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Naruse C, Sugihara K, Miyazaki T, Pan X, Sugiyama F, Asano M. A degron system targeting endogenous PD-1 inhibits the growth of tumor cells in mice. NAR Cancer 2022; 4:zcac019. [PMID: 35734392 PMCID: PMC9204894 DOI: 10.1093/narcan/zcac019] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 05/26/2022] [Accepted: 06/03/2022] [Indexed: 11/12/2022] Open
Abstract
Recently, targeted protein degradation systems have been developed using the ubiquitin-proteasome system. Here, we established Programmed cell death-1 (PD-1) knockdown mice as a model system for subjecting endogenous mouse proteins to the small molecule-assisted shutoff (SMASh) degron system. SMASh degron-tagged PD-1-mCherry in Jurkat cells and CD3+ splenocytes were degraded by the NS3/4A protease inhibitors, asunaprevir (ASV) or grazoprevir (GRV). Growth of MC-38 colon adenocarcinoma cells injected in Pdcd1-mCherry-SMASh homozygous knock-in (KI) mice was repressed by ASV or GRV. Moreover, growth of MC-38 cells was suppressed in wild-type mice transplanted with KI bone marrow cells after GRV treatment. This is the first study to use a degron tag targeting an endogenous mouse protein in vivo. Our experimental system using the SMASh degron may be employed for treating diseases and characterizing the cellular functions of essential proteins.
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Affiliation(s)
- Chie Naruse
- Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazushi Sugihara
- Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tatsuhiko Miyazaki
- Department of Pathology, Gifu University Hospital, 1-1 Yanagido, Gifu 501-1104, Japan
| | - Xuchi Pan
- Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Fumihiro Sugiyama
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Masahide Asano
- Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
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2
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Kenney AD, Aron SL, Gilbert C, Kumar N, Chen P, Eddy A, Zhang L, Zani A, Vargas-Maldonado N, Speaks S, Kawahara J, Denz PJ, Dorn L, Accornero F, Ma J, Zhu H, Rajaram MVS, Cai C, Langlois RA, Yount JS. Influenza virus replication in cardiomyocytes drives heart dysfunction and fibrosis. SCIENCE ADVANCES 2022; 8:eabm5371. [PMID: 35544568 PMCID: PMC9094651 DOI: 10.1126/sciadv.abm5371] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 03/24/2022] [Indexed: 05/04/2023]
Abstract
Cardiac dysfunction is a common complication of severe influenza virus infection, but whether this occurs due to direct infection of cardiac tissue or indirectly through systemic lung inflammation remains unclear. To test the etiology of this aspect of influenza disease, we generated a novel recombinant heart-attenuated influenza virus via genome incorporation of target sequences for miRNAs expressed in cardiomyocytes. Compared with control virus, mice infected with miR-targeted virus had significantly reduced heart viral titers, confirming cardiac attenuation of viral replication. However, this virus was fully replicative in the lungs and induced similar systemic inflammation and weight loss compared to control virus. The miR-targeted virus induced fewer cardiac conduction irregularities and significantly less fibrosis in mice lacking interferon-induced transmembrane protein 3 (IFITM3), which serve as a model for influenza-associated cardiac pathology. We conclude that robust virus replication in the heart is required for pathology, even when lung inflammation is severe.
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Affiliation(s)
- Adam D. Kenney
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, Viruses and Emerging Pathogens Program, The Ohio State University, Columbus, OH, USA
| | - Stephanie L. Aron
- Department of Microbiology and Immunology, The University of Minnesota, Minneapolis, MN, USA
| | - Clara Gilbert
- Department of Microbiology and Immunology, The University of Minnesota, Minneapolis, MN, USA
| | - Naresh Kumar
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
| | - Peng Chen
- Department of Physiology and Cell Biology, The Ohio State University, Columbus, OH, USA
| | - Adrian Eddy
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, Viruses and Emerging Pathogens Program, The Ohio State University, Columbus, OH, USA
| | - Lizhi Zhang
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, Viruses and Emerging Pathogens Program, The Ohio State University, Columbus, OH, USA
| | - Ashley Zani
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, Viruses and Emerging Pathogens Program, The Ohio State University, Columbus, OH, USA
| | - Nahara Vargas-Maldonado
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
| | - Samuel Speaks
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
| | - Jeffrey Kawahara
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, Viruses and Emerging Pathogens Program, The Ohio State University, Columbus, OH, USA
| | - Parker J. Denz
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, Viruses and Emerging Pathogens Program, The Ohio State University, Columbus, OH, USA
| | - Lisa Dorn
- Department of Physiology and Cell Biology, The Ohio State University, Columbus, OH, USA
| | - Federica Accornero
- Department of Physiology and Cell Biology, The Ohio State University, Columbus, OH, USA
| | - Jianjie Ma
- Department of Surgery, The Ohio State University, Columbus, OH, USA
| | - Hua Zhu
- Department of Surgery, The Ohio State University, Columbus, OH, USA
| | - Murugesan V. S. Rajaram
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
| | - Chuanxi Cai
- Department of Surgery, The Ohio State University, Columbus, OH, USA
| | - Ryan A. Langlois
- Department of Microbiology and Immunology, The University of Minnesota, Minneapolis, MN, USA
| | - Jacob S. Yount
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA
- Infectious Diseases Institute, Viruses and Emerging Pathogens Program, The Ohio State University, Columbus, OH, USA
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3
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tenOever BR. Synthetic Virology: Building Viruses to Better Understand Them. Cold Spring Harb Perspect Med 2020; 10:cshperspect.a038703. [PMID: 31871242 DOI: 10.1101/cshperspect.a038703] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Generally comprised of less than a dozen components, RNA viruses can be viewed as well-designed genetic circuits optimized to replicate and spread within a given host. Understanding the molecular design that enables this activity not only allows one to disrupt these circuits to study their biology, but it provides a reprogramming framework to achieve novel outputs. Recent advances have enabled a "learning by building" approach to better understand virus biology and create valuable tools. Below is a summary of how modifying the preexisting genetic framework of influenza A virus has been used to track viral movement, understand virus replication, and identify host factors that engage this viral circuitry.
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Affiliation(s)
- Benjamin R tenOever
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
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4
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Fay EJ, Aron SL, Macchietto MG, Markman MW, Esser-Nobis K, Gale M, Shen S, Langlois RA. Cell type- and replication stage-specific influenza virus responses in vivo. PLoS Pathog 2020; 16:e1008760. [PMID: 32790753 PMCID: PMC7447048 DOI: 10.1371/journal.ppat.1008760] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 08/25/2020] [Accepted: 06/29/2020] [Indexed: 12/22/2022] Open
Abstract
Influenza A viruses (IAVs) remain a significant global health burden. Activation of the innate immune response is important for controlling early virus replication and spread. It is unclear how early IAV replication events contribute to immune detection. Additionally, while many cell types in the lung can be infected, it is not known if all cell types contribute equally to establish the antiviral state in the host. Here, we use single-cycle influenza A viruses (scIAVs) to characterize the early immune response to IAV in vitro and in vivo. We found that the magnitude of virus replication contributes to antiviral gene expression within infected cells prior to the induction of a global response. We also developed a scIAV that is only capable of undergoing primary transcription, the earliest stage of virus replication. Using this tool, we uncovered replication stage-specific responses in vitro and in vivo. Using several innate immune receptor knockout cell lines, we identify RIG-I as the predominant antiviral detector of primary virus transcription and amplified replication in vitro. Through a Cre-inducible reporter mouse, we used scIAVs expressing Cre-recombinase to characterize cell type-specific responses in vivo. Individual cell types upregulate unique sets of antiviral genes in response to both primary virus transcription and amplified replication. We also identified antiviral genes that are only upregulated in response to direct infection. Altogether, these data offer insight into the early mechanisms of antiviral gene activation during influenza A infection.
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Affiliation(s)
- Elizabeth J. Fay
- Biochemistry, Molecular Biology and Biophysics Graduate Program, University of Minnesota, Minneapolis MN, United States of America
- Center for Immunology, University of Minnesota, Minneapolis MN, United States of America
| | - Stephanie L. Aron
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis MN, United States of America
| | - Marissa G. Macchietto
- Institute for Health Informatics, University of Minnesota, Minneapolis MN, United States of America
| | - Matthew W. Markman
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis MN, United States of America
| | - Katharina Esser-Nobis
- Department of Immunology and Center for Innate Immunity and Immune Disease, University of Washington, Seattle WA, United States of America
| | - Michael Gale
- Department of Immunology and Center for Innate Immunity and Immune Disease, University of Washington, Seattle WA, United States of America
| | - Steven Shen
- Institute for Health Informatics, University of Minnesota, Minneapolis MN, United States of America
| | - Ryan A. Langlois
- Biochemistry, Molecular Biology and Biophysics Graduate Program, University of Minnesota, Minneapolis MN, United States of America
- Center for Immunology, University of Minnesota, Minneapolis MN, United States of America
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis MN, United States of America
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5
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On the cutting edge: protease-based methods for sensing and controlling cell biology. Nat Methods 2020; 17:885-896. [PMID: 32661424 DOI: 10.1038/s41592-020-0891-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 06/09/2020] [Indexed: 02/06/2023]
Abstract
Sequence-specific proteases have proven to be versatile building blocks for tools that report or control cellular function. Reporting methods link protease activity to biochemical signals, whereas control methods rely on engineering proteases to respond to exogenous inputs such as light or chemicals. In turn, proteases have inherent control abilities, as their native functions are to release, activate or destroy proteins by cleavage, with the irreversibility of proteolysis allowing sustained downstream effects. As a result, protease-based synthetic circuits have been created for diverse uses such as reporting cellular signaling, tuning protein expression, controlling viral replication and detecting cancer states. Here, we comprehensively review the development and application of protease-based methods for reporting and controlling cellular function in eukaryotes.
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6
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Wu T, Yoon H, Xiong Y, Dixon-Clarke SE, Nowak RP, Fischer ES. Targeted protein degradation as a powerful research tool in basic biology and drug target discovery. Nat Struct Mol Biol 2020; 27:605-614. [PMID: 32541897 PMCID: PMC7923177 DOI: 10.1038/s41594-020-0438-0] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 04/23/2020] [Indexed: 12/16/2022]
Abstract
Controlled perturbation of protein activity is essential to study protein function in cells and living organisms. Small molecules that hijack the cellular protein ubiquitination machinery to selectively degrade proteins of interest, so-called degraders, have recently emerged as alternatives to selective chemical inhibitors, both as therapeutic modalities and as powerful research tools. These systems offer unprecedented temporal and spatial control over protein function. Here, we review recent developments in this field, with a particular focus on the use of degraders as research tools to interrogate complex biological problems.
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Affiliation(s)
- Tao Wu
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Hojong Yoon
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Yuan Xiong
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Sarah E Dixon-Clarke
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Radosław P Nowak
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Eric S Fischer
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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7
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Fiege JK, Stone IA, Dumm RE, Waring BM, Fife BT, Agudo J, Brown BD, Heaton NS, Langlois RA. Long-term surviving influenza infected cells evade CD8+ T cell mediated clearance. PLoS Pathog 2019; 15:e1008077. [PMID: 31557273 PMCID: PMC6782110 DOI: 10.1371/journal.ppat.1008077] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 10/08/2019] [Accepted: 09/11/2019] [Indexed: 01/02/2023] Open
Abstract
Influenza A virus (IAV) is a seasonal pathogen with the potential to cause devastating pandemics. IAV infects multiple epithelial cell subsets in the respiratory tract, eliciting damage to the lungs. Clearance of IAV is primarily dependent on CD8+ T cells, which must balance control of the infection with immunopathology. Using a virus expressing Cre recombinase to permanently label infected cells in a Cre-inducible reporter mouse, we previously discovered infected club cells that survive both lytic virus replication and CD8+ T cell-mediated clearance. In this study, we demonstrate that ciliated epithelial cells, type I and type II alveolar cells can also become survivor cells. Survivor cells are stable in the lung long-term and demonstrate enhanced proliferation compared to uninfected cells. When we investigated how survivor cells evade CD8+ T cell killing we observed that survivor cells upregulated the inhibitory ligand PD-L1, but survivor cells did not use PD-L1 to evade CD8+ T cell killing. Instead our data suggest that survivor cells are not inherently resistant to CD8+ T cell killing, but instead no longer present IAV antigen and cannot be detected by CD8+ T cells. Finally, we evaluate the failure of CD8+ T cells to kill these previously infected cells. This work demonstrates that additional cell types can survive IAV infection and that these cells robustly proliferate and are stable long term. By sparing previously infected cells, the adaptive immune system may be minimizing pathology associated with IAV infection.
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Affiliation(s)
- Jessica K. Fiege
- University of Minnesota, Department of Microbiology and Immunology and the Center for Immunology, Minneapolis, Minnesota, United States of America
| | - Ian A. Stone
- University of Minnesota, Department of Microbiology and Immunology and the Center for Immunology, Minneapolis, Minnesota, United States of America
| | - Rebekah E. Dumm
- Duke University School of Medicine, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
| | - Barbara M. Waring
- University of Minnesota, Department of Microbiology and Immunology and the Center for Immunology, Minneapolis, Minnesota, United States of America
| | - Brian T. Fife
- University of Minnesota, Department of Medicine and the Center for Immunology, Minneapolis, Minnesota, United States of America
| | - Judith Agudo
- Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences, New York City, New York, United States of America
| | - Brian D. Brown
- Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences, New York City, New York, United States of America
| | - Nicholas S. Heaton
- Duke University School of Medicine, Department of Molecular Genetics and Microbiology, Durham, North Carolina, United States of America
| | - Ryan A. Langlois
- University of Minnesota, Department of Microbiology and Immunology and the Center for Immunology, Minneapolis, Minnesota, United States of America
- * E-mail:
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