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Patange S, Maragh S. Fire Burn and Cauldron Bubble: What Is in Your Genome Editing Brew? Biochemistry 2023; 62:3500-3511. [PMID: 36306429 PMCID: PMC10734218 DOI: 10.1021/acs.biochem.2c00431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/28/2022] [Indexed: 11/28/2022]
Abstract
Genome editing is a rapidly evolving biotechnology with the potential to transform many sectors of industry such as agriculture, biomanufacturing, and medicine. This technology is enabled by an ever-growing portfolio of biomolecular reagents that span the central dogma, from DNA to RNA to protein. In this paper, we draw from our unique perspective as the National Metrology Institute of the United States to bring attention to the importance of understanding and reporting genome editing formulations accurately and promoting concepts to verify successful delivery into cells. Achieving the correct understanding may be hindered by the way units, quantities, and stoichiometries are reported in the field. We highlight the variability in how editing formulations are reported in the literature and examine how a reference molecule could be used to verify the delivery of a reagent into cells. We provide recommendations on how more accurate reporting of editing formulations and more careful verification of the steps in an editing experiment can help set baseline expectations of reagent performance, toward the aim of enabling genome editing studies to be more reproducible. We conclude with a future outlook on technologies that can further our control and enable our understanding of genome editing outcomes at the single-cell level.
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Affiliation(s)
- Simona Patange
- Biosystems and Biomaterials
Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Samantha Maragh
- Biosystems and Biomaterials
Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
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2
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Qi Y, Wang M, Jiang Q. PABPC1--mRNA stability, protein translation and tumorigenesis. Front Oncol 2022; 12:1025291. [PMID: 36531055 PMCID: PMC9753129 DOI: 10.3389/fonc.2022.1025291] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 11/08/2022] [Indexed: 09/29/2023] Open
Abstract
Mammalian poly A-binding proteins (PABPs) are highly conserved multifunctional RNA-binding proteins primarily involved in the regulation of mRNA translation and stability, of which PABPC1 is considered a central regulator of cytoplasmic mRNA homing and is involved in a wide range of physiological and pathological processes by regulating almost every aspect of RNA metabolism. Alterations in its expression and function disrupt intra-tissue homeostasis and contribute to the development of various tumors. There is increasing evidence that PABPC1 is aberrantly expressed in a variety of tumor tissues and cancers such as lung, gastric, breast, liver, and esophageal cancers, and PABPC1 might be used as a potential biomarker for tumor diagnosis, treatment, and clinical application in the future. In this paper, we review the abnormal expression, functional role, and molecular mechanism of PABPC1 in tumorigenesis and provide directions for further understanding the regulatory role of PABPC1 in tumor cells.
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Affiliation(s)
- Ya Qi
- Department of Gynecology and Obstetrics, Shengjing Hospital Affiliated of China Medical University, Shenyang, Liaoning, China
| | - Min Wang
- Department of Gynecology and Obstetrics, Shengjing Hospital Affiliated of China Medical University, Shenyang, Liaoning, China
| | - Qi Jiang
- Second Department of Clinical Medicine, China Medical University, Shenyang, Liaoning, China
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Adhikari B, Narain A, Wolf E. Generation of auxin inducible degron (AID) knock-in cell lines for targeted protein degradation in mammalian cells. STAR Protoc 2021; 2:100949. [PMID: 34849487 PMCID: PMC8609061 DOI: 10.1016/j.xpro.2021.100949] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Targeted protein degradation using degrons, such as the mini-Auxin-inducible degron (mAID), has an advantage over genetic silencing/knockout. However, the efficiency of sgRNA, homologous recombination, tedious expansion, and screening single clones makes the process of tagging endogenous proteins long and laborious. This protocol describes a practical and economical way to obtain AID-tagged endogenous proteins using CRISPR/Cas9-mediated homology-directed repair (HDR). We use the generation of endogenously AID-tagged SPT6 in U2OS cells as an example but provide sufficient details for usage in other cell types. For complete details on the use and execution of this protocol, please refer to Narain et al. (2021).
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Affiliation(s)
- Bikash Adhikari
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Ashwin Narain
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Elmar Wolf
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
- Mildred Scheel Early Career Center, University of Würzburg, Beethovenstraße 1A, 97080 Würzburg, Germany
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Amen T, Guihur A, Zelent C, Ursache R, Wilting J, Kaganovich D. Resveratrol and related stilbene derivatives induce stress granules with distinct clearance kinetics. Mol Biol Cell 2021; 32:ar18. [PMID: 34432484 PMCID: PMC8693967 DOI: 10.1091/mbc.e21-02-0066] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Stress granules (SGs) are ribonucleoprotein functional condensates that form under stress conditions in all eukaryotic cells. Although their stress-survival function is far from clear, SGs have been implicated in the regulation of many vital cellular pathways. Consequently, SG dysfunction is thought to be a mechanistic point of origin for many neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS). Additionally, SGs are thought to play a role in pathogenic pathways as diverse as viral infection and chemotherapy resistance. There is a growing consensus on the hypothesis that understanding the mechanistic regulation of SG physical properties is essential to understanding their function. Although the internal dynamics and condensation mechanisms of SGs have been broadly investigated, there have been fewer investigations into the timing of SG formation and clearance in live cells. Because the lifetime of SG persistence can be a key factor in their function and tendency toward pathological dysregulation, SG clearance mechanisms deserve particular attention. Here we show that resveratrol and its analogues piceatannol, pterostilbene, and 3,4,5,4'-tetramethoxystilbene induce G3BP-dependent SG formation with atypically rapid clearance kinetics. Resveratrol binds to G3BP, thereby reducing its protein-protein association valency. We suggest that altering G3BP valency is a pathway for the formation of uniquely transient SGs.
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Affiliation(s)
- Triana Amen
- Department of Experimental Neurodegeneration, University Medical Center Göttingen, 37073, Goettingen, Germany
| | - Anthony Guihur
- Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne, Switzerland
| | - Christina Zelent
- Department of Anatomy and Cell Biology, University Medical Center Göttingen, 37073, Goettingen, Germany
| | - Robertas Ursache
- Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne, Switzerland
| | - Jörg Wilting
- Department of Anatomy and Cell Biology, University Medical Center Göttingen, 37073, Goettingen, Germany
| | - Daniel Kaganovich
- Department of Experimental Neurodegeneration, University Medical Center Göttingen, 37073, Goettingen, Germany.,1Base Pharmaceuticals, Boston, MA, 02129, USA
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Amen T, Kaganovich D. Stress granules inhibit fatty acid oxidation by modulating mitochondrial permeability. Cell Rep 2021; 35:109237. [PMID: 34133922 PMCID: PMC8220302 DOI: 10.1016/j.celrep.2021.109237] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 03/29/2021] [Accepted: 05/18/2021] [Indexed: 12/17/2022] Open
Abstract
The formation of stress granules (SGs) is an essential aspect of the cellular response to many kinds of stress, but its adaptive role is far from clear. SG dysfunction is implicated in aging-onset neurodegenerative diseases, prompting interest in their physiological function. Here, we report that during starvation stress, SGs interact with mitochondria and regulate metabolic remodeling. We show that SG formation leads to a downregulation of fatty acid β-oxidation (FAO) through the modulation of mitochondrial voltage-dependent anion channels (VDACs), which import fatty acids (FAs) into mitochondria. The subsequent decrease in FAO during long-term starvation reduces oxidative damage and rations FAs for longer use. Failure to form SGs, whether caused by the genetic deletion of SG components or an amyotrophic lateral sclerosis (ALS)-associated mutation, translates into an inability to downregulate FAO. Because metabolic dysfunction is a common pathological element of neurodegenerative diseases, including ALS, our findings provide a direction for studying the clinical relevance of SGs.
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Affiliation(s)
- Triana Amen
- Department of Experimental Neurodegeneration, University Medical Center Goettingen, Goettingen, Germany
| | - Daniel Kaganovich
- 1Base Pharmaceuticals, Boston, MA 02129, USA; Department of Experimental Neurodegeneration, University Medical Center Goettingen, Goettingen, Germany.
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Amen T, Kaganovich D. Small Molecule Screen Reveals Joint Regulation of Stress Granule Formation and Lipid Droplet Biogenesis. Front Cell Dev Biol 2021; 8:606111. [PMID: 33972926 PMCID: PMC8105174 DOI: 10.3389/fcell.2020.606111] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/21/2020] [Indexed: 01/22/2023] Open
Abstract
Metabolic regulation is a necessary component of all stress response pathways, because all different mechanisms of stress-adaptation place high-energy demands on the cell. Mechanisms that integrate diverse stress response pathways with their metabolic components are therefore of great interest, but few are known. We show that stress granule (SG) formation, a common adaptive response to a variety of stresses, is reciprocally regulated by the pathways inducing lipid droplet accumulation. Inability to upregulate lipid droplets reduces stress granule formation. Stress granule formation in turn drives lipid droplet clustering and fatty acid accumulation. Our findings reveal a novel connection between stress response pathways and new modifiers of stress granule formation.
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Affiliation(s)
- Triana Amen
- Department of Experimental Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
| | - Daniel Kaganovich
- Department of Experimental Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany.,1Base Pharmaceuticals, Boston, MA, United States
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