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Caputo A, Sartini S, Levati E, Minato I, Elisi GM, Di Stasi A, Guillou C, Goekjian PG, Garcia P, Gueyrard D, Bach S, Comte A, Ottonello S, Rivara S, Montanini B. An Optimized Workflow for the Discovery of New Antimicrobial Compounds Targeting Bacterial RNA Polymerase Complex Formation. Antibiotics (Basel) 2022; 11:antibiotics11101449. [PMID: 36290107 PMCID: PMC9598883 DOI: 10.3390/antibiotics11101449] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 11/16/2022] Open
Abstract
Bacterial resistance represents a major health problem worldwide and there is an urgent need to develop first-in-class compounds directed against new therapeutic targets. We previously developed a drug-discovery platform to identify new antimicrobials able to disrupt the protein–protein interaction between the β’ subunit and the σ70 initiation factor of bacterial RNA polymerase, which is essential for transcription. As a follow-up to such work, we have improved the discovery strategy to make it less time-consuming and more cost-effective. This involves three sequential assays, easily scalable to a high-throughput format, and a subsequent in-depth characterization only limited to hits that passed the three tests. This optimized workflow, applied to the screening of 5360 small molecules from three synthetic and natural compound libraries, led to the identification of six compounds interfering with the β’–σ70 interaction, and thus was capable of inhibiting promoter-specific RNA transcription and bacterial growth. Upon supplementation with a permeability adjuvant, the two most potent transcription-inhibiting compounds displayed a strong antibacterial activity against Escherichia coli with minimum inhibitory concentration (MIC) values among the lowest (0.87–1.56 μM) thus far reported for β’–σ PPI inhibitors. The newly identified hit compounds share structural feature similarities with those of a pharmacophore model previously developed from known inhibitors.
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Affiliation(s)
- Alessia Caputo
- Laboratory of Biochemistry and Molecular Biology, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
- Interdepartmental Research Centre Biopharmanet-Tec, University of Parma, 43124 Parma, Italy
| | - Sara Sartini
- Laboratory of Biochemistry and Molecular Biology, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Elisabetta Levati
- Laboratory of Biochemistry and Molecular Biology, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Ilaria Minato
- Laboratory of Biochemistry and Molecular Biology, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
- Interdepartmental Research Centre Biopharmanet-Tec, University of Parma, 43124 Parma, Italy
| | - Gian Marco Elisi
- Department of Food and Drug, University of Parma, 43124 Parma, Italy
| | - Adriana Di Stasi
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Catherine Guillou
- Centre de Recherche de Gif, Institut de Chimie des Substances Naturelles, CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Peter G. Goekjian
- Laboratoire Chimie Organique 2 Glycochimie, ICBMS UMR 5246 CNRS-Université Claude Bernard Lyon 1, Université de Lyon, 69622 Villeurbanne, France
| | - Pierre Garcia
- Laboratoire Chimie Organique 2 Glycochimie, ICBMS UMR 5246 CNRS-Université Claude Bernard Lyon 1, Université de Lyon, 69622 Villeurbanne, France
| | - David Gueyrard
- Laboratoire Chimie Organique 2 Glycochimie, ICBMS UMR 5246 CNRS-Université Claude Bernard Lyon 1, Université de Lyon, 69622 Villeurbanne, France
| | - Stéphane Bach
- Sorbonne Université, CNRS, UMR 8227, Integrative Biology of Marine Models, Team Physiology and Cell Fate, Station Biologique de Roscoff, CS 90074, 29680 Roscoff, France
- Sorbonne Université, CNRS, FR 2424, Plateforme de criblage KISSf (Kinase Inhibitor Specialized Screening Facility), Station Biologique de Roscoff, 29680 Roscoff, France
- Centre of Excellence for Pharmaceutical Sciences, North-West University, Private Bag X6001, Potchefstroom 2520, South Africa
| | - Arnaud Comte
- Chimiothèque, ICBMS UMR 5246 CNRS-Université Claude Bernard Lyon 1, Université de Lyon, 69622 Villeurbanne, France
| | - Simone Ottonello
- Laboratory of Biochemistry and Molecular Biology, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
- Interdepartmental Research Centre Biopharmanet-Tec, University of Parma, 43124 Parma, Italy
| | - Silvia Rivara
- Interdepartmental Research Centre Biopharmanet-Tec, University of Parma, 43124 Parma, Italy
- Department of Food and Drug, University of Parma, 43124 Parma, Italy
| | - Barbara Montanini
- Laboratory of Biochemistry and Molecular Biology, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
- Interdepartmental Research Centre Biopharmanet-Tec, University of Parma, 43124 Parma, Italy
- Correspondence: ; Tel.: +39-0521-905654
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Burgess RR. What is in the black box? The discovery of the sigma factor and the subunit structure of E. coli RNA polymerase. J Biol Chem 2021; 297:101310. [PMID: 34673029 PMCID: PMC8569590 DOI: 10.1016/j.jbc.2021.101310] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/13/2021] [Indexed: 11/24/2022] Open
Abstract
This Reflections article is focused on the 5 years while I was a graduate student (1964-1969). During this period, I made some of the most significant discoveries of my career. I have written this article primarily for a protein biochemistry audience, my colleagues who shared this exciting time in science, and the many scientists over the last 50 years who have contributed to our knowledge of transcriptional machinery and their regulation. It is also written for today's graduate students, postdocs, and scientists who may not know much about the discoveries and technical advances that are now taken for granted, to show that even with methods primitive by today's standards, we were still able to make foundational advances. I also hope to provide a glimpse into how fortunate I was to be a graduate student over 50 years ago in the golden age of molecular biology.
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Affiliation(s)
- Richard R Burgess
- James D. Watson Professor Emeritus of Oncology, McArdle Laboratory for Cancer Research, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA.
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Abstract
The low G + C Gram-positive bacteria represent some of the most medically and industrially important microorganisms. They are relied on for the production of food and dietary supplements, enzymes and antibiotics, as well as being responsible for the majority of nosocomial infections and serving as a reservoir for antibiotic resistance. Control of gene expression in this group is more highly studied than in any bacteria other than the Gram-negative model Escherichia coli, yet until recently no structural information on RNA polymerase (RNAP) from this group was available. This review will summarize recent reports on the high-resolution structure of RNAP from the model low G + C representative Bacillus subtilis, including the role of auxiliary subunits δ and ε, and outline approaches for the development of antimicrobials to target RNAP from this group.
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Affiliation(s)
- Michael Miller
- School Of Environmental And Life Sciences, University Of Newcastle, Callaghan, NSW, Australia
| | - Aaron J Oakley
- School Of Environmental And Life Sciences, University Of Newcastle, Callaghan, NSW, Australia
| | - Peter J Lewis
- School Of Environmental And Life Sciences, University Of Newcastle, Callaghan, NSW, Australia.,School Of Chemistry And Molecular Bioscience, University Of Wollongong And Illawarra Health And Medical Research Institute, Wollongong, Nsw, Australia
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Musial-Siwek M, Jaffee MB, Imperiali B. Probing Polytopic Membrane Protein-Substrate Interactions by Luminescence Resonance Energy Transfer. J Am Chem Soc 2016; 138:3806-12. [PMID: 26918528 DOI: 10.1021/jacs.5b13426] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Integral membrane proteins play essential roles in all living systems; however, major technical hurdles challenge analyses of this class of proteins. Biophysical approaches that provide structural information to complement and leverage experimentally determined and computationally predicted structures are urgently needed. Herein we present the application of luminescence resonance energy transfer (LRET) for investigating the interactions of the polytopic membrane-bound oligosaccharyl transferases (OTases) with partner substrates. Monomeric OTases, such as the PglBs from Campylobacter jejuni and Campylobacter lari, catalyze transfer of glycans from membrane-associated undecaprenol diphosphate-linked substrates to proteins in the bacterial periplasm. LRET-based distance measurements are enabled by the inclusion of an encoded N-terminal lanthanide-binding tag (LBT), and LRET between the luminescent (LBT)-Tb(3+) donor complex and fluorescently labeled peptide and glycan substrates provides discrete distance measurements across the span of the membrane. LRET-based measurements of detergent-solubilized PglB from C. lari allowed direct comparison with the distances based on the previously reported the C. lari PglB crystal structure, thereby validating the approach in a defined system. Distance measurements between peptide and glycan substrates and the C. jejuni PglB offer new experimental information on substrate binding to the related, but structurally uncharacterized, eukaryotic OTase.
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Affiliation(s)
- Monika Musial-Siwek
- Departments of Biology and Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Marcie B Jaffee
- Departments of Biology and Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Barbara Imperiali
- Departments of Biology and Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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Ma C, Yang X, Lewis PJ. Bacterial Transcription Inhibitor of RNA Polymerase Holoenzyme Formation by Structure-Based Drug Design: From in Silico Screening to Validation. ACS Infect Dis 2016; 2:39-46. [PMID: 27622946 DOI: 10.1021/acsinfecdis.5b00058] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacterial transcription is a proven target for antibacterial research. However, most of the known inhibitors targeting transcription are from natural extracts or are hits from screens where the binding site remains unidentified. Using an RNA polymerase holoenzyme homology structure from the model Gram-positive organism Bacillus subtilis, we created a pharmacophore model and used it for in silico screening of a publicly available library for compounds able to inhibit holoenzyme formation. The hits demonstrated specific affinity to bacterial RNA polymerase and excellent activity using in vitro assays and showed no binding to the equivalent structure from human RNA polymerase II. The target specificity in live cells and antibacterial activity was demonstrated in microscopy and growth inhibition experiments. This is the first example of targeted inhibitor development for a bacterial RNA polymerase, outlining a complete discovery process from virtual screening to biochemical validation. This approach could serve as an appropriate platform for the future identification of inhibitors of bacterial transcription.
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Affiliation(s)
- Cong Ma
- School of Environmental and Life
Sciences, University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Xiao Yang
- School of Environmental and Life
Sciences, University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - Peter J. Lewis
- School of Environmental and Life
Sciences, University of Newcastle, Callaghan, New South Wales 2308, Australia
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Yang X, Ma C, Lewis PJ. Identification of inhibitors of bacterial RNA polymerase. Methods 2015; 86:45-50. [PMID: 25976836 DOI: 10.1016/j.ymeth.2015.05.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 04/28/2015] [Accepted: 05/05/2015] [Indexed: 01/09/2023] Open
Abstract
Very few clinically available antibiotics target bacterial RNA polymerase (RNAP) suggesting it is an underutilized target. The advent of detailed structural information of RNAP holoenzyme (HE) has allowed the design and in silico screening of novel transcription inhibitors. Here, we describe our approach for the design and testing of small molecule transcription inhibitors that work by preventing the interaction between the essential transcription initiation factor σ and RNAP. With the appropriate structural information this approach can be easily modified to other essential protein-protein interactions.
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Affiliation(s)
- Xiao Yang
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Cong Ma
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Peter J Lewis
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia.
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Surface plasmon resonance – more than a screening technology: insights in the binding mode of σ70:core RNAP inhibitors. Future Med Chem 2014; 6:1551-65. [DOI: 10.4155/fmc.14.105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Aim: Antibiotic resistance has become a major health problem. The σ70:core interface of bacterial RNA polymerase is a promising drug target. Recently, the coiled-coil and lid-rudder-system of the β’ subunit has been identified as an inhibition hot spot. Materials & methods & Results: By using surface plasmon resonance-based assays, inhibitors of the protein–protein interaction were identified and competition with σ70 was shown. Effective inhibition was verified in an in vitro transcription and a σ70:core assembly assay. For one hit series, we found a correlation between activity and affinity. Mutant interaction studies suggest the inhibitors’ binding site. Conclusion: Surface plasmon resonance is a valuable technology in drug design, that has been used in this study to identify and evaluate σ70:core RNA polymerase inhibitors.
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Hüsecken K, Negri M, Fruth M, Boettcher S, Hartmann RW, Haupenthal J. Peptide-based investigation of the Escherichia coli RNA polymerase σ(70):core interface as target site. ACS Chem Biol 2013; 8:758-66. [PMID: 23330640 DOI: 10.1021/cb3005758] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The number of bacterial strains that are resistant against antibiotics increased dramatically during the past decades. This fact stresses the urgent need for the development of new antibacterial agents with novel modes of action targeting essential enzymes such as RNA polymerase (RNAP). Bacterial RNAP is a large multi-subunit complex consisting of a core enzyme (subunits: α(2)ββ'ω) and a dissociable sigma factor (σ(70); holo enzyme: α(2)ββ'ωσ(70)) that is responsible for promoter recognition and transcription initiation. The interface between core RNAP and σ(70) represents a promising binding site. Nevertheless, detailed studies investigating its druggability are rare. Compounds binding to this region could inhibit this protein-protein interaction and thus holo enzyme formation, resulting in inhibition of transcription initiation. Sixteen peptides covering different regions of the Escherichia coli σ(70):core interface were designed; some of them-all derived from σ(70) 2.2 region-led to a strong RNAP inhibition. Indeed, an ELISA-based experiment confirmed the most active peptide P07 to inhibit the σ(70):core interaction. Furthermore, an abortive transcription assay revealed that P07 impedes transcription initiation. In order to study the mechanism of action of P07 in more detail, molecular dynamics simulations and a rational amino acid replacement study were performed, leading to the conclusion that P07 binds to the coiled-coil region in β' and that its flexible N-terminus inhibits the enzyme by interaction with the β' lid-rudder-system (LRS). This work revisits the β' coiled-coil as a hot spot for the protein-protein interaction inhibition and expands it by introduction of the LRS as target site.
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Affiliation(s)
- Kristina Hüsecken
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Department
of Drug Design and Optimization and ‡Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2_3, D-66123
Saarbrücken, Germany
| | - Matthias Negri
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Department
of Drug Design and Optimization and ‡Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2_3, D-66123
Saarbrücken, Germany
| | - Martina Fruth
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Department
of Drug Design and Optimization and ‡Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2_3, D-66123
Saarbrücken, Germany
| | - Stefan Boettcher
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Department
of Drug Design and Optimization and ‡Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2_3, D-66123
Saarbrücken, Germany
| | - Rolf W. Hartmann
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Department
of Drug Design and Optimization and ‡Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2_3, D-66123
Saarbrücken, Germany
| | - Joerg Haupenthal
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Department
of Drug Design and Optimization and ‡Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C2_3, D-66123
Saarbrücken, Germany
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The Listeria monocytogenes σB regulon and its virulence-associated functions are inhibited by a small molecule. mBio 2011; 2:mBio.00241-11. [PMID: 22128349 PMCID: PMC3225968 DOI: 10.1128/mbio.00241-11] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The stress-responsive alternative sigma factor σB is conserved across diverse Gram-positive bacterial genera. In Listeria monocytogenes, σB regulates transcription of >150 genes, including genes contributing to virulence and to bacterial survival under host-associated stress conditions, such as those encountered in the human gastrointestinal lumen. An inhibitor of L. monocytogenes σB activity was identified by screening ~57,000 natural and synthesized small molecules using a high-throughput cell-based assay. The compound fluoro-phenyl-styrene-sulfonamide (FPSS) (IC50 = 3.5 µM) downregulated the majority of genes previously identified as members of the σB regulon in L. monocytogenes 10403S, thus generating a transcriptional profile comparable to that of a 10403S ΔsigB strain. Specifically, of the 208 genes downregulated by FPSS, 75% had been identified previously as positively regulated by σB. Downregulated genes included key virulence and stress response genes, such as inlA, inlB, bsh, hfq, opuC, and bilE. From a functional perspective, FPSS also inhibited L. monocytogenes invasion of human intestinal epithelial cells and bile salt hydrolase activity. The ability of FPSS to inhibit σB activity in both L. monocytogenes and Bacillus subtilis indicates its utility as a specific inhibitor of σB across multiple Gram-positive genera. The σB transcription factor regulates expression of genes responsible for bacterial survival under changing environmental conditions and for virulence; therefore, this alternative sigma factor is important for transmission of L. monocytogenes and other Gram-positive bacteria. Regulation of σB activity is complex and tightly controlled, reflecting the key role of this factor in bacterial metabolism. We present multiple lines of evidence indicating that fluoro-phenyl-styrene-sulfonamide (FPSS) specifically inhibits activity of σB across Gram-positive bacterial genera, i.e., in both Listeria monocytogenes and Bacillus subtilis. Therefore, FPSS is an important new tool that will enable novel approaches for exploring complex regulatory networks in L. monocytogenes and other Gram-positive pathogens and for investigating small-molecule applications for controlling pathogen transmission.
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Glaser BT, Bergendahl V, Anthony LC, Olson B, Burgess RR. Studying the salt dependence of the binding of sigma70 and sigma32 to core RNA polymerase using luminescence resonance energy transfer. PLoS One 2009; 4:e6490. [PMID: 19649256 PMCID: PMC2715106 DOI: 10.1371/journal.pone.0006490] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2009] [Accepted: 06/19/2009] [Indexed: 12/04/2022] Open
Abstract
The study of protein-protein interactions is becoming increasingly important for understanding the regulation of many cellular processes. The ability to quantify the strength with which two binding partners interact is desirable but the accurate determination of equilibrium binding constants is a difficult process. The use of Luminescence Resonance Energy Transfer (LRET) provides a homogeneous binding assay that can be used for the detection of protein-protein interactions. Previously, we developed an LRET assay to screen for small molecule inhibitors of the interaction of σ70 with theβ' coiled-coil fragment (amino acids 100–309). Here we describe an LRET binding assay used to monitor the interaction of E. coli σ70 and σ32 with core RNA polymerase along with the controls to verify the system. This approach generates fluorescently labeled proteins through the random labeling of lysine residues which enables the use of the LRET assay for proteins for which the creation of single cysteine mutants is not feasible. With the LRET binding assay, we are able to show that the interaction of σ70 with core RNAP is much more sensitive to NaCl than to potassium glutamate (KGlu), whereas the σ32 interaction with core RNAP is insensitive to both salts even at concentrations >500 mM. We also find that the interaction of σ32 with core RNAP is stronger than σ70 with core RNAP, under all conditions tested. This work establishes a consistent set of conditions for the comparison of the binding affinities of the E.coli sigma factors with core RNA polymerase. The examination of the importance of salt conditions in the binding of these proteins could have implications in both in vitro assay conditions and in vivo function.
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Affiliation(s)
- Bryan T Glaser
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, USA
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