure that may lead to adverse health effects on humans. Even though a number of toxicological methodologies are available for assessing nanotoxicity, the effect of MOx NPs on cell metabolism in vitro and in vivo remains largely unknown, especially under the exposure to low-dose or supposedly low-toxicity MOx NPs. In this study, liquid chromatography-mass spectrometry (LC-MS) based metabolomics was used to reveal significantly altered metabolites and metabolic pathways in human bronchial epithelial cells exposed to four different types of MOx NPs (ZnO, SiO2, TiO2, and CeO2) at both high (25 μg/mL) and low (12.5 μg/mL) doses. We demonstrated that high-dose ZnO NPs caused severe cytotoxicity with altered metabolism of amino acids, nucleotides, nucleosides, tricarboxylic acid cycle, lipids, inflammation/redox, and fatty acid oxidation, as well as the elevation of toxic and DNA damage related metabolites. Fewer metabolomic alterations were induced by low-dose ZnO NPs. However, most metabolites significantly altered by high-dose ZnO NPs were also slightly changed by low-dose ZnO NPs. On the other hand, the cells exposed to SiO2, TiO2, and CeO2 NPs at either high or low dose displayed low cytotoxicity with similar metabolomic alterations, although each type of NPs induced distinct changes of certain metabolites. These three NPs significantly affected the metabolic pathways of sphingosine-1-phosphate, fatty acid oxidation, folate cycle, inflammation/redox, and lipid metabolism. In addition, dose-dependent effects were observed for a number of metabolites significantly altered by respective MOx NPs. Representative metabolites of the significantly altered metabolic pathways were successfully validated in vitro using enzymatic assays. More importantly, these representative metabolites were further validated in a mouse model after lung exposure to respective NPs, indicating that in vitro metabolomic findings may be used to effectively predict the toxicological effects in vivo. Despite functional assay results demonstrating that the changes in cellular functions were largely reflected by the metabolomic alterations, LC-MS-based metabolomics was sensitive enough to detect the subtle metabolomic changes when functional cellular assays showed no significant difference. Collectively, our studies have unveiled potential metabolic mechanisms of MOx NP-induced nanotoxicity in lung epithelial cells and demonstrated the sensitivity and feasibility of using metabolomic signatures to understand and predict nanotoxicity in vivo.
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Affiliation(s)
- Li Cui
- School of Dentistry and Jonsson Comprehensive Cancer Center , University of California , Los Angeles , California 90095 , United States
| | - Xiang Wang
- Division of NanoMedicine, Department of Medicine, California NanoSystems Institute , University of California , Los Angeles , California 90095 , United States
| | - Bingbing Sun
- State Key Laboratory of Fine Chemicals, School of Chemical Engineering , Dalian University of Technology , 2 Linggong Road , 116024 , Dalian , China
| | - Tian Xia
- Division of NanoMedicine, Department of Medicine, California NanoSystems Institute , University of California , Los Angeles , California 90095 , United States
| | - Shen Hu
- School of Dentistry and Jonsson Comprehensive Cancer Center , University of California , Los Angeles , California 90095 , United States
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Karkossa I, Bannuscher A, Hellack B, Bahl A, Buhs S, Nollau P, Luch A, Schubert K, von Bergen M, Haase A. An in-depth multi-omics analysis in RLE-6TN rat alveolar epithelial cells allows for nanomaterial categorization. Part Fibre Toxicol 2019; 16:38. [PMID: 31653258 PMCID: PMC6814995 DOI: 10.1186/s12989-019-0321-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 09/11/2019] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Nanomaterials (NMs) can be fine-tuned in their properties resulting in a high number of variants, each requiring a thorough safety assessment. Grouping and categorization approaches that would reduce the amount of testing are in principle existing for NMs but are still mostly conceptual. One drawback is the limited mechanistic understanding of NM toxicity. Thus, we conducted a multi-omics in vitro study in RLE-6TN rat alveolar epithelial cells involving 12 NMs covering different materials and including a systematic variation of particle size, surface charge and hydrophobicity for SiO2 NMs. Cellular responses were analyzed by global proteomics, targeted metabolomics and SH2 profiling. Results were integrated using Weighted Gene Correlation Network Analysis (WGCNA). RESULTS Cluster analyses involving all data sets separated Graphene Oxide, TiO2_NM105, SiO2_40 and Phthalocyanine Blue from the other NMs as their cellular responses showed a high degree of similarities, although apical in vivo results may differ. SiO2_7 behaved differently but still induced significant changes. In contrast, the remaining NMs were more similar to untreated controls. WGCNA revealed correlations of specific physico-chemical properties such as agglomerate size and redox potential to cellular responses. A key driver analysis could identify biomolecules being highly correlated to the observed effects, which might be representative biomarker candidates. Key drivers in our study were mainly related to oxidative stress responses and apoptosis. CONCLUSIONS Our multi-omics approach involving proteomics, metabolomics and SH2 profiling proved useful to obtain insights into NMs Mode of Actions. Integrating results allowed for a more robust NM categorization. Moreover, key physico-chemical properties strongly correlating with NM toxicity were identified. Finally, we suggest several key drivers of toxicity that bear the potential to improve future testing and assessment approaches.
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Affiliation(s)
- Isabel Karkossa
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research (UFZ), Permoserstraße 15, 04318, Leipzig, Germany
| | - Anne Bannuscher
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589, Berlin, Germany
| | - Bryan Hellack
- Institute of Energy and Environmental Technology (IUTA) e.V, Bliersheimerstraße 58-60, 47229, Duisburg, Germany.,German Environment Agency, 06844, Dessau-Roßlau, Germany
| | - Aileen Bahl
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589, Berlin, Germany
| | - Sophia Buhs
- Research Institute Children's Cancer Center and Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, 20251, Hamburg, Germany
| | - Peter Nollau
- Research Institute Children's Cancer Center and Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, 20251, Hamburg, Germany
| | - Andreas Luch
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589, Berlin, Germany
| | - Kristin Schubert
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research (UFZ), Permoserstraße 15, 04318, Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research (UFZ), Permoserstraße 15, 04318, Leipzig, Germany.,Institute of Biochemistry, Leipzig University, Brüderstraße 34, 04103, Leipzig, Germany
| | - Andrea Haase
- Department of Chemical and Product Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589, Berlin, Germany.
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17
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Holland L, Zhong W. Analytical developments in advancing safety in nanotechnology. Anal Bioanal Chem 2018; 410:6037-6039. [DOI: 10.1007/s00216-018-1298-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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