1
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Yoon J, Zhang YM, Her C, Grant RA, Ponomarenko AI, Ackermann BE, Hui T, Lin YS, Debelouchina GT, Shoulders MD. The immune-evasive proline-283 substitution in influenza nucleoprotein increases aggregation propensity without altering the native structure. SCIENCE ADVANCES 2024; 10:eadl6144. [PMID: 38640233 PMCID: PMC11029814 DOI: 10.1126/sciadv.adl6144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 03/15/2024] [Indexed: 04/21/2024]
Abstract
Nucleoprotein (NP) is a key structural protein of influenza ribonucleoprotein complexes and is central to viral RNA packing and trafficking. NP also determines the sensitivity of influenza to myxovirus resistance protein 1 (MxA), an innate immunity factor that restricts influenza replication. A few critical MxA-resistant mutations have been identified in NP, including the highly conserved proline-283 substitution. This essential proline-283 substitution impairs influenza growth, a fitness defect that becomes particularly prominent at febrile temperature (39°C) when host chaperones are depleted. Here, we biophysically characterize proline-283 NP and serine-283 NP to test whether the fitness defect is caused by the proline-283 substitution introducing folding defects. We show that the proline-283 substitution changes the folding pathway of NP, making NP more aggregation prone during folding, but does not alter the native structure of the protein. These findings suggest that influenza has evolved to hijack host chaperones to promote the folding of otherwise biophysically incompetent viral proteins that enable innate immune system escape.
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Affiliation(s)
- Jimin Yoon
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yu Meng Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Cheenou Her
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Robert A. Grant
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Anna I. Ponomarenko
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bryce E. Ackermann
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Tiffani Hui
- Department of Chemistry, Tufts University, Medford, MA, USA
| | - Yu-Shan Lin
- Department of Chemistry, Tufts University, Medford, MA, USA
| | - Galia T. Debelouchina
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Matthew D. Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
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2
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Abstract
Understanding the factors that shape viral evolution is critical for developing effective antiviral strategies, accurately predicting viral evolution, and preventing pandemics. One fundamental determinant of viral evolution is the interplay between viral protein biophysics and the host machineries that regulate protein folding and quality control. Most adaptive mutations in viruses are biophysically deleterious, resulting in a viral protein product with folding defects. In cells, protein folding is assisted by a dynamic system of chaperones and quality control processes known as the proteostasis network. Host proteostasis networks can determine the fates of viral proteins with biophysical defects, either by assisting with folding or by targeting them for degradation. In this review, we discuss and analyze new discoveries revealing that host proteostasis factors can profoundly shape the sequence space accessible to evolving viral proteins. We also discuss the many opportunities for research progress proffered by the proteostasis perspective on viral evolution and adaptation.
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Affiliation(s)
- Jimin Yoon
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
| | - Jessica E Patrick
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
| | - C Brandon Ogbunugafor
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- Santa Fe Institute, Santa Fe, New Mexico, USA
| | - Matthew D Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
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3
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Yoon J, Zhang YM, Her C, Grant RA, Ponomarenko AM, Ackermann BE, Debelouchina GT, Shoulders MD. The Immune-Evasive Proline 283 Substitution in Influenza Nucleoprotein Increases Aggregation Propensity Without Altering the Native Structure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.08.556894. [PMID: 37745335 PMCID: PMC10515774 DOI: 10.1101/2023.09.08.556894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Nucleoprotein (NP) is a key structural protein of influenza ribonucleoprotein complexes and is central to viral RNA packing and trafficking. In human cells, the interferon induced Myxovirus resistance protein 1 (MxA) binds to NP and restricts influenza replication. This selection pressure has caused NP to evolve a few critical MxA-resistant mutations, particularly the highly conserved Pro283 substitution. Previous work showed that this essential Pro283 substitution impairs influenza growth, and the fitness defect becomes particularly prominent at febrile temperature (39 °C) when host chaperones are depleted. Here, we biophysically characterize Pro283 NP and Ser283 NP to test if the fitness defect is owing to Pro283 substitution introducing folding defects. We show that the Pro283 substitution changes the folding pathway of NP without altering the native structure, making NP more aggregation prone during folding. These findings suggest that influenza has evolved to hijack host chaperones to promote the folding of otherwise biophysically incompetent viral proteins that enable innate immune system escape. Teaser Pro283 substitution in flu nucleoprotein introduces folding defects, and makes influenza uniquely dependent on host chaperones.
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4
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Choudhury A, Ratna A, Lim A, Sebastian RM, Moore CL, Filliol AA, Bledsoe J, Dai C, Schwabe RF, Shoulders MD, Mandrekar P. Loss of heat shock factor 1 promotes hepatic stellate cell activation and drives liver fibrosis. Hepatol Commun 2022; 6:2781-2797. [PMID: 35945902 PMCID: PMC9512451 DOI: 10.1002/hep4.2058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 06/24/2022] [Accepted: 07/05/2022] [Indexed: 11/26/2022] Open
Abstract
Liver fibrosis is an aberrant wound healing response that results from chronic injury and is mediated by hepatocellular death and activation of hepatic stellate cells (HSCs). While induction of oxidative stress is well established in fibrotic livers, there is limited information on stress‐mediated mechanisms of HSC activation. Cellular stress triggers an adaptive defense mechanism via master protein homeostasis regulator, heat shock factor 1 (HSF1), which induces heat shock proteins to respond to proteotoxic stress. Although the importance of HSF1 in restoring cellular homeostasis is well‐established, its potential role in liver fibrosis is unknown. Here, we show that HSF1 messenger RNA is induced in human cirrhotic and murine fibrotic livers. Hepatocytes exhibit nuclear HSF1, whereas stellate cells expressing alpha smooth muscle actin do not express nuclear HSF1 in human cirrhosis. Interestingly, despite nuclear HSF1, murine fibrotic livers did not show induction of HSF1 DNA binding activity compared with controls. HSF1‐deficient mice exhibit augmented HSC activation and fibrosis despite limited pro‐inflammatory cytokine response and display delayed fibrosis resolution. Stellate cell and hepatocyte‐specific HSF1 knockout mice exhibit higher induction of profibrogenic response, suggesting an important role for HSF1 in HSC activation and fibrosis. Stable expression of dominant negative HSF1 promotes fibrogenic activation of HSCs. Overactivation of HSF1 decreased phosphorylation of JNK and prevented HSC activation, supporting a protective role for HSF1. Our findings identify an unconventional role for HSF1 in liver fibrosis. Conclusion: Our results show that deficiency of HSF1 is associated with exacerbated HSC activation promoting liver fibrosis, whereas activation of HSF1 prevents profibrogenic HSC activation.
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Affiliation(s)
- Asmita Choudhury
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Anuradha Ratna
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Arlene Lim
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Rebecca M Sebastian
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Christopher L Moore
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Aveline A Filliol
- Institute of Human Nutrition, Columbia University Irving Medical Center, New York, New York, USA
| | - Jacob Bledsoe
- Department of Pathology, University of Massachusetts Memorial Medical Center, Worcester, Massachusetts, USA
| | - Chengkai Dai
- Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Robert F Schwabe
- Institute of Human Nutrition, Columbia University Irving Medical Center, New York, New York, USA
| | - Matthew D Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Pranoti Mandrekar
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
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5
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Peng H, Ramadurgum P, Woodard DR, Daniel S, Nakahara E, Renwick M, Aredo B, Datta S, Chen B, Ufret-Vincenty R, Hulleman JD. Utility of the DHFR-based destabilizing domain across mouse models of retinal degeneration and aging. iScience 2022; 25:104206. [PMID: 35521529 PMCID: PMC9062244 DOI: 10.1016/j.isci.2022.104206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 02/16/2022] [Accepted: 04/04/2022] [Indexed: 11/25/2022] Open
Abstract
The Escherichia coli dihydrofolate reductase (DHFR) destabilizing domain (DD) serves as a promising approach to conditionally regulate protein abundance in a variety of tissues. To test whether this approach could be effectively applied to a wide variety of aged and disease-related ocular mouse models, we evaluated the DHFR DD system in the eyes of aged mice (up to 24 months), a light-induced retinal degeneration (LIRD) model, and two genetic models of retinal degeneration (rd2 and Abca4−/− mice). The DHFR DD was effectively degraded in all model systems, including rd2 mice, which showed significant defects in chymotrypsin proteasomal activity. Moreover, trimethoprim (TMP) administration stabilized the DHFR DD in all mouse models. Thus, the DHFR DD-based approach allows for control of protein abundance in a variety of mouse models, laying the foundation to use this strategy for the conditional control of gene therapies to potentially treat multiple eye diseases. Destabilizing domains (DDs) confer conditional control of ocular protein abundance The DHFR DD is effectively turned over and stabilized in aged mouse’s retina DHFR DDs perform well in environmental and genetic retinal degenerative models
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Sun J, Zhang W, Zhao Y, Liu J, Wang F, Han Y, Jiang M, Li S, Tang D. Conditional control of chimeric antigen receptor T-cell activity through a destabilizing domain switch and its chemical ligand. Cytotherapy 2021; 23:1085-1096. [PMID: 34593327 DOI: 10.1016/j.jcyt.2021.07.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 07/20/2021] [Accepted: 07/25/2021] [Indexed: 11/15/2022]
Abstract
BACKGROUND AIMS Despite the impressive efficacy of chimeric antigen receptor (CAR) T-cell therapy, adverse effects, including cytokine release syndrome and neurotoxicity, impede its therapeutic application, thus making the modulation of CAR T-cell activity a priority. The destabilizing domain mutated from Escherichia coli dihydrofolate reductase (DHFR) is inherently unstable and degraded by proteasomes unless it is stabilized by its chemical ligand trimethoprim (TMP), a Food and Drug Administration-approved drug. Here the authors reveal a strategy to modulate CAR T-cell activity at the protein level by employing DHFR and TMP as a chemical switch system. METHODS First, the system was demonstrated to work in human primary T cells. To introduce the system to CAR T cells, DHFR was genetically fused to the carboxyl terminal of a third-generation CAR molecule targeting CD19 (CD19-CAR), constructing the CD19-CAR-DHFR fusion. RESULTS The CD19-CAR-DHFR molecule level was shown to be modulated by TMP. Importantly, the incorporation of DHFR had no impact on the recognition specificity and normal function of the CAR molecule. Little adverse effect on cell proliferation and apoptosis was detected. It was proved that TMP could regulate cytokine secretion and the in vitro cytotoxicity of CD19-CAR-DHFR T cells. Furthermore, the in vivo anti-tumor efficacy was demonstrated to be controllable through the manipulation of TMP administration. The approach to control CD19-CAR also succeeded in 19-BBZ(71), another CD19-targeting CAR with a different structure. CONCLUSIONS The proposed approach based on DHFR and TMP provides a facile strategy to bring CAR T-cell therapy under conditional user control, and the strategy may have the potential to be transplantable.
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Affiliation(s)
- Jiao Sun
- Institute of Medical Sciences, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China
| | - Wen Zhang
- Institute of Medical Sciences, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China.
| | - Yi Zhao
- Institute of Medical Sciences, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China
| | - Jiang Liu
- Institute of Medical Sciences, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China
| | - Fang Wang
- Institute of Medical Sciences, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China
| | - Ying Han
- Institute of Medical Sciences, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China
| | - Miao Jiang
- Institute of Medical Sciences, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China
| | - Shiwu Li
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Dongqi Tang
- Institute of Medical Sciences, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, People's Republic of China.
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7
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Ramadurgum P, Hulleman JD. Protocol for Designing Small-Molecule-Regulated Destabilizing Domains for In Vitro Use. STAR Protoc 2020; 1. [PMID: 32995752 PMCID: PMC7521665 DOI: 10.1016/j.xpro.2020.100069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The use of destabilizing domains (DDs) to conditionally control the abundance of a protein of interest (POI) through a small-molecule stabilizer has gained increasing traction both in vitro and in vivo. Yet there are specific considerations for the development and accurate control of user-defined POIs via DDs, as well as the identification of novel (and potentially synergistic) small-molecule stabilizers. Here, we describe a platform for achieving these goals. For complete details on the use and execution of this protocol, please refer to Ramadurgum et al. (2020). Conditional protein of interest (POI) regulation by destabilizing domain (DD) fusion Focus on the utility of the E. coli dihydrofolate reductase (ecDHFR) DD Dynamically define the levels of a POI through diverse ligands Simultaneous DD stabilization and control of synergistic cellular signaling pathways
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Affiliation(s)
- Prerana Ramadurgum
- Department of Ophthalmology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - John D Hulleman
- Department of Ophthalmology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA.,Department of Pharmacology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA.,Technical Contact.,Lead Contact
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8
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Nekongo EE, Ponomarenko AI, Dewal MB, Butty VL, Browne EP, Shoulders MD. HSF1 Activation Can Restrict HIV Replication. ACS Infect Dis 2020; 6:1659-1666. [PMID: 32502335 DOI: 10.1021/acsinfecdis.0c00166] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Host protein folding stress responses can play important roles in RNA virus replication and evolution. Prior work suggested a complicated interplay between the cytosolic proteostasis stress response, controlled by the transcriptional master regulator heat shock factor 1 (HSF1), and human immunodeficiency virus-1 (HIV-1). We sought to uncouple HSF1 transcription factor activity from cytotoxic proteostasis stress and thereby better elucidate the proposed role(s) of HSF1 in the HIV-1 lifecycle. To achieve this objective, we used chemical genetic, stress-independent control of HSF1 activity to establish whether and how HSF1 influences HIV-1 replication. Stress-independent HSF1 induction decreased both the total quantity and infectivity of HIV-1 virions. Moreover, HIV-1 was unable to escape HSF1-mediated restriction over the course of several serial passages. These results clarify the interplay between the host's heat shock response and HIV-1 infection and motivate continued investigation of chaperones as potential antiviral therapeutic targets.
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Affiliation(s)
- Emmanuel E. Nekongo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Anna I. Ponomarenko
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Mahender B. Dewal
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Vincent L. Butty
- BioMicro Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Edward P. Browne
- Department of Medicine, University of North Carolina School of Medicine, Chapel Hill, North Carolina 27516, United States
| | - Matthew D. Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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9
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Chen YP, Chen CT, Liu TP, Chien FC, Wu SH, Chen P, Mou CY. Catcher in the rel: Nanoparticles-antibody conjugate as NF-κB nuclear translocation blocker. Biomaterials 2020; 246:119997. [PMID: 32247937 DOI: 10.1016/j.biomaterials.2020.119997] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 02/23/2020] [Accepted: 03/20/2020] [Indexed: 12/11/2022]
Abstract
Transcription factor complex NF-κB (p65/p50) is localized to the cytoplasm by its inhibitor IκBα. Upon activation, the Rel proteins p65/p50 are released from IκBα and transported through nuclear pore to affect many gene expressions. While inhibitions of up or down stream signal pathways are often ineffective due to crosstalks and compensations, direct blocking of the Rel proteins p65/p50 has long been proposed as a potential target for cancer therapy. In this work, a nanoparticle/antibody complex targeting NF-κB is employed to catch the Rel protein p65 in perinuclear region and thus blocking the translocation near the nuclear pore gate. TAT peptide conjugated on mesoporous silica nanoparticles (MSN) help non-endocytosis cell-membrane transducing and converge toward perinuclear region, where the p65 specific antibody performed the targeting and catching against active NF-κB p65 effectively. The size of the p65 bound nanoparticle becomes too big to enter nucleus. Simultaneous treatment of mice with the hybrid MSN and doxorubicin conferred a significant therapeutic effect against 4T1 tumor-bearing mice. The new approach of anti-body therapy targeting on transcription factor with "nucleus focusing" and "size exclusion blocking" effects of the antibody-conjugated nanoparticle is general and may be applicable to modulating other transcription factors.
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Affiliation(s)
- Yi-Ping Chen
- Graduate Institute of Nanomedicine and Medical Engineering, Taipei Medical University, Taipei, 110, Taiwan; International Ph.D. Program in Biomedical Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei, 110, Taiwan
| | - Chien-Tsu Chen
- Department of Biochemistry and Molecular Cell Biology, College of Medicine, Taipei Medical University, Taipei, 110, Taiwan
| | - Tsang-Pai Liu
- Mackay Junior College of Medicine, Nursing and Management, Taipei, 112, Taiwan; Department of Surgery, Mackay Memorial Hospital, Taipei, 104, Taiwan
| | - Fan-Ching Chien
- Department of Optics and Photonics, National Central University, Chung-Li, 320, Taiwan
| | - Si-Han Wu
- Graduate Institute of Nanomedicine and Medical Engineering, Taipei Medical University, Taipei, 110, Taiwan; International Ph.D. Program in Biomedical Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei, 110, Taiwan.
| | - Peilin Chen
- Research Center of Applied Science, Academia Sinica, Taipei, 115, Taiwan.
| | - Chung-Yuan Mou
- Graduate Institute of Nanomedicine and Medical Engineering, Taipei Medical University, Taipei, 110, Taiwan; Department of Chemistry, National Taiwan University, Taipei, 106, Taiwan.
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10
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Abstract
Protein folding in the cell is mediated by an extensive network of >1,000 chaperones, quality control factors, and trafficking mechanisms collectively termed the proteostasis network. While the components and organization of this network are generally well established, our understanding of how protein-folding problems are identified, how the network components integrate to successfully address challenges, and what types of biophysical issues each proteostasis network component is capable of addressing remains immature. We describe a chemical biology-informed framework for studying cellular proteostasis that relies on selection of interesting protein-folding problems and precise researcher control of proteostasis network composition and activities. By combining these methods with multifaceted strategies to monitor protein folding, degradation, trafficking, and aggregation in cells, researchers continue to rapidly generate new insights into cellular proteostasis.
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Affiliation(s)
- Rebecca M Sebastian
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Matthew D Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
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11
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Peng H, Chau VQ, Phetsang W, Sebastian RM, Stone MRL, Datta S, Renwick M, Tamer YT, Toprak E, Koh AY, Blaskovich MA, Hulleman JD. Non-antibiotic Small-Molecule Regulation of DHFR-Based Destabilizing Domains In Vivo. Mol Ther Methods Clin Dev 2019; 15:27-39. [PMID: 31649953 PMCID: PMC6804886 DOI: 10.1016/j.omtm.2019.08.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 08/09/2019] [Indexed: 02/08/2023]
Abstract
The E. coli dihydrofolate reductase (DHFR) destabilizing domain (DD), which shows promise as a biologic tool and potential gene therapy approach, can be utilized to achieve spatial and temporal control of protein abundance in vivo simply by administration of its stabilizing ligand, the routinely prescribed antibiotic trimethoprim (TMP). However, chronic TMP use drives development of antibiotic resistance (increasing likelihood of subsequent infections) and disrupts the gut microbiota (linked to autoimmune and neurodegenerative diseases), tempering translational excitement of this approach in model systems and for treating human diseases. Herein, we identified a TMP-based, non-antibiotic small molecule, termed 14a (MCC8529), and tested its ability to control multiple DHFR-based reporters and signaling proteins. We found that 14a is non-toxic and can effectively stabilize DHFR DDs expressed in mammalian cells. Furthermore, 14a crosses the blood-retinal barrier and stabilizes DHFR DDs expressed in the mouse eye with kinetics comparable to that of TMP (≤6 h). Surprisingly, 14a stabilized a DHFR DD in the liver significantly better than TMP did, while having no effect on the mouse gut microbiota. Our results suggest that alternative small-molecule DHFR DD stabilizers (such as 14a) may be ideal substitutes for TMP in instances when conditional, non-antibiotic control of protein abundance is desired in the eye and beyond.
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Affiliation(s)
- Hui Peng
- Department of Ophthalmology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Viet Q. Chau
- Department of Ophthalmology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Wanida Phetsang
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
| | - Rebecca M. Sebastian
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139, USA
| | - M. Rhia L. Stone
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
| | - Shyamtanu Datta
- Department of Ophthalmology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Marian Renwick
- Department of Ophthalmology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Yusuf T. Tamer
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Erdal Toprak
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
- Department of Pharmacology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Andrew Y. Koh
- Department of Pediatrics, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
- Department of Microbiology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Mark A.T. Blaskovich
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, Brisbane, QLD 4072, Australia
| | - John D. Hulleman
- Department of Ophthalmology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
- Department of Pharmacology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
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12
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Fan Z, Wang J, Hao N, Li Y, Yin Y, Wang Z, Ding Y, Zhao J, Zhang K, Huang W. Ultrasensitive detection of transcription factors with a highly-efficient diaminoterephthalate fluorophore via an electrogenerated chemiluminescence strategy. Chem Commun (Camb) 2019; 55:11892-11895. [DOI: 10.1039/c9cc05692k] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Herein, we apply electrogenerated chemiluminescence (ECL) based method employing diaminoterephthalate analogue as ECL emitter and hairpin DNA as amplification strategy, for sensitive assay of transcription factors.
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13
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Small Molecule-Based Inducible Gene Therapies for Retinal Degeneration. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1185:65-69. [PMID: 31884590 DOI: 10.1007/978-3-030-27378-1_11] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The eye is an excellent target organ for gene therapy. It is physically isolated, easily accessible, immune-privileged, and postmitotic. Furthermore, potential gene therapies introduced into the eye can be evaluated by noninvasive methods such as fundoscopy, electroretinography, and optical coherence tomography. In the last two decades, great advances have been made in understanding the molecular underpinnings of retinal degenerative diseases. Building upon the development of modern techniques for gene delivery, many gene-based therapies have been effectively used to treat loss-of-function retinal diseases in mice and men. Significant effort has been invested into making gene delivery vehicles more efficient, less toxic, and non-immunogenic. However, one challenge for the treatment of more complex gain-of-function diseases, many of which might be benefited by the regulation of cellular stress-responsive signaling pathways, is the ability to control the strategy in a physiological (conditional) manner. This review is focused on promising retinal gene therapy strategies that rely on small molecule-based conditional regulation and the inherent limitations and challenges of these strategies that need to be addressed prior to their extensive use.
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14
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Datta S, Renwick M, Chau VQ, Zhang F, Nettesheim ER, Lipinski DM, Hulleman JD. A Destabilizing Domain Allows for Fast, Noninvasive, Conditional Control of Protein Abundance in the Mouse Eye - Implications for Ocular Gene Therapy. Invest Ophthalmol Vis Sci 2018; 59:4909-4920. [PMID: 30347085 PMCID: PMC6181441 DOI: 10.1167/iovs.18-24987] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 08/30/2018] [Indexed: 01/23/2023] Open
Abstract
Purpose Temporal and reversible control of protein expression in vivo is a central goal for many gene therapies, especially for strategies involving proteins that are detrimental to physiology if constitutively expressed. Accordingly, we explored whether protein abundance in the mouse retina could be effectively controlled using a destabilizing Escherichia coli dihydrofolate reductase (DHFR) domain whose stability is dependent on the small molecule, trimethoprim (TMP). Methods We intravitreally injected wild-type C57BL6/J mice with an adeno-associated vector (rAAV2/2[MAX]) constitutively expressing separate fluorescent reporters: DHFR fused to yellow fluorescent protein (DHFR.YFP) and mCherry. TMP or vehicle was administered to mice via oral gavage, drinking water, or eye drops. Ocular TMP levels post treatment were quantified by LC-MS/MS. Protein abundance was measured by fundus fluorescence imaging and western blotting. Visual acuity, response to light stimulus, retinal structure, and gene expression were evaluated after long-term (3 months) TMP treatment. Results Without TMP, DHFR.YFP was efficiently degraded in the retina. TMP achieved ocular concentrations of ∼13.6 μM (oral gavage), ∼331 nM (drinking water), and ∼636 nM (eye drops). Oral gavage and TMP eye drops stabilized DHFR.YFP as quickly as 6 hours, whereas continuous TMP drinking water could stabilize DHFR.YFP for ≥3 months. Stabilization was completely and repeatedly reversible following removal/addition of TMP in all regimens. Long-term TMP treatment had no impact on retina function/structure and had no effect on >99.9% of tested genes. Conclusions This DHFR-based conditional system is a rapid, efficient, and reversible tool to effectively control protein expression in the retina.
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Affiliation(s)
- Shyamtanu Datta
- Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - Marian Renwick
- Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - Viet Q. Chau
- Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - Fang Zhang
- Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - Emily R. Nettesheim
- Department of Ophthalmology, Eye Institute, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
| | - Daniel M. Lipinski
- Department of Ophthalmology, Eye Institute, Medical College of Wisconsin, Milwaukee, Wisconsin, United States
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neuroscience, University of Oxford, Oxford, United Kingdom
| | - John D. Hulleman
- Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
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15
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Wong MY, DiChiara AS, Suen PH, Chen K, Doan ND, Shoulders MD. Adapting Secretory Proteostasis and Function Through the Unfolded Protein Response. Curr Top Microbiol Immunol 2018; 414:1-25. [PMID: 28929194 DOI: 10.1007/82_2017_56] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cells address challenges to protein folding in the secretory pathway by engaging endoplasmic reticulum (ER)-localized protective mechanisms that are collectively termed the unfolded protein response (UPR). By the action of the transmembrane signal transducers IRE1, PERK, and ATF6, the UPR induces networks of genes whose products alleviate the burden of protein misfolding. The UPR also plays instructive roles in cell differentiation and development, aids in the response to pathogens, and coordinates the output of professional secretory cells. These functions add to and move beyond the UPR's classical role in addressing proteotoxic stress. Thus, the UPR is not just a reaction to protein misfolding, but also a fundamental driving force in physiology and pathology. Recent efforts have yielded a suite of chemical genetic methods and small molecule modulators that now provide researchers with both stress-dependent and -independent control of UPR activity. Such tools provide new opportunities to perturb the UPR and thereby study mechanisms for maintaining proteostasis in the secretory pathway. Numerous observations now hint at the therapeutic potential of UPR modulation for diseases related to the misfolding and aggregation of ER client proteins. Growing evidence also indicates the promise of targeting ER proteostasis nodes downstream of the UPR. Here, we review selected advances in these areas, providing a resource to inform ongoing studies of secretory proteostasis and function as they relate to the UPR.
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Affiliation(s)
- Madeline Y Wong
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139-4307, USA
| | - Andrew S DiChiara
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139-4307, USA
| | - Patreece H Suen
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139-4307, USA
| | - Kenny Chen
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139-4307, USA
| | - Ngoc-Duc Doan
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139-4307, USA
| | - Matthew D Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139-4307, USA.
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16
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The dTAG system for immediate and target-specific protein degradation. Nat Chem Biol 2018; 14:431-441. [PMID: 29581585 DOI: 10.1038/s41589-018-0021-8] [Citation(s) in RCA: 547] [Impact Index Per Article: 91.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 02/02/2018] [Indexed: 01/19/2023]
Abstract
Dissection of complex biological systems requires target-specific control of the function or abundance of proteins. Genetic perturbations are limited by off-target effects, multicomponent complexity, and irreversibility. Most limiting is the requisite delay between modulation to experimental measurement. To enable the immediate and selective control of single protein abundance, we created a chemical biology system that leverages the potency of cell-permeable heterobifunctional degraders. The dTAG system pairs a novel degrader of FKBP12F36V with expression of FKBP12F36V in-frame with a protein of interest. By transgene expression or CRISPR-mediated locus-specific knock-in, we exemplify a generalizable strategy to study the immediate consequence of protein loss. Using dTAG, we observe an unexpected superior antiproliferative effect of pan-BET bromodomain degradation over selective BRD4 degradation, characterize immediate effects of KRASG12V loss on proteomic signaling, and demonstrate rapid degradation in vivo. This technology platform will confer kinetic resolution to biological investigation and provide target validation in the context of drug discovery.
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17
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Laughlin-Toth S, Carter EK, Ivanov I, Wilson WD. DNA microstructure influences selective binding of small molecules designed to target mixed-site DNA sequences. Nucleic Acids Res 2017; 45:1297-1306. [PMID: 28180310 PMCID: PMC5388402 DOI: 10.1093/nar/gkw1232] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 11/18/2016] [Accepted: 11/23/2016] [Indexed: 12/18/2022] Open
Abstract
Specific targeting of protein–nucleic acid interactions is an area of current interest, for example, in the regulation of gene-expression. Most transcription factor proteins bind in the DNA major groove; however, we are interested in an approach using small molecules to target the minor groove to control expression by an allosteric mechanism. In an effort to broaden sequence recognition of DNA-targeted-small-molecules to include both A·T and G·C base pairs, we recently discovered that the heterocyclic diamidine, DB2277, forms a strong monomer complex with a DNA sequence containing 5΄-AAAGTTT-3΄. Competition mass spectrometry and surface plasmon resonance identified new monomer complexes, as well as unexpected binding of two DB2277 with certain sequences. Inherent microstructural differences within the experimental DNAs were identified through computational analyses to understand the molecular basis for recognition. These findings emphasize the critical nature of the DNA minor groove microstructure for sequence-specific recognition and offer new avenues to design synthetic small molecules for effective regulation of gene-expression.
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Affiliation(s)
- Sarah Laughlin-Toth
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - E Kathleen Carter
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - Ivaylo Ivanov
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - W David Wilson
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
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18
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Phillips AM, Gonzalez LO, Nekongo EE, Ponomarenko AI, McHugh SM, Butty VL, Levine SS, Lin YS, Mirny LA, Shoulders MD. Host proteostasis modulates influenza evolution. eLife 2017; 6. [PMID: 28949290 PMCID: PMC5614556 DOI: 10.7554/elife.28652] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 08/18/2017] [Indexed: 01/02/2023] Open
Abstract
Predicting and constraining RNA virus evolution require understanding the molecular factors that define the mutational landscape accessible to these pathogens. RNA viruses typically have high mutation rates, resulting in frequent production of protein variants with compromised biophysical properties. Their evolution is necessarily constrained by the consequent challenge to protein folding and function. We hypothesized that host proteostasis mechanisms may be significant determinants of the fitness of viral protein variants, serving as a critical force shaping viral evolution. Here, we test that hypothesis by propagating influenza in host cells displaying chemically-controlled, divergent proteostasis environments. We find that both the nature of selection on the influenza genome and the accessibility of specific mutational trajectories are significantly impacted by host proteostasis. These findings provide new insights into features of host–pathogen interactions that shape viral evolution, and into the potential design of host proteostasis-targeted antiviral therapeutics that are refractory to resistance. Influenza viruses, commonly called flu, can evade our immune system and develop resistance to treatments by changing frequently. Specifically, mutations in their genome cause influenza proteins to change in ways that can help the virus evade our defences. However, these mutations come at a cost and can prevent the viral proteins from forming functional and stable three-dimensional shapes – a process known as protein folding – thereby hampering the virus’ ability to replicate. In human cells, proteins called chaperones can help our other proteins fold properly. Influenza viruses do not have their own chaperones and, instead, hijack those of their host. Host chaperones are therefore crucial to the virus’ ability to replicate. However, until now, it was not known if host chaperones can influence how these viruses evolve. Here, Phillips et al. used mammalian cells to study how host chaperones affect an evolving influenza population. First, cells were engineered to either have normal chaperone levels, elevated chaperone levels, or inactive chaperones. Next, the H3N2 influenza strain was grown in these different conditions for nearly 200 generations and sequenced to determine how the virus evolved in each distinctive host chaperone environment. Phillips et al. discovered that host chaperones affect the rate at which mutations accumulate in the influenza population, and also the types of mutations in the influenza genome. For instance, when a chaperone called Hsp90 was inactivated, mutations became prevalent in the viral population more slowly than in cells with normal or elevated chaperone levels. Moreover, some specific mutations fared better in cells with high chaperone levels, whilst others worked better in cells with inactivated chaperones. These results suggest that influenza evolution is affected by host chaperone levels in complex and important ways. Moreover, whether chaperones will promote or hinder the effects of any single mutation is difficult to predict ahead of time. This discovery is significant, as the chaperones available to influenza can vary in different tissues, organisms and infectious conditions, and may therefore influence the virus' ability to change and evolve in a context-specific manner. The findings are likely to extend to other viruses such as HIV and Ebola, which also hijack host chaperones for the same purpose. More work is now needed to systematically quantify these effects so that we can better predict how specific chaperones will affect the ability of viruses to adapt, especially in pathologically relevant conditions like fever or viral host-switching. In the future, such insights could help shape the design of treatments to which viruses do not evolve resistance.
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Affiliation(s)
- Angela M Phillips
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| | - Luna O Gonzalez
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, United States
| | - Emmanuel E Nekongo
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| | - Anna I Ponomarenko
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| | - Sean M McHugh
- Department of Chemistry, Tufts University, Medford, United States
| | - Vincent L Butty
- BioMicro Center, Massachusetts Institute of Technology, Cambridge, United States
| | - Stuart S Levine
- BioMicro Center, Massachusetts Institute of Technology, Cambridge, United States
| | - Yu-Shan Lin
- Department of Chemistry, Tufts University, Medford, United States
| | - Leonid A Mirny
- Department of Physics, Massachusetts Institute of Technology, Cambridge, United States.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, United States
| | - Matthew D Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
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19
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Vu KT, Zhang F, Hulleman JD. Conditional, Genetically Encoded, Small Molecule-Regulated Inhibition of NFκB Signaling in RPE Cells. Invest Ophthalmol Vis Sci 2017; 58:4126-4137. [PMID: 28829844 PMCID: PMC5566385 DOI: 10.1167/iovs.17-22133] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Purpose Nuclear factor κB (NFκB) is a ubiquitously expressed, proinflammatory transcription factor that controls the expression of genes involved in cell survival, angiogenesis, complement activation, and inflammation. Studies have implicated NFκB-dependent cytokines or complement-related factors as being detrimentally involved in retinal diseases, thus making inhibition of NFκB signaling a potential therapeutic target. We sought to develop a conditional and reversible method that could regulate pathogenic NFκB signaling by the addition of a small molecule. Methods We developed a genetically based, trimethoprim (TMP)-regulated approach that conditionally inhibits NFκB signaling by fusing a destabilized dihydrofolate reductase (DHFR) domain to an inhibitor of NFκB, IκBα, in ARPE-19 cells. We then challenged ARPE-19 cells with a number of stimuli that have been demonstrated to trigger NFκB signaling, including LPS, TNFα, IL-1α, and A2E. Western blotting, electrophoretic mobility shift assay, quantitative PCR, ELISA, and NFκB reporter assays were used to evaluate the effectiveness of this DHFR-IκBα approach. Results This destabilized domain approach, coupled with doxycycline-inducibility, allowed for accurate control over the abundance of DHFR-IκBα. Stabilization of DHFR-IκBα with TMP prevented IL-1α-, A2E-, LPS-, and TNFα-induced NFκB-mediated upregulation and release of the proinflammatory cytokines IL-1β and IL-6 from ARPE-19 cells (by as much as 93%). This strategy is dosable, completely reversible, and can be cycled “on” or “off” within the same cell population repeatedly to confer protection at desired time points. Conclusions These studies lay the groundwork for the use of destabilized domains in retinal pigment epithelium (RPE) cells in vivo and in this context, demonstrate their utility for preventing inflammatory signaling.
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Affiliation(s)
- Khiem T Vu
- Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - Fang Zhang
- Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - John D Hulleman
- Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, Texas, United States.,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
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20
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Affiliation(s)
- George M. Burslem
- Departments of Molecular,
Cellular, and Developmental Biology, Chemistry, and Pharmacology, Yale University, 219 Prospect Street, New Haven, Connecticut 06511, United States
| | - Craig M. Crews
- Departments of Molecular,
Cellular, and Developmental Biology, Chemistry, and Pharmacology, Yale University, 219 Prospect Street, New Haven, Connecticut 06511, United States
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21
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Plate L, Wiseman RL. Regulating Secretory Proteostasis through the Unfolded Protein Response: From Function to Therapy. Trends Cell Biol 2017. [PMID: 28647092 DOI: 10.1016/j.tcb.2017.05.006] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Imbalances in secretory proteostasis induced by genetic, environmental, or aging-related insults are pathologically associated with etiologically diverse protein misfolding diseases. To protect the secretory proteome from these insults, organisms evolved stress-responsive signaling pathways that regulate the composition and activity of biologic pathways involved in secretory proteostasis maintenance. The most prominent of these is the endoplasmic reticulum (ER) unfolded protein response (UPR), which functions to regulate ER proteostasis in response to ER stress. While the signaling mechanisms involved in UPR activation are well defined, the impact of UPR activation on secretory proteostasis is only now becoming clear. Here, we highlight recent reports defining how activation of select UPR signaling pathways influences proteostasis within the ER and downstream secretory environments. Furthermore, we describe recent evidence that highlights the therapeutic potential for targeting UPR signaling pathways to correct pathologic disruption in secretory proteostasis associated with diverse types of protein misfolding diseases.
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Affiliation(s)
- Lars Plate
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - R Luke Wiseman
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
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22
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Fang A, Chen H, Li H, Liu M, Zhang Y, Yao S. Glutathione regulation-based dual-functional upconversion sensing-platform for acetylcholinesterase activity and cadmium ions. Biosens Bioelectron 2017; 87:545-551. [DOI: 10.1016/j.bios.2016.08.111] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 08/25/2016] [Accepted: 08/30/2016] [Indexed: 11/28/2022]
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23
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Maji B, Moore CL, Zetsche B, Volz SE, Zhang F, Shoulders MD, Choudhary A. Multidimensional chemical control of CRISPR-Cas9. Nat Chem Biol 2016; 13:9-11. [PMID: 27820801 DOI: 10.1038/nchembio.2224] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 09/23/2016] [Indexed: 11/09/2022]
Abstract
Cas9-based technologies have transformed genome engineering and the interrogation of genomic functions, but methods to control such technologies across numerous dimensions-including dose, time, specificity, and mutually exclusive modulation of multiple genes-are still lacking. We conferred such multidimensional controls to diverse Cas9 systems by leveraging small-molecule-regulated protein degron domains. Application of our strategy to both Cas9-mediated genome editing and transcriptional activities opens new avenues for systematic genome interrogation.
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Affiliation(s)
- Basudeb Maji
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.,Renal Division, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Christopher L Moore
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Bernd Zetsche
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Sara E Volz
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Matthew D Shoulders
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Amit Choudhary
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA.,Renal Division, Brigham and Women's Hospital, Boston, Massachusetts, USA
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24
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Baranczak A, Kelly JW. A current pharmacologic agent versus the promise of next generation therapeutics to ameliorate protein misfolding and/or aggregation diseases. Curr Opin Chem Biol 2016; 32:10-21. [PMID: 26859714 DOI: 10.1016/j.cbpa.2016.01.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 01/14/2016] [Accepted: 01/14/2016] [Indexed: 12/18/2022]
Abstract
The list of protein aggregation-associated degenerative diseases is long and growing, while the portfolio of disease-modifying strategies is very small. In this review and perspective, we assess what has worked to slow the progression of an aggregation-associated degenerative disease, covering the underlying mechanism of pharmacologic action and what we have learned about the etiology of the transthyretin amyloid diseases and likely amyloidoses in general. Next, we introduce emerging therapies that should apply more generally to protein misfolding and/or aggregation diseases, approaches that rely on adapting the protein homeostasis or proteostasis network for disease amelioration.
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Affiliation(s)
- Aleksandra Baranczak
- Department of Chemistry and The Skaggs Institute for Chemical Biology, La Jolla, CA 92037, USA; Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Jeffery W Kelly
- Department of Chemistry and The Skaggs Institute for Chemical Biology, La Jolla, CA 92037, USA; Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.
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25
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Moore CL, Dewal MB, Nekongo EE, Santiago S, Lu NB, Levine SS, Shoulders MD. Transportable, Chemical Genetic Methodology for the Small Molecule-Mediated Inhibition of Heat Shock Factor 1. ACS Chem Biol 2016; 11:200-10. [PMID: 26502114 DOI: 10.1021/acschembio.5b00740] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Proteostasis in the cytosol is governed by the heat shock response. The master regulator of the heat shock response, heat shock factor 1 (HSF1), and key chaperones whose levels are HSF1-regulated have emerged as high-profile targets for therapeutic applications ranging from protein misfolding-related disorders to cancer. Nonetheless, a generally applicable methodology to selectively and potently inhibit endogenous HSF1 in a small molecule-dependent manner in disease model systems remains elusive. Also problematic, the administration of even highly selective chaperone inhibitors often has the side effect of activating HSF1 and thereby inducing a compensatory heat shock response. Herein, we report a ligand-regulatable, dominant negative version of HSF1 that addresses these issues. Our approach, which required engineering a new dominant negative HSF1 variant, permits dosable inhibition of endogenous HSF1 with a selective small molecule in cell-based model systems of interest. The methodology allows us to uncouple the pleiotropic effects of chaperone inhibitors and environmental toxins from the concomitantly induced compensatory heat shock response. Integration of our method with techniques to activate HSF1 enables the creation of cell lines in which the cytosolic proteostasis network can be up- or down-regulated by orthogonal small molecules. Selective, small molecule-mediated inhibition of HSF1 has distinctive implications for the proteostasis of both chaperone-dependent globular proteins and aggregation-prone intrinsically disordered proteins. Altogether, this work provides critical methods for continued exploration of the biological roles of HSF1 and the therapeutic potential of heat shock response modulation.
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Affiliation(s)
- Christopher L. Moore
- Department
of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Mahender B. Dewal
- Department
of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Emmanuel E. Nekongo
- Department
of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Sebasthian Santiago
- Department
of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Nancy B. Lu
- Department
of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Stuart S. Levine
- BioMicro
Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Matthew D. Shoulders
- Department
of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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26
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Toure M, Crews CM. Niedermolekulare PROTACs: neue Wege zum Abbau von Proteinen. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201507978] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Momar Toure
- Departments of Chemistry; Molecular, Cellular & Developmental Biology; Pharmacology; Yale University; New Haven CT 06511 USA
| | - Craig M. Crews
- Departments of Chemistry; Molecular, Cellular & Developmental Biology; Pharmacology; Yale University; New Haven CT 06511 USA
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27
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Toure M, Crews CM. Small-Molecule PROTACS: New Approaches to Protein Degradation. Angew Chem Int Ed Engl 2016; 55:1966-73. [DOI: 10.1002/anie.201507978] [Citation(s) in RCA: 379] [Impact Index Per Article: 47.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Indexed: 01/12/2023]
Affiliation(s)
- Momar Toure
- Departments of Chemistry; Molecular, Cellular & Developmental Biology, Pharmacology; Yale University; New Haven CT 06511 USA
| | - Craig M. Crews
- Departments of Chemistry; Molecular, Cellular & Developmental Biology, Pharmacology; Yale University; New Haven CT 06511 USA
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28
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Feng J, Jester BW, Tinberg CE, Mandell DJ, Antunes MS, Chari R, Morey KJ, Rios X, Medford JI, Church GM, Fields S, Baker D. A general strategy to construct small molecule biosensors in eukaryotes. eLife 2015; 4. [PMID: 26714111 PMCID: PMC4739774 DOI: 10.7554/elife.10606] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 12/17/2015] [Indexed: 12/22/2022] Open
Abstract
Biosensors for small molecules can be used in applications that range from metabolic engineering to orthogonal control of transcription. Here, we produce biosensors based on a ligand-binding domain (LBD) by using a method that, in principle, can be applied to any target molecule. The LBD is fused to either a fluorescent protein or a transcriptional activator and is destabilized by mutation such that the fusion accumulates only in cells containing the target ligand. We illustrate the power of this method by developing biosensors for digoxin and progesterone. Addition of ligand to yeast, mammalian, or plant cells expressing a biosensor activates transcription with a dynamic range of up to ~100-fold. We use the biosensors to improve the biotransformation of pregnenolone to progesterone in yeast and to regulate CRISPR activity in mammalian cells. This work provides a general methodology to develop biosensors for a broad range of molecules in eukaryotes. DOI:http://dx.doi.org/10.7554/eLife.10606.001 Small molecules play essential roles in organisms, and so methods to sense these molecules within living cells could have wide-ranging uses in both biology and biotechnology. However, current methods for making new “biosensors” are limited and only a narrow range of small molecules can be detected. One approach to biosensor design in yeast and other eukaryotic organisms uses proteins called ligand-binding domains, which bind to small molecules. Here, Feng, Jester, Tinberg, Mandell et al. have developed a new method to make biosensors from ligand-binding domains that could, in principle, be applied to any target small molecule. The new method involves taking a ligand-binding domain that is either engineered or occurs in nature and linking it to something that can be readily detected, such as a protein that fluoresces or that controls gene expression. This combined biosensor protein is then engineered, via mutations, such that it is unstable unless it binds to the small molecule. This means that, in the absence of the small molecule, these proteins are destroyed inside living cells. However, the binding of a target molecule to one of these proteins protects it from degradation, which allows the signal to be detected. Feng, Jester, Tinberg, Mandell et al. use this method to create biosensors for a human hormone called progesterone and a drug called digoxin, which is used to treat heart disease. Further experiments used the biosensors to optimize the production of progesterone in yeast and to regulate the activity of a gene editing protein called Cas9 in human cells. The biosensors can be also used to produce long-term environmental sensors in plant cells. This approach makes it possible to produce a wide variety of biosensors for different organisms. The next step is to continue to explore the ability of various proteins to be converted into biosensors, and to find out how easy it is to transfer a biosensor produced in one species to another. DOI:http://dx.doi.org/10.7554/eLife.10606.002
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Affiliation(s)
- Justin Feng
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, United States.,Department of Genetics, Harvard Medical School, Boston, United States
| | - Benjamin W Jester
- Department of Genome Sciences, University of Washington, Seattle, United States.,Howard Hughes Medical Institute, University of Washington, Seattle, United States
| | - Christine E Tinberg
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Daniel J Mandell
- Department of Genetics, Harvard Medical School, Boston, United States.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, United States
| | - Mauricio S Antunes
- Department of Biology, Colorado State University, Fort Collins, United States
| | - Raj Chari
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Kevin J Morey
- Department of Biology, Colorado State University, Fort Collins, United States
| | - Xavier Rios
- Department of Genetics, Harvard Medical School, Boston, United States
| | - June I Medford
- Department of Biology, Colorado State University, Fort Collins, United States
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, United States.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, United States
| | - Stanley Fields
- Department of Genome Sciences, University of Washington, Seattle, United States.,Howard Hughes Medical Institute, University of Washington, Seattle, United States.,Department of Medicine, University of Washington, Seattle, United States
| | - David Baker
- Howard Hughes Medical Institute, University of Washington, Seattle, United States.,Department of Biochemistry, University of Washington, Seattle, United States
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29
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Eisele YS, Monteiro C, Fearns C, Encalada SE, Wiseman RL, Powers ET, Kelly JW. Targeting protein aggregation for the treatment of degenerative diseases. Nat Rev Drug Discov 2015; 14:759-80. [PMID: 26338154 PMCID: PMC4628595 DOI: 10.1038/nrd4593] [Citation(s) in RCA: 278] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The aggregation of specific proteins is hypothesized to underlie several degenerative diseases, which are collectively known as amyloid disorders. However, the mechanistic connection between the process of protein aggregation and tissue degeneration is not yet fully understood. Here, we review current and emerging strategies to ameliorate aggregation-associated degenerative disorders, with a focus on disease-modifying strategies that prevent the formation of and/or eliminate protein aggregates. Persuasive pharmacological and genetic evidence now supports protein aggregation as the cause of postmitotic tissue dysfunction or loss. However, a more detailed understanding of the factors that trigger and sustain aggregate formation and of the structure-activity relationships underlying proteotoxicity is needed to develop future disease-modifying therapies.
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Affiliation(s)
- Yvonne S. Eisele
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Cecilia Monteiro
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Colleen Fearns
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Sandra E. Encalada
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
- Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, California 92037, USA
- Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, La Jolla, California 92037, USA
| | - R. Luke Wiseman
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Evan T. Powers
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Jeffery W. Kelly
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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30
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Dewal MB, DiChiara AS, Antonopoulos A, Taylor RJ, Harmon CJ, Haslam SM, Dell A, Shoulders MD. XBP1s Links the Unfolded Protein Response to the Molecular Architecture of Mature N-Glycans. CHEMISTRY & BIOLOGY 2015; 22:1301-12. [PMID: 26496683 PMCID: PMC4621487 DOI: 10.1016/j.chembiol.2015.09.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 09/06/2015] [Accepted: 09/09/2015] [Indexed: 12/24/2022]
Abstract
The molecular architecture of the mature N-glycome is dynamic, with consequences for both normal and pathologic processes. Elucidating cellular mechanisms that modulate the N-linked glycome is, therefore, crucial. The unfolded protein response (UPR) is classically responsible for maintaining proteostasis in the secretory pathway by defining levels of chaperones and quality control proteins. Here, we employ chemical biology methods for UPR regulation to show that stress-independent activation of the UPR's XBP1s transcription factor also induces a panel of N-glycan maturation-related enzymes. The downstream consequence is a distinctive shift toward specific hybrid and complex N-glycans on N-glycoproteins produced from XBP1s-activated cells, which we characterize by mass spectrometry. Pulse-chase studies attribute this shift specifically to altered N-glycan processing, rather than to changes in degradation or secretion rates. Our findings implicate XBP1s in a new role for N-glycoprotein biosynthesis, unveiling an important link between intracellular stress responses and the molecular architecture of extracellular N-glycoproteins.
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Affiliation(s)
- Mahender B Dewal
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Andrew S DiChiara
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | | | - Rebecca J Taylor
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Chyleigh J Harmon
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Stuart M Haslam
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Anne Dell
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Matthew D Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.
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31
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Buckley DL, Raina K, Darricarrere N, Hines J, Gustafson JL, Smith IE, Miah AH, Harling JD, Crews CM. HaloPROTACS: Use of Small Molecule PROTACs to Induce Degradation of HaloTag Fusion Proteins. ACS Chem Biol 2015; 10:1831-7. [PMID: 26070106 DOI: 10.1021/acschembio.5b00442] [Citation(s) in RCA: 280] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Small molecule-induced protein degradation is an attractive strategy for the development of chemical probes. One method for inducing targeted protein degradation involves the use of PROTACs, heterobifunctional molecules that can recruit specific E3 ligases to a desired protein of interest. PROTACs have been successfully used to degrade numerous proteins in cells, but the peptidic E3 ligase ligands used in previous PROTACs have hindered their development into more mature chemical probes or therapeutics. We report the design of a novel class of PROTACs that incorporate small molecule VHL ligands to successfully degrade HaloTag7 fusion proteins. These HaloPROTACs will inspire the development of future PROTACs with more drug-like properties. Additionally, these HaloPROTACs are useful chemical genetic tools, due to their ability to chemically knock down widely used HaloTag7 fusion proteins in a general fashion.
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Affiliation(s)
| | | | | | | | | | - Ian E. Smith
- Protein Degradation Discovery Performance Unit, GlaxoSmithKline, Stevenage, SG1 2NY, United Kingdom
| | - Afjal H. Miah
- Protein Degradation Discovery Performance Unit, GlaxoSmithKline, Stevenage, SG1 2NY, United Kingdom
| | - John D. Harling
- Protein Degradation Discovery Performance Unit, GlaxoSmithKline, Stevenage, SG1 2NY, United Kingdom
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32
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Chung HK, Jacobs CL, Huo Y, Yang J, Krumm SA, Plemper RK, Tsien RY, Lin MZ. Tunable and reversible drug control of protein production via a self-excising degron. Nat Chem Biol 2015. [PMID: 26214256 PMCID: PMC4543534 DOI: 10.1038/nchembio.1869] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
An effective method for direct chemical control over the production of specific proteins would be widely useful. We describe Small Molecule-Assisted Shutoff (SMASh), a technique in which proteins are fused to a degron that removes itself in the absence of drug, leaving untagged protein. Clinically tested HCV protease inhibitors can then block degron removal, inducing rapid degradation of subsequently synthesized protein copies. SMASh allows reversible and dose-dependent shutoff of various proteins in multiple mammalian cell types and in yeast. We also used SMASh to confer drug responsiveness onto a RNA virus for which no licensed inhibitors exist. As SMASh does not require permanent fusion of a large domain, it should be useful when control over protein production with minimal structural modification is desired. Furthermore, as SMASh only involves a single genetic modification and does not rely on modulating protein-protein interactions, it should be easy to generalize to multiple biological contexts.
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Affiliation(s)
- Hokyung K Chung
- Department of Biology, Stanford University, Stanford, California, USA
| | - Conor L Jacobs
- Department of Biology, Stanford University, Stanford, California, USA
| | - Yunwen Huo
- Department of Pediatrics, Stanford University, Stanford, California, USA
| | - Jin Yang
- Department of Pharmacology, University of California, San Diego, La Jolla, California, USA
| | - Stefanie A Krumm
- Department of Pediatrics, Emory University, Atlanta, Georgia, USA
| | - Richard K Plemper
- 1] Department of Pediatrics, Emory University, Atlanta, Georgia, USA. [2] Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia, USA
| | - Roger Y Tsien
- 1] Department of Pharmacology, University of California, San Diego, La Jolla, California, USA. [2] Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA. [3] Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California, USA
| | - Michael Z Lin
- 1] Department of Pediatrics, Stanford University, Stanford, California, USA. [2] Department of Bioengineering, Stanford University, Stanford, California, USA
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33
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Jalles A, Maciel P. The disruption of proteostasis in neurodegenerative disorders. AIMS MOLECULAR SCIENCE 2015. [DOI: 10.3934/molsci.2015.3.259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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34
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Hebert DN, Lamriben L, Powers ET, Kelly JW. The intrinsic and extrinsic effects of N-linked glycans on glycoproteostasis. Nat Chem Biol 2014; 10:902-10. [PMID: 25325701 PMCID: PMC4232232 DOI: 10.1038/nchembio.1651] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 08/28/2014] [Indexed: 01/29/2023]
Abstract
Proteins that traffic through the eukaryotic secretory pathway are commonly modified with N-linked carbohydrates. These bulky amphipathic modifications at asparagines intrinsically enhance solubility and folding energetics through carbohydrate-protein interactions. N-linked glycans can also extrinsically enhance glycoprotein folding by using the glycoprotein homeostasis or 'glycoproteostasis' network, which comprises numerous glycan binding and/or modification enzymes or proteins that synthesize, transfer, sculpt and use N-linked glycans to direct folding and trafficking versus degradation and trafficking of nascent N-glycoproteins through the cellular secretory pathway. If protein maturation is perturbed by misfolding, aggregation or both, stress pathways are often activated that result in transcriptional remodeling of the secretory pathway in an attempt to alleviate the insult (or insults). The inability to achieve glycoproteostasis is linked to several pathologies, including amyloidoses, cystic fibrosis and lysosomal storage diseases. Recent progress on genetic and pharmacologic adaptation of the glycoproteostasis network provides hope that drugs of this mechanistic class can be developed for these maladies in the near future.
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Affiliation(s)
- Daniel N. Hebert
- Department of Biochemistry and Molecular Biology, Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA 01003
| | - Lydia Lamriben
- Department of Biochemistry and Molecular Biology, Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, MA 01003
| | - Evan T. Powers
- Departments of Chemistry and Molecular and Experimental Medicine and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037
| | - Jeffery W. Kelly
- Departments of Chemistry and Molecular and Experimental Medicine and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037
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35
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Zhang X, Liu Y, Genereux JC, Nolan C, Singh M, Kelly JW. Heat-shock response transcriptional program enables high-yield and high-quality recombinant protein production in Escherichia coli. ACS Chem Biol 2014; 9:1945-9. [PMID: 25051296 PMCID: PMC4168666 DOI: 10.1021/cb5004477] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The biosynthesis of soluble, properly
folded recombinant proteins
in large quantities from Escherichia coli is desirable
for academic research and industrial protein production. The basal E. coli protein homeostasis (proteostasis) network capacity
is often insufficient to efficiently fold overexpressed proteins.
Herein we demonstrate that a transcriptionally reprogrammed E. coli proteostasis network is generally superior for producing
soluble, folded, and functional recombinant proteins. Reprogramming
is accomplished by overexpressing a negative feedback deficient heat-shock
response
transcription factor before and during overexpression of the protein-of-interest.
The advantage of transcriptional reprogramming versus simply overexpressing
select proteostasis network components (e.g., chaperones and co-chaperones,
which has been explored previously) is that a large number of proteostasis
network components are upregulated at their evolved stoichiometry,
thus maintaining the system capabilities of the proteostasis network
that are currently incompletely understood. Transcriptional proteostasis
network reprogramming mediated by stress-responsive signaling in the
absence of stress should also be useful for protein production in
other cells.
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Affiliation(s)
- Xin Zhang
- Department of Chemistry, ‡Department of Molecular and Experimental
Medicine, and §Department of
Chemical Physiology, ∥The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yu Liu
- Department of Chemistry, ‡Department of Molecular and Experimental
Medicine, and §Department of
Chemical Physiology, ∥The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Joseph C. Genereux
- Department of Chemistry, ‡Department of Molecular and Experimental
Medicine, and §Department of
Chemical Physiology, ∥The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Chandler Nolan
- Department of Chemistry, ‡Department of Molecular and Experimental
Medicine, and §Department of
Chemical Physiology, ∥The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Meha Singh
- Department of Chemistry, ‡Department of Molecular and Experimental
Medicine, and §Department of
Chemical Physiology, ∥The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jeffery W. Kelly
- Department of Chemistry, ‡Department of Molecular and Experimental
Medicine, and §Department of
Chemical Physiology, ∥The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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36
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The systemic amyloid precursor transthyretin (TTR) behaves as a neuronal stress protein regulated by HSF1 in SH-SY5Y human neuroblastoma cells and APP23 Alzheimer's disease model mice. J Neurosci 2014; 34:7253-65. [PMID: 24849358 DOI: 10.1523/jneurosci.4936-13.2014] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Increased neuronal synthesis of transthyretin (TTR) may favorably impact on Alzheimer's disease (AD) because TTR has been shown to inhibit Aβ aggregation and detoxify cell-damaging conformers. The mechanism whereby hippocampal and cortical neurons from AD patients and APP23 AD model mice produce more TTR is unknown. We now show that TTR expression in SH-SY5Y human neuroblastoma cells, primary hippocampal neurons and the hippocampus of APP23 mice, is significantly enhanced by heat shock factor 1 (HSF1). Chromatin immunoprecipitation (ChIP) assays demonstrated occupation of TTR promoter heat shock elements by HSF1 in APP23 hippocampi, primary murine hippocampal neurons, and SH-SY5Y cells, but not in mouse liver, cultured human hepatoma (HepG2) cells, or AC16 cultured human cardiomyocytes. Treating SH-SY5Y human neuroblastoma cells with heat shock or the HSF1 stimulator celastrol increased TTR transcription in parallel with that of HSP40, HSP70, and HSP90. With both treatments, ChIP showed increased occupancy of heat shock elements in the TTR promoter by HSF1. In vivo celastrol increased the HSF1 ChIP signal in hippocampus but not in liver. Transfection of a human HSF1 construct into SH-SY5Y cells increased TTR transcription and protein production, which could be blocked by shHSF1 antisense. The effect is neuron specific. In cultured HepG2 cells, HSF1 was either suppressive or had no effect on TTR expression confirming the differential effects of HSF1 on TTR transcription in different cell types.
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37
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Ryno LM, Genereux J, Naito T, Morimoto RI, Powers ET, Shoulders MD, Wiseman RL. Characterizing the altered cellular proteome induced by the stress-independent activation of heat shock factor 1. ACS Chem Biol 2014; 9:1273-83. [PMID: 24689980 PMCID: PMC4076015 DOI: 10.1021/cb500062n] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Accepted: 04/01/2014] [Indexed: 01/18/2023]
Abstract
The heat shock response is an evolutionarily conserved, stress-responsive signaling pathway that adapts cellular proteostasis in response to pathologic insult. In metazoans, the heat shock response primarily functions through the posttranslational activation of heat shock factor 1 (HSF1), a stress-responsive transcription factor that induces the expression of cytosolic proteostasis factors including chaperones, cochaperones, and folding enzymes. HSF1 is a potentially attractive therapeutic target to ameliorate pathologic imbalances in cellular proteostasis associated with human disease, although the underlying impact of stress-independent HSF1 activation on cellular proteome composition remains to be defined. Here, we employ a highly controllable, ligand-regulated HSF1 that activates HSF1 to levels compatible with those that could be achieved using selective small molecule HSF1 activators. Using a combination of RNAseq and quantitative proteomics, we define the impact of stress-independent HSF1 activation on the composition of the cellular proteome. We show that stress-independent HSF1 activation selectively remodels cytosolic proteostasis pathways without globally influencing the composition of the cellular proteome. Furthermore, we show that stress-independent HSF1 activation decreases intracellular aggregation of a model polyglutamine-containing protein and reduces the cellular toxicity of environmental toxins like arsenite that disrupt cytosolic proteostasis. Collectively, our results reveal a proteome-level view of stress-independent HSF1 activation, providing a framework to establish therapeutic approaches to correct pathologic imbalances in cellular proteostasis through the selective targeting of HSF1.
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Affiliation(s)
- Lisa M. Ryno
- Department
of Molecular & Experimental Medicine, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Joseph
C. Genereux
- Department
of Molecular & Experimental Medicine, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Tadasuke Naito
- Department
of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, Illinois 60208, United States
| | - Richard I. Morimoto
- Department
of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, Illinois 60208, United States
| | - Evan T. Powers
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Matthew D. Shoulders
- Department
of Molecular & Experimental Medicine, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, United States
- Department
of Chemistry, Massachusetts Institute of
Technology, Cambridge, Massachusetts 02139, United States
| | - R. Luke Wiseman
- Department
of Molecular & Experimental Medicine, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, United States
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38
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Buckley DL, Crews CM. Small-molecule control of intracellular protein levels through modulation of the ubiquitin proteasome system. Angew Chem Int Ed Engl 2014; 53:2312-30. [PMID: 24459094 PMCID: PMC4348030 DOI: 10.1002/anie.201307761] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Indexed: 12/25/2022]
Abstract
Traditionally, biological probes and drugs have targeted the activities of proteins (such as enzymes and receptors) that can be readily controlled by small molecules. The remaining majority of the proteome has been deemed "undruggable". By using small-molecule modulators of the ubiquitin proteasome, protein levels, rather than protein activity, can be targeted instead, thus increasing the number of druggable targets. Whereas targeting of the proteasome itself can lead to a global increase in protein levels, the targeting of other components of the UPS (e.g., the E3 ubiquitin ligases) can lead to an increase in protein levels in a more targeted fashion. Alternatively, multiple strategies for inducing protein degradation with small-molecule probes are emerging. With the ability to induce and inhibit the degradation of targeted proteins, small-molecule modulators of the UPS have the potential to significantly expand the druggable portion of the proteome beyond traditional targets, such as enzymes and receptors.
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Affiliation(s)
- Dennis L. Buckley
- Departments of Chemistry; Molecular, Cellular & Developmental, Biology; Pharmacology, Yale University, New Haven, Connecticut 06511, United States
| | - Craig M. Crews
- Departments of Chemistry; Molecular, Cellular & Developmental, Biology; Pharmacology, Yale University, New Haven, Connecticut 06511, United States
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39
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Buckley DL, Crews CM. Steuerung der intrazellulären Proteinmenge durch niedermolekulare Modulatoren des Ubiquitin-Proteasom-Systems. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201307761] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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