1
|
Severi AA, Akbari B. CRISPR-Cas9 delivery strategies and applications: Review and update. Genesis 2024; 62:e23598. [PMID: 38727638 DOI: 10.1002/dvg.23598] [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: 12/15/2023] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 06/28/2024]
Abstract
Nowadays, a significant part of the investigations carried out in the medical field belong to cancer treatment. Generally, conventional cancer treatments, including chemotherapy, radiotherapy, and surgery, which have been used for a long time, are not sufficient, especially in malignant cancers. Because genetic mutations cause cancers, researchers are trying to treat these diseases using genetic engineering tools. One of them is clustered regularly interspaced short palindromic repeats (CRISPR), a powerful tool in genetic engineering in the last decade. CRISPR, which forms the CRISPR-Cas structure with its endonuclease protein, Cas, is known as a part of the immune system (adaptive immunity) in bacteria and archaea. Among the types of Cas proteins, Cas9 endonuclease has been used in many scientific studies due to its high accuracy and efficiency. This review reviews the CRISPR system, focusing on the history, classification, delivery methods, applications, new generations, and challenges of CRISPR-Cas9 technology.
Collapse
Affiliation(s)
- Ali Alizadeh Severi
- Department of Medical Biotechnology, School of Medicine, Kermanshah University of Medical Science, Kermanshah, Iran
| | - Bahman Akbari
- Department of Medical Biotechnology, School of Medicine, Kermanshah University of Medical Science, Kermanshah, Iran
| |
Collapse
|
2
|
Wang L, Miao J, Ding M, Zhang W, Pan L. Exploring the mechanism of nonylphenol-induced ovarian developmental delay of manila clams, Ruditapes philippinarum: Applying RNAi to toxicological analysis. CHEMOSPHERE 2024; 356:141905. [PMID: 38579946 DOI: 10.1016/j.chemosphere.2024.141905] [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: 01/14/2024] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 04/07/2024]
Abstract
Nonylphenol (NP) contamination in the coastal environment of China poses ecological risks to aquatic organisms. However, the endocrine disruptive impacts of NP on bivalves, particularly on ovarian development, remain poorly understood. In this study, Manila clams Ruditapes philippinarum at the developing stage of gonad were exposed to 1.0 μg/L NP for 21 days. Utilizing RNA interference (RNAi) to suppress ER gene expression, we observed a delay in ovarian development as evidenced by histological observations under both NP and NPRi (NP with ER-RNAi) treatment, with Vtg elevation exclusive to the NP group. Comprehensive analyses encompassing transcriptomics, real-time quantitative PCR, and steroid hormone measurement revealed significant alterations in aldosterone synthesis, estrogen signaling, and thyroid hormone synthesis. These pathways showed similar perturbations in both NP and NPRi groups compared to controls. Notably, the NPRi group exhibited distinct enrichment in PPAR and insulin signaling pathways, may implicating these in ER function suppression. Steroid hormone biosynthesis was notably reduced in both treatments, pointing to a profound impact on hormone synthesis. The contrast between in vivo and in vitro findings suggests that NP's detrimental effects on ovarian development may primarily involve neuroendocrine regulation of steroidogenesis. This investigation highlights the complex dynamics of NP-induced endocrine disruption in bivalves, emphasizing the pivotal role of ER and associated pathways.
Collapse
Affiliation(s)
- Lu Wang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, PR China
| | - Jingjing Miao
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, PR China.
| | - Min Ding
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, PR China; Marine Environmental Monitoring Central Station of Qinhuangdao, SOA, PR China
| | - Wei Zhang
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, PR China
| | - Luqing Pan
- The Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, PR China
| |
Collapse
|
3
|
Zhao F, Ding X, Liu Z, Yan X, Chen Y, Jiang Y, Chen S, Wang Y, Kang T, Xie C, He M, Zheng J. Application of CRISPR/Cas9-based genome editing in ecotoxicology. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 336:122458. [PMID: 37633433 DOI: 10.1016/j.envpol.2023.122458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 08/28/2023]
Abstract
Chemicals are widely used and released into the environment, and their degradation, accumulation, migration, and transformation processes in the environment can pose a threat to the ecosystem. The advancement in analytical methods with high-throughput screening of biomolecules has revolutionized the way toxicologists used to explore the effects of chemicals on organisms. CRISPR/Cas is a newly developed tool, widely used in the exploration of basic science and biologically engineered products given its high efficiency and low cost. For example, it can edit target genes efficiently, and save loss of the crop yield caused by environmental pollution as well as gain a better understanding of the toxicity mechanisms from various chemicals. This review briefly introduces the development history of CRISPR/Cas and summarizes the current application of CRISPR/Cas in ecotoxicology, including its application on improving crop yield and drug resistance towards agricultural pollution, antibiotic pollution and other threats. The benefits by applying the CRISPR/Cas9 system in conventional toxicity mechanism studies are fully demonstrated here together with its foreseeable expansions in other area of ecotoxicology. Finally, the prospects and disadvantages of CRISPR/Cas system in the field of ecotoxicology are also discussed.
Collapse
Affiliation(s)
- Fang Zhao
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China; State Environmental Protection Key laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Sciences. Ministry of Environmental Protection, Guangzhou, China; School of Public Health, Guizhou Medical University, Guizhou, China
| | - Xiaofan Ding
- Faculty of Health Sciences, University of Macau, Taipa, Macao SAR, China
| | - Zimeng Liu
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Xiao Yan
- State Environmental Protection Key laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Sciences. Ministry of Environmental Protection, Guangzhou, China
| | - Yanzhen Chen
- Faculty of Health Sciences, University of Macau, Taipa, Macao SAR, China
| | - Yaxin Jiang
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Shunjie Chen
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Yuanfang Wang
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Tingting Kang
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Chun Xie
- School of Public Health, Guizhou Medical University, Guizhou, China
| | - Mian He
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China.
| | - Jing Zheng
- State Environmental Protection Key laboratory of Environmental Pollution Health Risk Assessment, South China Institute of Environmental Sciences. Ministry of Environmental Protection, Guangzhou, China
| |
Collapse
|
4
|
Tian M, Xia P, Yan L, Gou X, Yu H, Zhang X. Human functional genomics reveals toxicological mechanism underlying genotoxicants-induced inflammatory responses under low doses exposure. CHEMOSPHERE 2023; 314:137658. [PMID: 36584827 DOI: 10.1016/j.chemosphere.2022.137658] [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: 11/01/2022] [Revised: 12/10/2022] [Accepted: 12/24/2022] [Indexed: 06/17/2023]
Abstract
Understanding the toxicological mechanisms of chemicals is essential for accurate assessments of environmental health risks. Inflammation could play a critical role in the adverse health outcomes caused by genotoxicants; however, the toxicological mechanisms underlying genotoxicants-induced inflammatory response are still limited. Here, functional genomics CRISPR screens were performed to enhance the mechanistic understanding of the genotoxicants-induced inflammatory response at low doses exposure. Key genes and pathways associated with the activities of immune cells and the production of cytokines were identified by CRISPR screens of 6 model genotoxicants. Gene network analysis revealed that three genes (TLR10, HCAR2 and TRIM6) were involved in the regulation of neutrophil apoptosis and cytokine release, and TLR10 shared a similar functional pattern with HCAR2 and TRIM6. Furthermore, adverse outcome pathway (AOP) network analysis revealed that TLR10 was involved in the molecular initiating events (MIEs) or key events (KEs) in the inflammatory response AOPs of all the 6 genotoxicants, which provided mechanistic links between TLR10 and genotoxicants-induced inflammation and respiratory diseases. Finally, functional validation tests demonstrated that TLR10 exhibited inhibitory effects on genotoxicants-induced inflammatory responses in both epithelial and immune cells. This study highlights the powerful utility of the integration of CRISPR screen and AOP network analysis in illuminating the toxicological causal mechanisms of environmental chemicals.
Collapse
Affiliation(s)
- Mingming Tian
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, People's Republic of China
| | - Pu Xia
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, People's Republic of China
| | - Lu Yan
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, People's Republic of China
| | - Xiao Gou
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, People's Republic of China
| | - Hongxia Yu
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, People's Republic of China
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, People's Republic of China; Jiangsu Province Ecology and Environment Protection Key Laboratory of Chemical Safety and Health Risk, Nanjing, 210023, Jiangsu, China.
| |
Collapse
|
5
|
Rani V, Prabhu A. CRISPR-Cas9 based non-viral approaches in nanoparticle elicited therapeutic delivery. J Drug Deliv Sci Technol 2022. [DOI: 10.1016/j.jddst.2022.103737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
|
6
|
Tian M, Xia P, Yan L, Gou X, Giesy JP, Dai J, Yu H, Zhang X. Toxicological Mechanism of Individual Susceptibility to Formaldehyde-Induced Respiratory Effects. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:6511-6524. [PMID: 35438505 DOI: 10.1021/acs.est.1c07945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Understanding the mechanisms of individual susceptibility to exposure to environmental pollutants has been a challenge in health risk assessment. Here, an integrated approach combining a CRISPR screen in human cells and epidemiological analysis was developed to identify the individual susceptibility to the adverse health effects of air pollutants by taking formaldehyde (FA) and the associated chronic obstructive pulmonary disease (COPD) as a case study. Among the primary hits of CRISPR screening of FA in human A549 cells, HTR4 was the only gene genetically associated with COPD susceptibility in global populations. However, the association between HTR4 and FA-induced respiratory toxicity is unknown in the literature. Adverse outcome pathway (AOP) network analysis of CRISPR screen hits provided a potential mechanistic link between activation of HTR4 (molecular initiating event) and FA-induced lung injury (adverse outcome). Systematic toxicology tests (in vitro and animal experiments) were conducted to reveal the HTR4-involved biological mechanisms underlying the susceptibility to adverse health effects of FA. Functionality and enhanced expression of HTR4 were required for susceptibility to FA-induced lung injury, and FA-induced epigenetic changes could result in enhanced expression of HTR4. Specific epigenetic and genetic characteristics of HTR4 were associated with the progression and prevalence of COPD, respectively, and these genetic risk factors for COPD could be potential biomarkers of individual susceptibility to adverse respiratory effects of FA. These biomarkers could be of great significance for defining subpopulations susceptible to exposure to FA and reducing uncertainty in the next-generation health risk assessment of air pollutants. Our study delineated a novel toxicological pathway mediated by HTR4 in FA-induced lung injury, which could provide a mechanistic understanding of the potential biomarkers of individual susceptibility to adverse respiratory effects of FA.
Collapse
Affiliation(s)
- Mingming Tian
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, People's Republic of China
| | - Pu Xia
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, People's Republic of China
| | - Lu Yan
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, People's Republic of China
| | - Xiao Gou
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, People's Republic of China
| | - John P Giesy
- Department of Veterinary Biomedical Sciences and Toxicology Centre, University of Saskatchewan Saskatoon, Saskatoon SK S7N 5B3, Canada
- Zoology Department, Center for Integrative Toxicology, Michigan State University, 1129 Farm Lane Road, East Lansing, Michigan 48824, United States
- Department of Environmental Science, Baylor University, Waco, Texas 76798, United States
| | - Jiayin Dai
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | - Hongxia Yu
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, People's Republic of China
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, People's Republic of China
| |
Collapse
|
7
|
Tian M, Xia P, Gou X, Yan L, Yu H, Zhang X. CRISPR screen identified that UGT1A9 was required for bisphenols-induced mitochondria dyshomeostasis. ENVIRONMENTAL RESEARCH 2022; 205:112427. [PMID: 34861229 DOI: 10.1016/j.envres.2021.112427] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 11/07/2021] [Accepted: 11/20/2021] [Indexed: 06/13/2023]
Abstract
Exposure to bisphenols chemicals could cause various adverse health effects, including non-alcoholic fatty liver disease (NAFLD), which have been associated with cellular mitochondria stress. However, the biological mechanism underlying the mitochondria stress-mediated cell death by bisphenols was poorly understood. Here, CRISPR screens were performed to identify the critical genes which were involved in cell death caused by exposure to four bisphenols (BPA, BPB, BPE and BPS). Results of CRISPR screens showed that UGT1A9 was the primary genetic factor facilitating cell death induced by all of the four bisphenols. Systematic toxicological tests demonstrated that UGT1A9 was required for BPA-induced mitochondria dyshomeostasis in vitro and in vivo, and UGT1A9-mediated mitochondria dyshomeostasis was an important cause of facilitating cell death. Liver injury caused by exposure to BPA in wild-type mice was accompanied with suppression of mitophagy and increased expression of C-Caspase 3, but UGT1A9 knockout attenuated these adverse effects induced by BPA. Finally, molecular epidemiology analysis suggested that the five genetic variants of UGT1A9 could be potential genetic risk factors of NAFLD when people were exposed to BPA. The biological mechanism uncovered here provided mechanistic evidence for identification of susceptible populations of liver injury associated with exposure to BPA.
Collapse
Affiliation(s)
- Mingming Tian
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, People's Republic of China
| | - Pu Xia
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, People's Republic of China
| | - Xiao Gou
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, People's Republic of China
| | - Lu Yan
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, People's Republic of China
| | - Hongxia Yu
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, People's Republic of China
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, 210023, People's Republic of China.
| |
Collapse
|
8
|
The application of genome-wide CRISPR-Cas9 screens to dissect the molecular mechanisms of toxins. Comput Struct Biotechnol J 2022; 20:5076-5084. [PMID: 36187925 PMCID: PMC9489804 DOI: 10.1016/j.csbj.2022.09.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 11/29/2022] Open
Abstract
Many toxins are life-threatening to both animals and humans. However, specific antidotes are not available for most of those toxins. The molecular mechanisms underlying the toxicology of well-known toxins are not yet fully characterized. Recently, the advance in CRISPR-Cas9 technologies has greatly accelerated the process of revealing the toxic mechanisms of some common toxins on hosts from a genome-wide perspective. The high-throughput CRISPR screen has made it feasible to untangle complicated interactions between a particular toxin and its corresponding targeting tissue(s). In this review, we present an overview of recent advances in molecular dissection of toxins’ cytotoxicity by using genome-wide CRISPR screens, summarize the components essential for toxin-specific CRISPR screens, and propose new strategies for future research.
Collapse
|
9
|
Chatterjee N, Zhang X. CRISPR approach in environmental chemical screening focusing on population variability. J Toxicol Sci 2021; 46:499-507. [PMID: 34719552 DOI: 10.2131/jts.46.499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
A significant barrier to include population variability in risk assessment is our incomplete understanding of inter-individual variability and the differential susceptibility to environmental exposures induced adverse outcomes. By combining genome editing tools with the population diversity model, this article intended to highlight a potential strategy to identify and characterize the inter-individual variability factors, the determinant gene anchoring to a particular phenotype. The goal could be achieved by integrating the perturbed CRISPR-based unbiased functional genomics screening, genome-wide or a focused subset of genes, in a population-based in vitro model system (such as the lymphoblastoid cell lines, LCL, available from HapMap and 1000 Genomes project). Then data can be translated to genetic variability and individual (or subpopulation) susceptibility by incorporating ethnicity and corresponding genome-wide association studies (GWAS) with functional genomics screening results. This approach can provide complementary data for next-generation risk assessment, in particular, for environmental stressors. The current paper outlined the previous work conducted with a population-based in vitro model system, perturbed CRISPR-based functional toxicogenomic screening of environmental chemicals, and finally, the potential strategies to combine these two platforms with their opportunities and challenges to achieve a mechanistic understanding of population variability.
Collapse
Affiliation(s)
- Nivedita Chatterjee
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, China.,INL-International Iberian Nanotechnology Laboratory, Portugal
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, China
| |
Collapse
|
10
|
Lujan H, Romer E, Salisbury R, Hussain S, Sayes C. Determining the Biological Mechanisms of Action for Environmental Exposures: Applying CRISPR/Cas9 to Toxicological Assessments. Toxicol Sci 2021; 175:5-18. [PMID: 32105327 DOI: 10.1093/toxsci/kfaa028] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Toxicology is a constantly evolving field, especially in the area of developing alternatives to animal testing. Toxicological research must evolve and utilize adaptive technologies in an effort to improve public, environmental, and occupational health. The most commonly cited mechanisms of toxic action after exposure to a chemical or particle test substance is oxidative stress. However, because oxidative stress involves a plethora of genes and proteins, the exact mechanism(s) are not commonly defined. Exact mechanisms of toxicity can be revealed using an emerging laboratory technique referred to as CRISPR (clustered regularly interspaced short palindromic repeats). This article reviews the most common CRISPR techniques utilized today and how each may be applied in Toxicological Sciences. Specifically, the CRISPR/CRISPR-associated protein complex is used for single gene knock-outs, whereas CRISPR interference/activation is used for silencing or activating (respectively) ribonucleic acid. Finally, CRISPR libraries are used for knocking-out entire gene pathways. This review highlights the application of CRISPR in toxicology to elucidate the exact mechanism through which toxicants perturb normal cellular functions.
Collapse
Affiliation(s)
- Henry Lujan
- Department of Environmental Science, Baylor University, Waco, Texas 76706
| | - Eric Romer
- Molecular Bioeffects Branch, Bioeffects Division, 711th Human Performance Wing, Air Force Research Laboratory, Dayton, Ohio 45433
| | - Richard Salisbury
- Molecular Bioeffects Branch, Bioeffects Division, 711th Human Performance Wing, Air Force Research Laboratory, Dayton, Ohio 45433
| | - Saber Hussain
- Molecular Bioeffects Branch, Bioeffects Division, 711th Human Performance Wing, Air Force Research Laboratory, Dayton, Ohio 45433
| | - Christie Sayes
- Department of Environmental Science, Baylor University, Waco, Texas 76706
| |
Collapse
|
11
|
Fritsche E, Haarmann-Stemmann T, Kapr J, Galanjuk S, Hartmann J, Mertens PR, Kämpfer AAM, Schins RPF, Tigges J, Koch K. Stem Cells for Next Level Toxicity Testing in the 21st Century. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2006252. [PMID: 33354870 DOI: 10.1002/smll.202006252] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/13/2020] [Indexed: 06/12/2023]
Abstract
The call for a paradigm change in toxicology from the United States National Research Council in 2007 initiates awareness for the invention and use of human-relevant alternative methods for toxicological hazard assessment. Simple 2D in vitro systems may serve as first screening tools, however, recent developments infer the need for more complex, multicellular organotypic models, which are superior in mimicking the complexity of human organs. In this review article most critical organs for toxicity assessment, i.e., skin, brain, thyroid system, lung, heart, liver, kidney, and intestine are discussed with regards to their functions in health and disease. Embracing the manifold modes-of-action how xenobiotic compounds can interfere with physiological organ functions and cause toxicity, the need for translation of such multifaceted organ features into the dish seems obvious. Currently used in vitro methods for toxicological applications and ongoing developments not yet arrived in toxicity testing are discussed, especially highlighting the potential of models based on embryonic stem cells and induced pluripotent stem cells of human origin. Finally, the application of innovative technologies like organs-on-a-chip and genome editing point toward a toxicological paradigm change moves into action.
Collapse
Affiliation(s)
- Ellen Fritsche
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, 40225, Germany
- Medical Faculty, Heinrich-Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | | | - Julia Kapr
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, 40225, Germany
| | - Saskia Galanjuk
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, 40225, Germany
| | - Julia Hartmann
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, 40225, Germany
| | - Peter R Mertens
- Department of Nephrology and Hypertension, Diabetes and Endocrinology, Otto-von-Guericke-University Magdeburg, Magdeburg, 39106, Germany
| | - Angela A M Kämpfer
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, 40225, Germany
| | - Roel P F Schins
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, 40225, Germany
| | - Julia Tigges
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, 40225, Germany
| | - Katharina Koch
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, 40225, Germany
| |
Collapse
|
12
|
Editorial overview: The environment and man: A Study in mechanistic toxicology. CURRENT OPINION IN TOXICOLOGY 2020. [DOI: 10.1016/j.cotox.2020.03.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
13
|
Rager JE, Carberry C, Fry RC. Use of Genome Editing Tools in Environmental Health Research. CURRENT OPINION IN TOXICOLOGY 2019; 18:13-17. [PMID: 31656878 DOI: 10.1016/j.cotox.2019.02.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The nature and types of genome editing tools are rapidly expanding and becoming increasingly incorporated into research efforts aimed at understanding human disease. The majority of research involving genome editing has been driven by medical research, with a limited but increasing number of studies currently published in the field of environmental health and toxicology. This review aims to address this research gap by providing a high-level summary of current genome editing techniques and presenting examples of how some of these techniques have been used toxicologically to evaluate environmental exposure-induced disease. Specific strategies surrounding the evaluation of hazardous chemicals, chemical mechanism of action / adverse outcome pathways, and inter-individual response variability are also discussed to aid in the translation of genome editing methods towards toxicological and environmental health research.
Collapse
Affiliation(s)
- Julia E Rager
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill.,The Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill.,Curriculum in Toxicology, The University of North Carolina at Chapel Hill
| | - Celeste Carberry
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill
| | - Rebecca C Fry
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill.,The Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill.,Curriculum in Toxicology, The University of North Carolina at Chapel Hill
| |
Collapse
|
14
|
Zhang X, Xia P, Wang P, Yang J, Baird DJ. Omics Advances in Ecotoxicology. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:3842-3851. [PMID: 29481739 DOI: 10.1021/acs.est.7b06494] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Toxic substances in the environment generate adverse effects at all levels of biological organization from the molecular level to community and ecosystem. Given this complexity, it is not surprising that ecotoxicologists have struggled to address the full consequences of toxic substance release at ecosystem level, due to the limits of observational and experimental tools to reveal the changes in deep structure at different levels of organization. -Omics technologies, consisting of genomics and ecogenomics, have the power to reveal, in unprecedented detail, the cellular processes of an individual or biodiversity of a community in response to environmental change with high sample/observation throughput. This represents a historic opportunity to transform the way we study toxic substances in ecosystems, through direct linkage of ecological effects with the systems biology of organisms. Three recent examples of -omics advance in the assessment of toxic substances are explored here: (1) the use of functional genomics in the discovery of novel molecular mechanisms of toxicity of chemicals in the environment; (2) the development of laboratory pipelines of dose-dependent, reduced transcriptomics to support high-throughput chemical testing at the biological pathway level; and (3) the use of eDNA metabarcoding approaches for assessing chemical effects on biological communities in mesocosm experiments and through direct observation in field monitoring. -Omics advances in ecotoxicological studies not only generate new knowledge regarding mechanisms of toxicity and environmental effect, improving the relevance and immediacy of laboratory toxicological assessment, but can provide a wholly new paradigm for ecotoxicology by linking ecological models to mechanism-based, systems biology approaches.
Collapse
Affiliation(s)
- Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment , Nanjing University , Nanjing 210023 , China
| | - Pu Xia
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment , Nanjing University , Nanjing 210023 , China
| | - Pingping Wang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment , Nanjing University , Nanjing 210023 , China
| | - Jianghu Yang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment , Nanjing University , Nanjing 210023 , China
| | - Donald J Baird
- Environment & Climate Change Canada @ Canadian Rivers Institute, Department of Biology , University of New Brunswick , Fredericton , New Brunswick E3B 5A3 , Canada
| |
Collapse
|
15
|
Abstract
Since the sequence of the human genome is complete, the main issue is how to understand the information written in the DNA sequence. Despite numerous genome-wide studies that have already been performed, the challenge to determine the function of genes, gene products, and also their interaction is still open. As changes in the human genome are highly likely to cause pathological conditions, functional analysis is vitally important for human health. For many years there have been a variety of technologies and tools used in functional genome analysis. However, only in the past decade there has been rapid revolutionizing progress and improvement in high-throughput methods, which are ranging from traditional real-time polymerase chain reaction to more complex systems, such as next-generation sequencing or mass spectrometry. Furthermore, not only laboratory investigation, but also accurate bioinformatic analysis is required for reliable scientific results. These methods give an opportunity for accurate and comprehensive functional analysis that involves various fields of studies: genomics, epigenomics, proteomics, and interactomics. This is essential for filling the gaps in the knowledge about dynamic biological processes at both cellular and organismal level. However, each method has both advantages and limitations that should be taken into account before choosing the right method for particular research in order to ensure successful study. For this reason, the present review paper aims to describe the most frequent and widely-used methods for the comprehensive functional analysis.
Collapse
Affiliation(s)
- Evelina Gasperskaja
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University Vilnius, Lithuania
| | - Vaidutis Kučinskas
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University Vilnius, Lithuania
| |
Collapse
|
16
|
Park HR, Oh R, Wagner P, Panganiban R, Lu Q. New Insights Into Cellular Stress Responses to Environmental Metal Toxicants. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 331:55-82. [PMID: 28325215 DOI: 10.1016/bs.ircmb.2016.10.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Exposures to metal toxicants in the environment disrupt normal physiological functions and have been linked to the development of a myriad of human diseases. While the molecular and cellular mechanisms underlying metal toxicities remain to be fully understood, it is well appreciated that metal toxicants induce cellular stresses and that how cells respond to the stresses plays an important role in metal toxicity. In this review, we focus on how metal exposures induce stresses in the endoplasmic reticulum (ER) to elicit the unfolded protein response (UPR). We document the emerging evidence that induction of ER stress and UPR in the development of human diseases is associated with metal exposures. We also discuss the role of the interplay between ER stress and oxidative stress in metal toxicity. Finally, we review recent advances in functional genomics approaches and discuss how applications of these new tools could help elucidate the molecular mechanisms underlying cellular stresses induced by environmental metal toxicants.
Collapse
Affiliation(s)
- H-R Park
- Program in Molecular and Integrative Physiological Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - R Oh
- Program in Molecular and Integrative Physiological Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - P Wagner
- Program in Molecular and Integrative Physiological Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - R Panganiban
- Program in Molecular and Integrative Physiological Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Q Lu
- Program in Molecular and Integrative Physiological Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, United States.
| |
Collapse
|
17
|
Xia P, Zhang X, Xie Y, Guan M, Villeneuve DL, Yu H. Functional Toxicogenomic Assessment of Triclosan in Human HepG2 Cells Using Genome-Wide CRISPR-Cas9 Screening. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:10682-10692. [PMID: 27459410 DOI: 10.1021/acs.est.6b02328] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
There are thousands of chemicals used by humans and detected in the environment for which limited or no toxicological data are available. Rapid and cost-effective approaches for assessing the toxicological properties of chemicals are needed. We used CRISPR-Cas9 functional genomic screening to identify the potential molecular mechanism of a widely used antimicrobial triclosan (TCS) in HepG2 cells. Resistant genes at IC50 (the concentration causing a 50% reduction in cell viability) were significantly enriched in the adherens junction pathway, MAPK signaling pathway, and PPAR signaling pathway, suggesting a potential role in the molecular mechanism of TCS-induced cytotoxicity. Evaluation of the top-ranked resistant genes, FTO (encoding an mRNA demethylase) and MAP2K3 (a MAP kinase kinase family gene), revealed that their loss conferred resistance to TCS. In contrast, sensitive genes at IC10 and IC20 were specifically enriched in pathways involved with immune responses, which was concordant with transcriptomic profiling of TCS at concentrations of <IC10. It is suggested that the CRISPR-Cas9 fingerprint may reveal the patterns of TCS toxicity at low concentration levels. Moreover, we retrieved the potential connection between CRISPR-Cas9 fingerprint and disease terms, obesity, and breast cancer from an existing chemical-gene-disease database. Overall, CRISPR-Cas9 functional genomic screening offers an alternative approach for chemical toxicity testing.
Collapse
Affiliation(s)
- Pu Xia
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University , Nanjing 210023, People's Republic of China
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University , Nanjing 210023, People's Republic of China
| | - Yuwei Xie
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University , Nanjing 210023, People's Republic of China
| | - Miao Guan
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University , Nanjing 210023, People's Republic of China
| | - Daniel L Villeneuve
- Mid-Continent Ecology Division, United States Environmental Protection Agency , Duluth, Minnesota 55804, United States
| | - Hongxia Yu
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University , Nanjing 210023, People's Republic of China
| |
Collapse
|
18
|
Shen H, McHale CM, Haider SI, Jung C, Zhang S, Smith MT, Zhang L. Identification of Genes That Modulate Susceptibility to Formaldehyde and Imatinib by Functional Genomic Screening in Human Haploid KBM7 Cells. Toxicol Sci 2016; 151:10-22. [PMID: 27008852 DOI: 10.1093/toxsci/kfw032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Though current functional genomic screening systems are useful for investigating human susceptibility to chemical toxicity, they have limitations. Well-established, high-throughput yeast mutant screens identify only evolutionarily conserved processes. RNA interference can be applied in human cells but is limited by incomplete gene knockout and off-target effects. Human haploid cell screening is advantageous as it requires knockdown of only a single copy of each gene. A human haploid cell mutant library (KBM7-Mu), derived from a chronic myeloid leukemia (CML) patient, was recently developed and has been used to identify genes that modulate sensitivity to infectious agents and pharmaceutical drugs. Here, we sought to improve the KBM7-Mu screening process to enable efficient screening of environmental chemicals. We developed a semi-solid medium based screening approach that cultures individual mutant colonies from chemically resistant cells, faster (by 2-3 weeks) and with less labor than the original liquid medium-based approach. As proof of principle, we identified genetic mutants that confer resistance to the carcinogen formaldehyde (FA, 12 genes, 18 hits) and the CML chemotherapeutic agent imatinib (6 genes, 13 hits). Validation experiments conducted on KBM7 mutants lacking each of the 18 genes confirmed resistance of 6 FA mutants (CTC1, FCRLA, GOT1, LPR5, M1AP, and MAP2K5) and 1 imatinib-resistant mutant (LYRM9). Despite the improvements to the method, it remains technically challenging to limit false positive findings. Nonetheless, our findings demonstrate the broad applicability of this optimized haploid approach to screen toxic chemicals to identify novel susceptibility genes and gain insight into potential mechanisms of toxicity.
Collapse
Affiliation(s)
- Hua Shen
- Superfund Research Program, School of Public Health, University of California, Berkeley, California 94720
| | - Cliona M McHale
- Superfund Research Program, School of Public Health, University of California, Berkeley, California 94720
| | - Syed I Haider
- Superfund Research Program, School of Public Health, University of California, Berkeley, California 94720
| | - Cham Jung
- Superfund Research Program, School of Public Health, University of California, Berkeley, California 94720
| | - Susie Zhang
- Superfund Research Program, School of Public Health, University of California, Berkeley, California 94720
| | - Martyn T Smith
- Superfund Research Program, School of Public Health, University of California, Berkeley, California 94720
| | - Luoping Zhang
- Superfund Research Program, School of Public Health, University of California, Berkeley, California 94720
| |
Collapse
|
19
|
Abstract
Neuroscience research has been revolutionized by the use of recombinant viral vector technology from the basic, preclinical and clinical levels. Currently, multiple recombinant viral vector types are employed with each having its strengths and weaknesses depending on the proposed application. Helper-dependent adenoviral vectors (HdAd) are emerging as ideal viral vectors that solve a major need in the neuroscience field: (1) expression of transgenes that are too large to be packaged by other viral vectors and (2) rapid onset of transgene expression in the absence of cytotoxicity. Here, we describe the methods for large-scale production of HdAd viral vectors for in vivo use with neurospecific transgene expression.
Collapse
|