1
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Owutey SL, Procuniar KA, Akoto E, Davis JC, Vachon RM, O'Malley LF, Schneider HO, Smaldino PJ, True JD, Kalinski AL, Rubenstein EM. Endoplasmic reticulum and inner nuclear membrane ubiquitin-conjugating enzymes Ubc6 and Ubc7 confer resistance to hygromycin B in Saccharomyces cerevisiae. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001276. [PMID: 39139584 PMCID: PMC11320122 DOI: 10.17912/micropub.biology.001276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 07/25/2024] [Accepted: 07/25/2024] [Indexed: 08/15/2024]
Abstract
Aberrant endoplasmic reticulum (ER) and inner nuclear membrane (INM) proteins are destroyed through ER-associated degradation (ERAD) and INM-associated degradation (INMAD). We previously showed the Hrd1, Doa10, and Asi ERAD and INMAD ubiquitin ligases (E3s) in Saccharomyces cerevisiae confer resistance to hygromycin B, which distorts the ribosome decoding center. Here, we assessed the requirement of Ubc6 and Ubc7, the primary ERAD and INMAD ubiquitin-conjugating enzymes (E2s) for hygromycin B resistance. Loss of either E2 sensitized cells to hygromycin B, with UBC7 deletion having a greater impact, consistent with characterized roles for Ubc6 and Ubc7 in ER and INM protein quality control.
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Affiliation(s)
| | | | | | - Jacob C Davis
- Department of Biology, Ball State University
- Department of Anesthesiology, University of North Carolina
| | | | | | - Hayden O Schneider
- Department of Biology, Ball State University
- Division of Molecular Cardiovascular Biology, Cincinnati Children’s Hospital Medical Center
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2
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Pallares RM, An DD, Hebert S, Loguinov A, Proctor M, Villalobos JA, Bjornstad KA, Rosen CJ, Vulpe C, Abergel RJ. Screening the complex biological behavior of late lanthanides through genome-wide interactions. Metallomics 2023; 15:mfad039. [PMID: 37336558 DOI: 10.1093/mtomcs/mfad039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 05/26/2023] [Indexed: 06/21/2023]
Abstract
Despite their similar physicochemical properties, recent studies have demonstrated that lanthanides can display different biological behaviors. Hence, the lanthanide series can be divided into three parts, namely early, mid, and late lanthanides, based on their interactions with biological systems. In particular, the late lanthanides demonstrate distinct, but poorly understood biological activity. In the current study, we employed genome-wide functional screening to help understand biological effects of exposure to Yb(III) and Lu(III), which were selected as representatives of the late lanthanides. As a model organism, we used Saccharomyces cerevisiae, since it shares many biological functions with humans. Analysis of the functional screening results indicated toxicity of late lanthanides is consistent with disruption of vesicle-mediated transport, and further supported a role for calcium transport processes and mitophagy in mitigating toxicity. Unexpectedly, our analysis suggested that late lanthanides target proteins with SH3 domains, which may underlie the observed toxicity. This study provides fundamental insights into the unique biological chemistry of late lanthanides, which may help devise new avenues toward the development of decorporation strategies and bio-inspired separation processes.
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Affiliation(s)
- Roger M Pallares
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Institute for Experimental Molecular Imaging (ExMI), RWTH Aachen University Hospital, Forckenbeckstr. 55, Aachen 52074, Germany
| | - Dahlia D An
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Solene Hebert
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Alex Loguinov
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Michael Proctor
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Jonathan A Villalobos
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kathleen A Bjornstad
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Chris J Rosen
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Christopher Vulpe
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Rebecca J Abergel
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Nuclear Engineering, University of California, Berkeley, CA 94720, USA
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3
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Pallares R, An DD, Hébert S, Loguinov A, Proctor M, Villalobos JA, Bjornstad KA, Rosen CJ, Vulpe CD, Abergel RJ. Identifying Toxicity Mechanisms Associated with Early Lanthanide Exposure through Multidimensional Genome-Wide Screening. ACS OMEGA 2022; 7:34412-34419. [PMID: 36188298 PMCID: PMC9521019 DOI: 10.1021/acsomega.2c04045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 09/01/2022] [Indexed: 06/16/2023]
Abstract
Lanthanides are a series of elements essential to a wide range of applications, from clean energy production to healthcare. Despite their presence in multiple products and technologies, their toxicological characteristics have been only partly studied. Recently, our group has employed a genomic approach to extensively characterize the toxicity mechanisms of lanthanides. Even though we identified substantially different behaviors for mid and late lanthanides, the toxicological profiles of early lanthanides remained elusive. Here, we overcome this gap by describing a multidimensional genome-wide toxicogenomic study for two early lanthanides, namely, lanthanum and praseodymium. We used Saccharomyces cerevisiae as a model system since its genome shares many biological pathways with humans. By performing functional analysis and protein-protein interaction network analysis, we identified the main genes and proteins that participate in the yeast response to counter metal harmful effects. Moreover, our analysis also highlighted key enzymes that are dysregulated by early lanthanides, inducing cytotoxicity. Several of these genes and proteins have human orthologues, indicating that they may also participate in the human response against the metals. By highlighting the key genes and proteins in lanthanide-induced toxicity, this work may contribute to the development of new prophylactic and therapeutic strategies against lanthanide harmful exposures.
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Affiliation(s)
- Roger
M. Pallares
- Chemical
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Dahlia D. An
- Chemical
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Solène Hébert
- Chemical
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Alex Loguinov
- Center
for Environmental and Human Toxicology, Department of Physiological
Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida 32611, United States
| | - Michael Proctor
- Center
for Environmental and Human Toxicology, Department of Physiological
Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida 32611, United States
| | - Jonathan A. Villalobos
- Chemical
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Kathleen A. Bjornstad
- Chemical
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Chris J. Rosen
- Chemical
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Chris D. Vulpe
- Center
for Environmental and Human Toxicology, Department of Physiological
Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida 32611, United States
| | - Rebecca J. Abergel
- Chemical
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
- Department
of Nuclear Engineering, University of California, Berkeley, California 94720, United States
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4
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Pallares RM, An DD, Hébert S, Faulkner D, Loguinov A, Proctor M, Villalobos JA, Bjornstad KA, Rosen CJ, Vulpe C, Abergel RJ. Delineating toxicity mechanisms associated with MRI contrast enhancement through a multidimensional toxicogenomic profiling of gadolinium. Mol Omics 2022; 18:237-248. [PMID: 35040455 DOI: 10.1039/d1mo00267h] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Gadolinium is a metal used in contrast agents for magnetic resonance imaging. Although gadolinium is widely used in clinical settings, many concerns regarding its toxicity and bioaccumulation after gadolinium-based contrast agent administration have been raised and published over the last decade. To date, most toxicological studies have focused on identifying acute effects following gadolinium exposure, rather than investigating associated toxicity mechanisms. In this study, we employ functional toxicogenomics to assess mechanistic interactions of gadolinium with Saccharomyces cerevisiae. Furthermore, we determine which mechanisms are conserved in humans, and their implications for diseases related to the use of gadolinium-based contrast agents in medicine. A homozygous deletion pool of 4291 strains were screened to identify biological functions and pathways disturbed by the metal. Gene ontology and pathway enrichment analyses showed endocytosis and vesicle-mediated transport as the main yeast response to gadolinium, while certain metabolic processes, such as glycosylation, were the primary disrupted functions after the metal treatments. Cluster and protein-protein interaction network analyses identified proteins mediating vesicle-mediated transport through the Golgi apparatus and the vacuole, and vesicle cargo exocytosis as key components to reduce the metal toxicity. Moreover, the metal seemed to induce cytotoxicity by disrupting the function of enzymes (e.g. transferases and proteases) and chaperones involved in metabolic processes. Several of the genes and proteins associated with gadolinium toxicity are conserved in humans, suggesting that they may participate in pathologies linked to gadolinium-based contrast agent exposures. We thereby discuss the potential role of these conserved genes and gene products in gadolinium-induced nephrogenic systemic fibrosis, and propose potential prophylactic strategies to prevent its adverse health effects.
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Affiliation(s)
- Roger M Pallares
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Dahlia D An
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Solène Hébert
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - David Faulkner
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Alex Loguinov
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Michael Proctor
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Jonathan A Villalobos
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Kathleen A Bjornstad
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Chris J Rosen
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Christopher Vulpe
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Rebecca J Abergel
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,Department of Nuclear Engineering, University of California, Berkeley, CA, 94720, USA
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5
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Pallares RM, An DD, Hébert S, Faulkner D, Loguinov A, Proctor M, Villalobos JA, Bjornstad KA, Rosen CJ, Vulpe C, Abergel RJ. Multidimensional genome-wide screening in yeast provides mechanistic insights into europium toxicity. Metallomics 2021; 13:6409834. [PMID: 34694395 DOI: 10.1093/mtomcs/mfab061] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 10/19/2021] [Indexed: 11/13/2022]
Abstract
Europium is a lanthanide metal that is highly valued in optoelectronics. Even though europium is used in many commercial products, its toxicological profile has only been partially characterized, with most studies focusing on identifying lethal doses in different systems or bioaccumulation in vivo. This paper describes a genome-wide toxicogenomic study of europium in Saccharomyces cerevisiae, which shares many biological functions with humans. By using a multidimensional approach and functional and network analyses, we have identified a group of genes and proteins associated with the yeast responses to ameliorate metal toxicity, which include metal discharge paths through vesicle-mediated transport, paths to regulate biologically relevant cations, and processes to reduce metal-induced stress. Furthermore, the analyses indicated that europium promotes yeast toxicity by disrupting the function of chaperones and cochaperones, which have metal-binding sites. Several of the genes and proteins highlighted in our study have human orthologues, suggesting they may participate in europium-induced toxicity in humans. By identifying the endogenous targets of europium as well as the already existing paths that can decrease its toxicity, we can determine specific genes and proteins that may help to develop future therapeutic strategies.
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Affiliation(s)
- Roger M Pallares
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Dahlia D An
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Solène Hébert
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - David Faulkner
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Alex Loguinov
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Michael Proctor
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Jonathan A Villalobos
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kathleen A Bjornstad
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Chris J Rosen
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Christopher Vulpe
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA
| | - Rebecca J Abergel
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Department of Nuclear Engineering, University of California, Berkeley, CA 94720, USA
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6
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Genome-wide toxicogenomic study of the lanthanides sheds light on the selective toxicity mechanisms associated with critical materials. Proc Natl Acad Sci U S A 2021; 118:2025952118. [PMID: 33903247 DOI: 10.1073/pnas.2025952118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Lanthanides are a series of critical elements widely used in multiple industries, such as optoelectronics and healthcare. Although initially considered to be of low toxicity, concerns have emerged during the last few decades over their impact on human health. The toxicological profile of these metals, however, has been incompletely characterized, with most studies to date solely focusing on one or two elements within the group. In the current study, we assessed potential toxicity mechanisms in the lanthanide series using a functional toxicogenomics approach in baker's yeast, which shares many cellular pathways and functions with humans. We screened the homozygous deletion pool of 4,291 Saccharomyces cerevisiae strains with the lanthanides and identified both common and unique functional effects of these metals. Three very different trends were observed within the lanthanide series, where deletions of certain proteins on membranes and organelles had no effect on the cellular response to early lanthanides while inducing yeast sensitivity and resistance to middle and late lanthanides, respectively. Vesicle-mediated transport (primarily endocytosis) was highlighted by both gene ontology and pathway enrichment analyses as one of the main functions disturbed by the majority of the metals. Protein-protein network analysis indicated that yeast response to lanthanides relied on proteins that participate in regulatory paths used for calcium (and other biologically relevant cations), and lanthanide toxicity included disruption of biosynthetic pathways by enzyme inhibition. Last, multiple genes and proteins identified in the network analysis have human orthologs, suggesting that those may also be targeted by lanthanides in humans.
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7
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Atias N, Kupiec M, Sharan R. Systematic identification and correction of annotation errors in the genetic interaction map of Saccharomyces cerevisiae. Nucleic Acids Res 2015; 44:e50. [PMID: 26602688 PMCID: PMC4797274 DOI: 10.1093/nar/gkv1284] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 11/04/2015] [Indexed: 01/05/2023] Open
Abstract
The yeast mutant collections are a fundamental tool in deciphering genomic organization and function. Over the last decade, they have been used for the systematic exploration of ∼6 000 000 double gene mutants, identifying and cataloging genetic interactions among them. Here we studied the extent to which these data are prone to neighboring gene effects (NGEs), a phenomenon by which the deletion of a gene affects the expression of adjacent genes along the genome. Analyzing ∼90,000 negative genetic interactions observed to date, we found that more than 10% of them are incorrectly annotated due to NGEs. We developed a novel algorithm, GINGER, to identify and correct erroneous interaction annotations. We validated the algorithm using a comparative analysis of interactions from Schizosaccharomyces pombe. We further showed that our predictions are significantly more concordant with diverse biological data compared to their mis-annotated counterparts. Our work uncovered about 9500 new genetic interactions in yeast.
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Affiliation(s)
- Nir Atias
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
| | - Martin Kupiec
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv 69978, Israel
| | - Roded Sharan
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
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8
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Braconi D, Bernardini G, Santucci A. Saccharomyces cerevisiae as a model in ecotoxicological studies: A post-genomics perspective. J Proteomics 2015; 137:19-34. [PMID: 26365628 DOI: 10.1016/j.jprot.2015.09.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 08/29/2015] [Accepted: 09/02/2015] [Indexed: 12/13/2022]
Abstract
The budding yeast Saccharomyces cerevisiae represents a well-consolidated and widely used eukaryotic model, with a number of features that make it an ideal organism to carry out functional toxicological studies. Several advantages are permitted by the use of yeast cells, as the possibility to identify molecular biomarkers, unknown mechanisms of action and novel potential targets. Thanks to the evolutionary conservation, yeast can provide also useful clues allowing the prioritization of more complex analyses and toxicity predictions in higher eukaryotes. The last two decades were incredibly fruitful for yeast "omics", but referring to the analysis of the effects of pesticides on yeast much still remains to be done. Furthermore, a deeper knowledge of the effects of environmental pollutants on biotechnological processes associated with the use of yeasts is to be hoped.
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Affiliation(s)
- Daniela Braconi
- Dipartimento di Biotecnologie, Chimica e Farmacia, via A. Moro 2, Università degli Studi di Siena, 53100 Siena, Italy
| | - Giulia Bernardini
- Dipartimento di Biotecnologie, Chimica e Farmacia, via A. Moro 2, Università degli Studi di Siena, 53100 Siena, Italy
| | - Annalisa Santucci
- Dipartimento di Biotecnologie, Chimica e Farmacia, via A. Moro 2, Università degli Studi di Siena, 53100 Siena, Italy.
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9
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Yeast toxicogenomics: lessons from a eukaryotic cell model and cell factory. Curr Opin Biotechnol 2015; 33:183-91. [DOI: 10.1016/j.copbio.2015.03.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 02/16/2015] [Accepted: 03/05/2015] [Indexed: 12/21/2022]
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10
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Shen H, McHale CM, Smith MT, Zhang L. Functional genomic screening approaches in mechanistic toxicology and potential future applications of CRISPR-Cas9. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2015; 764:31-42. [PMID: 26041264 DOI: 10.1016/j.mrrev.2015.01.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 01/14/2015] [Accepted: 01/16/2015] [Indexed: 01/25/2023]
Abstract
Characterizing variability in the extent and nature of responses to environmental exposures is a critical aspect of human health risk assessment. Chemical toxicants act by many different mechanisms, however, and the genes involved in adverse outcome pathways (AOPs) and AOP networks are not yet characterized. Functional genomic approaches can reveal both toxicity pathways and susceptibility genes, through knockdown or knockout of all non-essential genes in a cell of interest, and identification of genes associated with a toxicity phenotype following toxicant exposure. Screening approaches in yeast and human near-haploid leukemic KBM7 cells have identified roles for genes and pathways involved in response to many toxicants but are limited by partial homology among yeast and human genes and limited relevance to normal diploid cells. RNA interference (RNAi) suppresses mRNA expression level but is limited by off-target effects (OTEs) and incomplete knockdown. The recently developed gene editing approach called clustered regularly interspaced short palindrome repeats-associated nuclease (CRISPR)-Cas9, can precisely knock-out most regions of the genome at the DNA level with fewer OTEs than RNAi, in multiple human cell types, thus overcoming the limitations of the other approaches. It has been used to identify genes involved in the response to chemical and microbial toxicants in several human cell types and could readily be extended to the systematic screening of large numbers of environmental chemicals. CRISPR-Cas9 can also repress and activate gene expression, including that of non-coding RNA, with near-saturation, thus offering the potential to more fully characterize AOPs and AOP networks. Finally, CRISPR-Cas9 can generate complex animal models in which to conduct preclinical toxicity testing at the level of individual genotypes or haplotypes. Therefore, CRISPR-Cas9 is a powerful and flexible functional genomic screening approach that can be harnessed to provide unprecedented mechanistic insight in the field of modern toxicology.
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Affiliation(s)
- Hua Shen
- Superfund Research Program, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA 94720, USA
| | - Cliona M McHale
- Superfund Research Program, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA 94720, USA
| | - Martyn T Smith
- Superfund Research Program, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA 94720, USA
| | - Luoping Zhang
- Superfund Research Program, Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA 94720, USA.
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Gaytán BD, Vulpe CD. Functional toxicology: tools to advance the future of toxicity testing. Front Genet 2014; 5:110. [PMID: 24847352 PMCID: PMC4017141 DOI: 10.3389/fgene.2014.00110] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 04/12/2014] [Indexed: 11/16/2022] Open
Abstract
The increased presence of chemical contaminants in the environment is an undeniable concern to human health and ecosystems. Historically, by relying heavily upon costly and laborious animal-based toxicity assays, the field of toxicology has often neglected examinations of the cellular and molecular mechanisms of toxicity for the majority of compounds—information that, if available, would strengthen risk assessment analyses. Functional toxicology, where cells or organisms with gene deletions or depleted proteins are used to assess genetic requirements for chemical tolerance, can advance the field of toxicity testing by contributing data regarding chemical mechanisms of toxicity. Functional toxicology can be accomplished using available genetic tools in yeasts, other fungi and bacteria, and eukaryotes of increased complexity, including zebrafish, fruit flies, rodents, and human cell lines. Underscored is the value of using less complex systems such as yeasts to direct further studies in more complex systems such as human cell lines. Functional techniques can yield (1) novel insights into chemical toxicity; (2) pathways and mechanisms deserving of further study; and (3) candidate human toxicant susceptibility or resistance genes.
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Affiliation(s)
- Brandon D Gaytán
- Department of Nutritional Science and Toxicology, University of California Berkeley Berkeley, CA, USA
| | - Chris D Vulpe
- Department of Nutritional Science and Toxicology, University of California Berkeley Berkeley, CA, USA
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