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Chen Z, Wang Y, Zhang G, Zheng J, Tian L, Song Y, Liu X. Role of LRP5/6/GSK-3β/β-catenin in the differences in exenatide- and insulin-promoted T2D osteogenesis and osteomodulation. Br J Pharmacol 2024; 181:3556-3575. [PMID: 38804080 DOI: 10.1111/bph.16421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/10/2024] [Accepted: 04/15/2024] [Indexed: 05/29/2024] Open
Abstract
BACKGROUND AND PURPOSE Insulin and exenatide are two hypoglycaemic agents that exhibit different osteogenic effects. This study compared the differences between exenatide and insulin in osseointegration in a rat model of Type 2 diabetes (T2D) and explored the mechanisms promoting osteogenesis in this model of T2D. EXPERIMENTAL APPROACH In vivo, micro-CT was used to detect differences in the peri-implant bone microstructure in vivo. Histology, dual-fluorescent labelling, immunofluorescence and immunohistochemistry were used to detect differences in tissue, cell and protein expression around the implants. In vitro, RT-PCR and western blotting were used to measure the expression of osteogenesis- and Wnt signalling-related genes and proteins in bone marrow mesenchymal stromal cells (BMSCs) from rats with T2D (TBMSCs) after PBS, insulin and exenatide treatment. RT-PCR was used to detect the expression of Wnt bypass cascade reactions under Wnt inactivation. KEY RESULTS Micro-CT and section staining showed exenatide extensively promoted peri-implant osseointegration. Both in vivo and in vitro experiments showed exenatide substantially increased the expression of osteogenesis-related and activated the LRP5/6/GSK-3β/β-catenin-related Wnt pathway. Furthermore, exenatide suppressed expression of Bmpr1a to inhibit lipogenesis and promoted expression of Btrc to suppress inflammation. CONCLUSION AND IMPLICATIONS Compared to insulin, exenatide significantly improved osteogenesis in T2D rats and TBMSCs. In addition to its dependence on LRP5/6/GSK-3β/β-catenin signalling for osteogenic differentiation, exenatide-mediated osteomodulation also involves inhibition of inflammation and adipogenesis by BMPR1A and β-TrCP, respectively.
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Affiliation(s)
- Zijun Chen
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Engineering Research Center for Dental Materials and Advanced Manufacture, School of Stomatology, Air Force Medical University, Xi'an, China
| | - Yuxi Wang
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Engineering Research Center for Dental Materials and Advanced Manufacture, School of Stomatology, Air Force Medical University, Xi'an, China
| | - Guanhua Zhang
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Engineering Research Center for Dental Materials and Advanced Manufacture, School of Stomatology, Air Force Medical University, Xi'an, China
| | - Jian Zheng
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Engineering Research Center for Dental Materials and Advanced Manufacture, School of Stomatology, Air Force Medical University, Xi'an, China
| | - Lei Tian
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Engineering Research Center for Dental Materials and Advanced Manufacture, School of Stomatology, Air Force Medical University, Xi'an, China
| | - Yingliang Song
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Engineering Research Center for Dental Materials and Advanced Manufacture, School of Stomatology, Air Force Medical University, Xi'an, China
| | - Xiangdong Liu
- State Key Laboratory of Military Stomatology and National Clinical Research Center for Oral Diseases and Shaanxi Engineering Research Center for Dental Materials and Advanced Manufacture, School of Stomatology, Air Force Medical University, Xi'an, China
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2
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Huang KT, Aye Y. Toward decoding spatiotemporal signaling activities of reactive immunometabolites with precision immuno-chemical biology tools. Commun Chem 2024; 7:195. [PMID: 39223329 PMCID: PMC11369232 DOI: 10.1038/s42004-024-01282-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024] Open
Abstract
Immune-cell reprogramming driven by mitochondria-derived reactive electrophilic immunometabolites (mt-REMs-e.g., fumarate, itaconate) is an emerging phenomenon of major biomedical importance. Despite their localized production, mt-REMs elicit significantly large local and global footprints within and across cells, through mechanisms involving electrophile signaling. Burgeoning efforts are being put into profiling mt-REMs' potential protein-targets and phenotypic mapping of their multifaceted inflammatory behaviors. Yet, precision indexing of mt-REMs' first-responders with spatiotemporal intelligence and locale-specific function assignments remain elusive. Highlighting the latest advances and overarching challenges, this perspective aims to stimulate thoughts and spur interdisciplinary innovations to address these unmet chemical-biotechnological needs at therapeutic immuno-signaling frontiers.
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Affiliation(s)
- Kuan-Ting Huang
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Yimon Aye
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
- University of Oxford, Oxford, UK.
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3
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Yuan L, Wang Y, Li N, Yang X, Sun X, Tian H, Zhang Y. Mechanism of Action and Therapeutic Implications of Nrf2/HO-1 in Inflammatory Bowel Disease. Antioxidants (Basel) 2024; 13:1012. [PMID: 39199256 PMCID: PMC11351392 DOI: 10.3390/antiox13081012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 07/29/2024] [Accepted: 08/17/2024] [Indexed: 09/01/2024] Open
Abstract
Oxidative stress (OS) is a key factor in the generation of various pathophysiological conditions. Nuclear factor erythroid 2 (NF-E2)-related factor 2 (Nrf2) is a major transcriptional regulator of antioxidant reactions. Heme oxygenase-1 (HO-1), a gene regulated by Nrf2, is one of the most critical cytoprotective molecules. In recent years, Nrf2/HO-1 has received widespread attention as a major regulatory pathway for intracellular defense against oxidative stress. It is considered as a potential target for the treatment of inflammatory bowel disease (IBD). This review highlights the mechanism of action and therapeutic significance of Nrf2/HO-1 in IBD and IBD complications (intestinal fibrosis and colorectal cancer (CRC)), as well as the potential of phytochemicals targeting Nrf2/HO-1 in the treatment of IBD. The results suggest that the therapeutic effects of Nrf2/HO-1 on IBD mainly involve the following aspects: (1) Controlling of oxidative stress to reduce intestinal inflammation and injury; (2) Regulation of intestinal flora to repair the intestinal mucosal barrier; and (3) Prevention of ferroptosis in intestinal epithelial cells. However, due to the complex role of Nrf2/HO-1, a more nuanced understanding of the exact mechanisms involved in Nrf2/HO-1 is the way forward for the treatment of IBD in the future.
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Affiliation(s)
- Lingling Yuan
- Department of Gastroenterology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610072, China; (L.Y.); (Y.W.); (X.Y.); (X.S.); (H.T.)
| | - Yingyi Wang
- Department of Gastroenterology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610072, China; (L.Y.); (Y.W.); (X.Y.); (X.S.); (H.T.)
| | - Na Li
- Department of Infection, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610072, China;
| | - Xuli Yang
- Department of Gastroenterology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610072, China; (L.Y.); (Y.W.); (X.Y.); (X.S.); (H.T.)
| | - Xuhui Sun
- Department of Gastroenterology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610072, China; (L.Y.); (Y.W.); (X.Y.); (X.S.); (H.T.)
| | - Huai’e Tian
- Department of Gastroenterology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610072, China; (L.Y.); (Y.W.); (X.Y.); (X.S.); (H.T.)
| | - Yi Zhang
- Department of Gastroenterology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610072, China; (L.Y.); (Y.W.); (X.Y.); (X.S.); (H.T.)
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4
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Long MJC, Aye Y. Climbing into their Skin to Understand Contextual Protein-Protein Associations and Localizations: Functional Investigations in Transgenic Live Model Organisms. Chembiochem 2024; 25:e202400005. [PMID: 38511872 DOI: 10.1002/cbic.202400005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/07/2024] [Indexed: 03/22/2024]
Abstract
Borrowing some quotes from Harper Lee's novel "To Kill A Mockingbird" to help frame our manuscript, we discuss methods to profile local proteomes. We initially focus on chemical biology regimens that function in live organisms and use reactive biotin species for this purpose. We then consider ways to add new dimensions to these experimental regimens, principally by releasing less reactive (i. e., more selective) (preter)natural electrophiles. Although electrophile release methods may have lower resolution and label fewer proteins than biotinylation methods, their ability to probe simultaneously protein function and locale raises new and interesting possibilities for the field.
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Affiliation(s)
| | - Yimon Aye
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, 1015, Switzerland
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5
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Peng S, Shen L, Yu X, Zhang L, Xu K, Xia Y, Zha L, Wu J, Luo H. The role of Nrf2 in the pathogenesis and treatment of ulcerative colitis. Front Immunol 2023; 14:1200111. [PMID: 37359553 PMCID: PMC10285877 DOI: 10.3389/fimmu.2023.1200111] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/22/2023] [Indexed: 06/28/2023] Open
Abstract
Ulcerative colitis (UC) is a chronic inflammatory bowel disease involving mainly the colorectal mucosa and submucosa, the incidence of which has been on the rise in recent years. Nuclear factor erythroid 2-related factor 2 (Nrf2), known for its key function as a transcription factor, is pivotal in inducing antioxidant stress and regulating inflammatory responses. Numerous investigations have demonstrated the involvement of the Nrf2 pathway in maintaining the development and normal function of the intestine, the development of UC, and UC-related intestinal fibrosis and carcinogenesis; meanwhile, therapeutic agents targeting the Nrf2 pathway have been widely investigated. This paper reviews the research progress of the Nrf2 signaling pathway in UC.
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Affiliation(s)
- Shuai Peng
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Digestive Diseases, Wuhan, China
| | - Lei Shen
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Digestive Diseases, Wuhan, China
| | - Xiaoyun Yu
- Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Li Zhang
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Ke Xu
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yuan Xia
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Digestive Diseases, Wuhan, China
| | - Lanlan Zha
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Digestive Diseases, Wuhan, China
| | - Jing Wu
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Digestive Diseases, Wuhan, China
| | - Hesheng Luo
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Digestive Diseases, Wuhan, China
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6
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Huang KT, Poganik JR, Parvez S, Raja S, Miller B, Long MJC, Fetcho JR, Aye Y. Z-REX: shepherding reactive electrophiles to specific proteins expressed tissue specifically or ubiquitously, and recording the resultant functional electrophile-induced redox responses in larval fish. Nat Protoc 2023; 18:1379-1415. [PMID: 37020146 PMCID: PMC11150335 DOI: 10.1038/s41596-023-00809-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 12/05/2022] [Indexed: 04/07/2023]
Abstract
This Protocol Extension describes the adaptation of an existing Protocol detailing the use of targetable reactive electrophiles and oxidants, an on-demand redox targeting toolset in cultured cells. The adaptation described here is for use of reactive electrophiles and oxidants technologies in live zebrafish embryos (Z-REX). Zebrafish embryos expressing a Halo-tagged protein of interest (POI)-either ubiquitously or tissue specifically-are treated with a HaloTag-specific small-molecule probe housing a photocaged reactive electrophile (either natural electrophiles or synthetic electrophilic drug-like fragments). The reactive electrophile is then photouncaged at a user-defined time, enabling proximity-assisted electrophile-modification of the POI. Functional and phenotypic ramifications of POI-specific modification can then be monitored, by coupling to standard downstream assays, such as click chemistry-based POI-labeling and target-occupancy quantification; immunofluorescence or live imaging; RNA-sequencing and real-time quantitative polymerase chain reaction analyses of downstream-transcript modulations. Transient expression of requisite Halo-POI in zebrafish embryos is achieved by messenger RNA injection. Procedures associated with generation of transgenic zebrafish expressing a tissue-specific Halo-POI are also described. The Z-REX experiments can be completed in <1 week using standard techniques. To successfully execute Z-REX, researchers should have basic skills in fish husbandry, imaging and pathway analysis. Experience with protein or proteome manipulation is useful. This Protocol Extension is aimed at helping chemical biologists study precision redox events in a model organism and fish biologists perform redox chemical biology.
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Affiliation(s)
- Kuan-Ting Huang
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Jesse R Poganik
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Saba Parvez
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT, USA
| | - Sruthi Raja
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Brian Miller
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, USA
| | | | - Joseph R Fetcho
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, USA.
| | - Yimon Aye
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
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7
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Long MJC, Liu J, Aye Y. Finding a vocation for validation: taking proteomics beyond association and location. RSC Chem Biol 2023; 4:110-120. [PMID: 36794020 PMCID: PMC9906375 DOI: 10.1039/d2cb00214k] [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: 10/06/2022] [Accepted: 12/01/2022] [Indexed: 12/03/2022] Open
Abstract
First established in the seventies, proteomics, chemoproteomics, and most recently, spatial/proximity-proteomics technologies have empowered researchers with new capabilities to illuminate cellular communication networks that govern sophisticated decision-making processes. With an ever-growing inventory of these advanced proteomics tools, the onus is upon the researchers to understand their individual advantages and limitations, such that we can ensure rigorous implementation and conclusions derived from critical data interpretations backed up by orthogonal series of functional validations. This perspective-based on the authors' experience in applying varied proteomics workflows in complex living models-underlines key book-keeping considerations, comparing and contrasting most-commonly-deployed modern proteomics profiling technologies. We hope this article stimulates thoughts among expert users and equips new-comers with practical knowhow of what has become an indispensable tool in chemical biology, drug discovery, and broader life-science investigations.
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Affiliation(s)
- Marcus J. C. Long
- University of Lausanne (UNIL)Switzerland,NCCR Chemical Biology, University of Geneva (UNIGE)Switzerland
| | - Jinmin Liu
- Swiss Federal Institute of Technology Lausanne (EPFL) Switzerland .,NCCR Chemical Biology, University of Geneva (UNIGE) Switzerland
| | - Yimon Aye
- Swiss Federal Institute of Technology Lausanne (EPFL) Switzerland .,NCCR Chemical Biology, University of Geneva (UNIGE) Switzerland
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8
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Van Hall-Beauvais A, Poganik JR, Huang KT, Parvez S, Zhao Y, Lin HY, Liu X, Long MJC, Aye Y. Z-REX uncovers a bifurcation in function of Keap1 paralogs. eLife 2022; 11:e83373. [PMID: 36300632 PMCID: PMC9754640 DOI: 10.7554/elife.83373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/12/2022] [Indexed: 11/13/2022] Open
Abstract
Studying electrophile signaling is marred by difficulties in parsing changes in pathway flux attributable to on-target, vis-à-vis off-target, modifications. By combining bolus dosing, knockdown, and Z-REX-a tool investigating on-target/on-pathway electrophile signaling, we document that electrophile labeling of one zebrafish-Keap1-paralog (zKeap1b) stimulates Nrf2- driven antioxidant response (AR) signaling (like the human-ortholog). Conversely, zKeap1a is a dominant-negative regulator of electrophile-promoted Nrf2-signaling, and itself is nonpermissive for electrophile-induced Nrf2-upregulation. This behavior is recapitulated in human cells: (1) zKeap1b-expressing cells are permissive for augmented AR-signaling through reduced zKeap1b-Nrf2 binding following whole-cell electrophile treatment; (2) zKeap1a-expressing cells are non-permissive for AR-upregulation, as zKeap1a-Nrf2 binding capacity remains unaltered upon whole-cell electrophile exposure; (3) 1:1 ZKeap1a:zKeap1b-co-expressing cells show no Nrf2-release from the Keap1-complex following whole-cell electrophile administration, rendering these cells unable to upregulate AR. We identified a zKeap1a-specific point-mutation (C273I) responsible for zKeap1a's behavior during electrophilic stress. Human-Keap1(C273I), of known diminished Nrf2-regulatory capacity, dominantly muted electrophile-induced Nrf2-signaling. These studies highlight divergent and interdependent electrophile signaling behaviors, despite conserved electrophile sensing.
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Affiliation(s)
| | - Jesse R Poganik
- Swiss Federal Institute of Technology LausanneLausanneSwitzerland
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical SchoolBostonUnited States
| | - Kuan-Ting Huang
- Swiss Federal Institute of Technology LausanneLausanneSwitzerland
| | - Saba Parvez
- Department of Pharmacology and Toxicology, College of Pharmacy, University of UtahSalt Lake CityUnited States
| | - Yi Zhao
- Swiss Federal Institute of Technology LausanneLausanneSwitzerland
- BayRay Innovation Center, Shenzhen Bay LaboratoryShenzhenChina
| | - Hong-Yu Lin
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen UniversityXiamenChina
| | - Xuyu Liu
- Swiss Federal Institute of Technology LausanneLausanneSwitzerland
- School of Chemistry, The University of SydneySydneyAustralia
- The Heart Research Institute, NewtownNewtownAustralia
| | - Marcus John Curtis Long
- Department of Biochemistry, Faculty of Biology and Medicine, University of LausanneLausanneSwitzerland
| | - Yimon Aye
- Swiss Federal Institute of Technology LausanneLausanneSwitzerland
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9
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Fragoulis A, Schenkel J, Schröder N, Brandt EF, Weiand M, Neu T, Ramadori P, Caspers T, Kant S, Pufe T, Mohs A, Trautwein C, Longerich T, Streetz KL, Wruck CJ. Nrf2 induces malignant transformation of hepatic progenitor cells by inducing β-catenin expression. Redox Biol 2022; 57:102453. [PMID: 36209041 PMCID: PMC9618468 DOI: 10.1016/j.redox.2022.102453] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 07/22/2022] [Accepted: 08/19/2022] [Indexed: 11/28/2022] Open
Abstract
The Nrf2 signaling pathway prevents cancer initiation, but genetic mutations that activate this pathway are found in various types of cancer. The molecular mechanisms underlying this Janus-headed character are still not understood. Here, we show that sustained Nrf2 activation induces proliferation and dedifferentiation of a Wnt-responsive perivenular hepatic progenitor cell population, transforming them into metastatic cancer cells. The neoplastic lesions display many histological features known from human hepatoblastoma. We describe an Nrf2-induced upregulation of β-catenin expression and its activation as the underlying mechanism for the observed malignant transformation. Thus, we have identified the Nrf2–β-catenin axis promoting proliferation of hepatic stem cells and triggering tumorigenesis. These findings support the concept that different functional levels of Nrf2 control both the protection against various toxins as well as liver regeneration by activating hepatic stem cells. Activation of the hepatic stem cell compartment confers the observation that unbridled Nrf2 activation may trigger tumorigenesis.
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Affiliation(s)
| | - Julia Schenkel
- Department of Anatomy and Cell Biology, Uniklinik RWTH Aachen, Germany
| | - Nicole Schröder
- Department of Anatomy and Cell Biology, Uniklinik RWTH Aachen, Germany
| | | | - Mathias Weiand
- Department of Anatomy and Cell Biology, Uniklinik RWTH Aachen, Germany
| | - Tabita Neu
- Department of Anatomy and Cell Biology, Uniklinik RWTH Aachen, Germany
| | - Pierluigi Ramadori
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tim Caspers
- Department of Anatomy and Cell Biology, Uniklinik RWTH Aachen, Germany
| | - Sebastian Kant
- Institute of Molecular and Cellular Anatomy, Uniklinik RWTH Aachen, Germany
| | - Thomas Pufe
- Department of Anatomy and Cell Biology, Uniklinik RWTH Aachen, Germany
| | - Antje Mohs
- Department of Medicine III, Uniklinik RWTH Aachen, Germany
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10
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Long MJC, Aye Y. Keap 1: The new Janus word on the block. Bioorg Med Chem Lett 2022; 71:128766. [PMID: 35537607 DOI: 10.1016/j.bmcl.2022.128766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 04/27/2022] [Indexed: 11/19/2022]
Abstract
Here we draw insights from the latest serendipitous findings made on the opposing roles of a proposed drug-target protein Keap1. We weigh up how natural reactive electrophiles and electrophilic small-molecule drugs in clinical use directly impinge on seemingly conflicting, yet both Keap1-electrophile-modification-dependent, cell-survival- vs. cell-death-promoting behaviors. In the process, we convey how understanding reactive chemical-signal regulation at the single-protein-specific level is an enabling necessity in deconstructing otherwise intricate reactive-small-molecule-responsive cellular pathways. We hope this opinion piece further spurs the broader interests of basic and pharmaceutical research communities toward better understanding of molecular mechanisms underpinning reactive small-molecule-regulated signaling subsystems.
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Affiliation(s)
- Marcus J C Long
- NCCR Chemical Biology and University of Geneva, 1211 Geneva, Switzerland; University of Lausanne (UNIL), Lausanne, Switzerland
| | - Yimon Aye
- Swiss Federal Institute of Technology Lausanne (EPFL), 1015 Lausanne, Switzerland.
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11
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Veale CGL, Talukdar A, Vauzeilles B. ICBS 2021: Looking Toward the Next Decade of Chemical Biology. ACS Chem Biol 2022; 17:728-743. [PMID: 35293726 DOI: 10.1021/acschembio.2c00209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Clinton G. L. Veale
- Department of Chemistry, University of Cape Town, Rondebosch, Cape Town, 7700, South Africa
| | - Arindam Talukdar
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Boris Vauzeilles
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198, Gif-sur-Yvette, France
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12
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Long MJC, Miranda Herrera PA, Aye Y. Hitting the Bullseye: Endogenous Electrophiles Show Remarkable Nuance in Signaling Regulation. Chem Res Toxicol 2022; 35:1636-1648. [PMID: 35394758 DOI: 10.1021/acs.chemrestox.2c00006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Our bodies produce a host of electrophilic species that can label specific endogenous proteins in cells. The signaling roles of these molecules are under active debate. However, in our opinion, it is becoming increasingly likely that electrophiles can rewire cellular signaling processes at endogenous levels. Attention is turning more to understanding how nuanced electrophile signaling in cells is. In this Perspective, we describe recent work from our laboratory that has started to inform on different levels of context-specific regulation of proteins by electrophiles. We discuss the relevance of these data to the field and to the broader application of electrophile signaling to precision medicine development, beyond the traditional views of their pleiotropic cytotoxic roles.
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Affiliation(s)
- Marcus J C Long
- National Centre of Competence in Research Chemical Biology, University of Geneva, 1211 Geneva, Switzerland.,Department of Biochemistry, Faculty of Biology and Medicine, University of Lausanne, 1066 Epalinges, Switzerland
| | - Pierre A Miranda Herrera
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Swiss Federal Institute of Technology Lausanne, 1015 Lausanne, Switzerland.,National Centre of Competence in Research Chemical Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Yimon Aye
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, Swiss Federal Institute of Technology Lausanne, 1015 Lausanne, Switzerland.,National Centre of Competence in Research Chemical Biology, University of Geneva, 1211 Geneva, Switzerland
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13
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Function-guided proximity mapping unveils electrophilic-metabolite sensing by proteins not present in their canonical locales. Proc Natl Acad Sci U S A 2022; 119:2120687119. [PMID: 35082156 PMCID: PMC8812531 DOI: 10.1073/pnas.2120687119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2021] [Indexed: 11/18/2022] Open
Abstract
Enzyme-assisted posttranslational modifications (PTMs) constitute a major means of signaling across different cellular compartments. However, how nonenzymatic PTMs-despite their direct relevance to covalent drug development-impinge on cross-compartment signaling remains inaccessible as current target-identification (target-ID) technologies offer limited spatiotemporal resolution, and proximity mapping tools are also not guided by specific, biologically-relevant, ligand chemotypes. Here we establish a quantitative and direct profiling platform (Localis-rex) that ranks responsivity of compartmentalized subproteomes to nonenzymatic PTMs. In a setup that contrasts nucleus- vs. cytoplasm-specific responsivity to reactive-metabolite modification (hydroxynonenylation), ∼40% of the top-enriched protein sensors investigated respond in compartments of nonprimary origin or where the canonical activity of the protein sensor is inoperative. CDK9-a primarily nuclear-localized kinase-was hydroxynonenylated only in the cytoplasm. Site-specific CDK9 hydroxynonenylation-which we identified in untreated cells-drives its nuclear translocation, downregulating RNA-polymerase-II activity, through a mechanism distinct from that of commonly used CDK9 inhibitors. Taken together, this work documents an unmet approach to quantitatively profile and decode localized and context-specific signaling/signal-propagation programs orchestrated by reactive covalent ligands.
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14
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Long MJC, Ly P, Aye Y. A primer on harnessing non-enzymatic post-translational modifications for drug design. RSC Med Chem 2021; 12:1797-1807. [PMID: 34825181 PMCID: PMC8597429 DOI: 10.1039/d1md00157d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 10/08/2021] [Indexed: 11/21/2022] Open
Abstract
Of the manifold concepts in drug discovery and design, covalent drugs have re-emerged as one of the most promising over the past 20-or so years. All such drugs harness the ability of a covalent bond to drive an interaction between a target biomolecule, typically a protein, and a small molecule. Formation of a covalent bond necessarily prolongs target engagement, opening avenues to targeting shallower binding sites, protein complexes, and other difficult to drug manifolds, amongst other virtues. This opinion piece discusses frameworks around which to develop covalent drugs. Our argument, based on results from our research program on natural electrophile signaling, is that targeting specific residues innately involved in native signaling programs are ideally poised to be targeted by covalent drugs. We outline ways to identify electrophile-sensing residues, and discuss how studying ramifications of innate signaling by endogenous molecules can provide a means to predict drug mechanism and function and assess on- versus off-target behaviors.
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Affiliation(s)
| | - Phillippe Ly
- Swiss Federal Institute of Technology in Lausanne (EPFL) 1015 Lausanne Switzerland
| | - Yimon Aye
- Swiss Federal Institute of Technology in Lausanne (EPFL) 1015 Lausanne Switzerland
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15
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Valle MS, Russo C, Malaguarnera L. Protective role of vitamin D against oxidative stress in diabetic retinopathy. Diabetes Metab Res Rev 2021; 37:e3447. [PMID: 33760363 DOI: 10.1002/dmrr.3447] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 02/01/2021] [Accepted: 02/15/2021] [Indexed: 02/06/2023]
Abstract
Diabetic retinopathy (DR) is a microvascular complication of diabetes mellitus. There is much evidence showing that a high level of mitochondrial overproduction of reactive oxygen species in the diabetic retina contributes in modifying cellular signalling and leads to retinal cell damage and finally to the development of DR pathogenesis. In the last few decades, it has been reported that vitamin D is involved in DR pathogenesis. Vitamin D, traditionally known as an essential nutrient crucial in bone metabolism, has also been proven to be a very effective antioxidant. It has been demonstrated that it modulates the production of advanced glycosylated end products, as well as several pathways including protein kinase C, the polyol pathway leading to the reduction of free radical formation. It prevents the translocation of nuclear factor kappa B, preventing the inflammatory response, acting as an immunomodulator, and modulates autophagy and apoptosis. In this review, we explore the molecular mechanisms by which vitamin D protects the eye from oxidative stress, in order to evaluate whether vitamin D supplementation may be useful to mitigate the deleterious effects of free radicals in DR.
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Affiliation(s)
- Maria Stella Valle
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Cristina Russo
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Lucia Malaguarnera
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
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16
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Poganik JR, Huang KT, Parvez S, Zhao Y, Raja S, Long MJC, Aye Y. Wdr1 and cofilin are necessary mediators of immune-cell-specific apoptosis triggered by Tecfidera. Nat Commun 2021; 12:5736. [PMID: 34593792 PMCID: PMC8484674 DOI: 10.1038/s41467-021-25466-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 08/11/2021] [Indexed: 01/10/2023] Open
Abstract
Despite the emerging importance of reactive electrophilic drugs, deconvolution of their principal targets remains difficult. The lack of genetic tractability/interventions and reliance on secondary validation using other non-specific compounds frequently complicate the earmarking of individual binders as functionally- or phenotypically-sufficient pathway regulators. Using a redox-targeting approach to interrogate how on-target binding of pleiotropic electrophiles translates to a phenotypic output in vivo, we here systematically track the molecular components attributable to innate immune cell toxicity of the electrophilic-drug dimethyl fumarate (Tecfidera®). In a process largely independent of canonical Keap1/Nrf2-signaling, Keap1-specific modification triggers mitochondrial-targeted neutrophil/macrophage apoptosis. On-target Keap1–ligand-engagement is accompanied by dissociation of Wdr1 from Keap1 and subsequent coordination with cofilin, intercepting Bax. This phagocytic-specific cell-killing program is recapitulated by whole-animal administration of dimethyl fumarate, where individual depletions of the players identified above robustly suppress apoptosis. The mechanism-of-action of many electrohilic drugs remains poorly understood. Here, the authors use a redox-targeting approach to elucidate the basis for the innate immune cell toxicity of dimethyl fumarate, showing that it modifies Keap1 to trigger mitochondrial-targeted neutrophil/macrophage apoptosis.
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Affiliation(s)
- Jesse R Poganik
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kuan-Ting Huang
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Saba Parvez
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT, USA
| | - Yi Zhao
- BayRay Innovation Center, Shenzhen Bay Laboratory (SZBL), Guangdong, China
| | - Sruthi Raja
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | | | - Yimon Aye
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
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17
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Long MJC, Rogg C, Aye Y. An Oculus to Profile and Probe Target Engagement In Vivo: How T-REX Was Born and Its Evolution into G-REX. Acc Chem Res 2021; 54:618-631. [PMID: 33228351 DOI: 10.1021/acs.accounts.0c00537] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Here we provide a personal account of innovation and design principles underpinning a method to interrogate precision electrophile signaling that has come to be known as "REX technologies". This Account is framed in the context of trying to improve methods of target mining and understanding of individual target-ligand engagement by a specific natural electrophile and the ramifications of this labeling event in cells and organisms. We start by explaining from a practical standpoint why gleaning such understanding is critical: we are constantly assailed by a battery of electrophilic molecules that exist as a consequence of diet, food preparation, ineluctable endogenous metabolic processes, and potentially disease. The resulting molecules, which are detectable in the body, appear to be able to modify function of specific proteins. Aside from potentially being biologically relevant in their own right, these labeling events are essentially identical to protein-covalent drug interactions. Thus, on what proteins and even in what ways a covalent drug will work can be understood through the eyes of natural electrophiles; extending this logic leads to the postulate that target identification of specific electrophiles can inform on drug design. However, when we entered this field, there was no way to interrogate how a specific labeling event impacted a specific protein in an unperturbed cell. Methods to evaluate stoichiometry of labeling, and even chemospecificity of a specific phenotype were limited. There were further no generally accepted ways to study electrophile signaling that did not hugely disturb physiology.We developed T-REX, a method to study single-protein-specific electrophile engagement, to interrogate how single-protein electrophile labeling shapes pathway flux. Using T-REX, we discovered that labeling of several proteins by a specific electrophile, even at low occupancy, leads to biologically relevant signaling outputs. Further experimentation using T-REX showed that in some instances, single-protein isoforms were electrophile responsive against other isoforms, such as Akt3. Selective electrophile-labeling of Akt3 elicited inhibition of Akt-pathway flux in cells and in zebrafish embryos. Using these data, we rationally designed a molecule to selectively target Akt3. This was a fusion of the naturally derived electrophile and an isoform-nonspecific, reversible Akt inhibitor in phase-II trials, MK-2206. The resulting molecule was a selective inhibitor of Akt3 and was shown to fare better than MK-2206 in breast cancer xenograft mouse models. Recently, we have also developed a means to screen electrophile sensors that is unbiased and uses a precise burst of electrophiles. Using this method, dubbed G-REX, in conjunction with T-REX, we discovered new DNA-damage response upregulation pathways orchestrated by simple natural electrophiles. We thus emphasize how deriving a quantitative understanding of electrophile signaling that is linked to thorough and precise mechanistic studies can open doors to numerous medicinally and biologically relevant insights, from gleaning better understanding of target engagement and target mining to rational design of targeted covalent medicines.
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Affiliation(s)
- Marcus J. C. Long
- Department of Molecular Biology, University of Geneva, 30 quai Ernest-Ansermet, 1211 Geneva, Switzerland
| | - Chloé Rogg
- Institute of Chemical Sciences and Engineering (ISIC), Swiss Federal Institute of Technology Lausanne (EPFL), Route Cantonale, 1015 Lausanne, Switzerland
| | - Yimon Aye
- Institute of Chemical Sciences and Engineering (ISIC), Swiss Federal Institute of Technology Lausanne (EPFL), Route Cantonale, 1015 Lausanne, Switzerland
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18
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Long MJC, Wang L, Aye Y. Getting the Right Grip? How Understanding Electrophile Selectivity Profiles Could Illuminate Our Understanding of Redox Signaling. Antioxid Redox Signal 2020; 33:1077-1091. [PMID: 31578876 PMCID: PMC7583342 DOI: 10.1089/ars.2019.7894] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Significance: Electrophile signaling is coming into focus as a bona fide cell signaling mechanism. The electrophilic regulation occurs typically through a sensing event (i.e., labeling of a protein) and a signaling event (the labeling event having an effect of the proteins activity, association, etc.). Recent Advances: Herein, we focus on the first step of this process, electrophile sensing. Electrophile sensing is typically a deceptively simple reaction between the thiol of a protein cysteine, of which there are around 200,000 in the human proteome, and a Michael acceptor, of which there are numerous flavors, including enals and enones. Recent data overall paint a picture that despite being a simple chemical reaction, electrophile sensing is a discerning process, showing labeling preferences that are often not in line with reactivity of the electrophile. Critical Issues: With a view to trying to decide what brings about highly electrophile-reactive protein cysteines, and how reactive these sensors may be, we discuss aspects of the thermodynamics and kinetics of covalent/noncovalent binding. Data made available by several laboratories indicate that it is likely that specific proteins exhibit highly stereo- and chemoselective electrophile sensing, which we take as good evidence for recognition between the electrophile and the protein before forming a covalent bond. Future Directions: We propose experiments that could help us gain a better and more quantitative understanding of the mechanisms through which sensing comes about. We further extoll the importance of performing more detailed experiments on labeling and trying to standardize the way we assess protein-specific electrophile sensing.
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Affiliation(s)
- Marcus J C Long
- 47 Pudding Gate, Bishop Burton, Beverley East Riding of Yorkshire, United Kingdom
| | - Lingxi Wang
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Yimon Aye
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
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19
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Zhang Q, Yin X, Zhang Y. MicroRNA-221 Promotes Cell Proliferation and Inhibits Apoptosis in Osteosarcoma Cells by Directly Targeting FBXW11 and Regulating Wnt Signaling. Arch Med Res 2020; 52:191-199. [PMID: 33131925 DOI: 10.1016/j.arcmed.2020.10.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 10/09/2020] [Accepted: 10/22/2020] [Indexed: 12/25/2022]
Abstract
BACKGROUND AND OBJECTIVES MicroRNAs play a crucial role in the progression of various cancers, and microRNA-221 (miR-221) has been observed to be significantly overexpressed in osteosarcoma (OS) cells. FBXW11, a vital F-box protein of the ubiquitin-proteasome system, mediates the proliferation and survival of cancer cells by targeting multiple substrates for degradation. FBXW11 inhibits OS growth and metastasis by antagonizing the β-catenin/Wnt signaling pathway. Therefore, we hypothesized that miR-221 targets FBXW11 to mediate Wnt signaling and promote OS proliferation. METHODS In this study, we demonstrated the increased expression of miR-221 and FBXW11 in OS tissues and cell lines by real-time polymerase chain reaction (RT-PCR). Moreover, to elucidate the regulatory mechanism(s) of miR-221 and FBXW11 in progression, cell viability and apoptosis were analyzed by the MTT assay and flow cytometry, respectively. RESULTS The results showed that the overexpression of miR-221 in OS cells dramatically promoted cell growth and cell cycle progression, and inhibited apoptosis, whereas miR-221 inhibitors conversely inhibited proliferation and promoted apoptosis in OS cells. The data also showed that FBXW11 directly targeted miR-221 and miR-221 regulated OS cell proliferation and apoptosis by binding to FBXW11. We further confirmed that miR-221 targeted FBXW11 to promote proliferation and inhibit apoptosis in OS cell lines by inhibiting Wnt signaling. INTERPRETATION AND CONCLUSIONS Overall, our study revealed a functional mechanism for miR-221 in OS. Further studies will elucidate its role in the progression of OS and inhibiting miR-221 may represent a useful treatment strategy.
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Affiliation(s)
- Qingzhu Zhang
- Department of Orthopedics, Affiliated Hospital of Chengde Medical University, Chengde, China
| | - Xuelian Yin
- Department of Stomatology, Affiliated Hospital of Chengde Medical University, Chengde, China
| | - Yi Zhang
- Department of Orthopedic Trauma, Affiliated Hospital of Chengde Medical University, Chengde, China.
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20
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Long MJC, Zhao Y, Aye Y. Neighborhood watch: tools for defining locale-dependent subproteomes and their contextual signaling activities. RSC Chem Biol 2020; 1:42-55. [PMID: 34458747 PMCID: PMC8341840 DOI: 10.1039/d0cb00041h] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 05/16/2020] [Indexed: 12/21/2022] Open
Abstract
Transient associations between numerous organelles-e.g., the endoplasmic reticulum and the mitochondria-forge highly-coordinated, particular environments essential for cross-compartment information flow. Our perspective summarizes chemical-biology tools that have enabled identifying proteins present within these itinerant communities against the bulk proteome, even when a particular protein's presence is fleeting/substoichiometric. However, proteins resident at these ephemeral junctions also experience transitory changes to their interactomes, small-molecule signalomes, and, importantly, functions. Thus, a thorough census of sub-organellar communities necessitates functionally probing context-dependent signaling properties of individual protein-players. Our perspective accordingly further discusses how repurposing of existing tools could allow us to glean a functional understanding of protein-specific signaling activities altered as a result of organelles pulling together. Collectively, our perspective strives to usher new chemical-biology techniques that could, in turn, open doors to modulate functions of specific subproteomes/organellar junctions underlying the nuanced regulatory subsystem broadly termed as contactology.
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Affiliation(s)
| | - Yi Zhao
- Swiss Federal Institute of Technology Lausanne (EPFL), Institute of Chemical Sciences and Engineering 1015 Lausanne Switzerland
| | - Yimon Aye
- Swiss Federal Institute of Technology Lausanne (EPFL), Institute of Chemical Sciences and Engineering 1015 Lausanne Switzerland
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21
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Poganik JR, Van Hall-Beauvais AK, Long MJC, Disare MT, Zhao Y, Aye Y. The mRNA-Binding Protein HuR Is a Kinetically-Privileged Electrophile Sensor. Helv Chim Acta 2020; 103:e2000041. [PMID: 34113045 PMCID: PMC8188987 DOI: 10.1002/hlca.202000041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 04/11/2020] [Indexed: 12/11/2022]
Abstract
The key mRNA-binding proteins HuR and AUF1 are reported stress sensors in mammals. Intrigued by recent reports of sensitivity of these proteins to the electrophilic lipid prostaglandin A2 and other redox signals, we here examined their sensing abilities to a prototypical redox-linked lipid-derived electrophile, 4-hydroxynonenal (HNE). Leveraging our T-REX electrophile delivery platform, we found that only HuR, and not AUF1, is a kinetically-privileged sensor of HNE in HEK293T cells, and sensing functions through a specific cysteine, C13. Cells depleted of HuR, upon treatment with HNE, manifest unique alterations in cell viability and Nrf2-transcription-factor-driven antioxidant response (AR), which our recent work shows is regulated by HuR at the Nrf2-mRNA level. Mutagenesis studies showed that C13-specific sensing alone is not sufficient to explain HuR-dependent stress responsivities, further highlighting a complex context-dependent layer of Nrf2/AR regulation through HuR.
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Affiliation(s)
- Jesse R Poganik
- Institute of Chemical Sciences & Engineering (ISIC), Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015 Lausanne
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York, 14853 New York, United States
| | - Alexandra K Van Hall-Beauvais
- Institute of Chemical Sciences & Engineering (ISIC), Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015 Lausanne
| | - Marcus J C Long
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York, 14853 New York, United States
| | - Michael T Disare
- Department of Chemistry & Chemical Biology, Cornell University, Ithaca, New York, 14853 New York, United States
| | - Yi Zhao
- Institute of Chemical Sciences & Engineering (ISIC), Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015 Lausanne
| | - Yimon Aye
- Institute of Chemical Sciences & Engineering (ISIC), Swiss Federal Institute of Technology Lausanne (EPFL), CH-1015 Lausanne
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22
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Reclassifying Hepatic Cell Death during Liver Damage: Ferroptosis-A Novel Form of Non-Apoptotic Cell Death? Int J Mol Sci 2020; 21:ijms21051651. [PMID: 32121273 PMCID: PMC7084577 DOI: 10.3390/ijms21051651] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 02/10/2020] [Accepted: 02/14/2020] [Indexed: 12/11/2022] Open
Abstract
Ferroptosis has emerged as a new type of cell death in different pathological conditions, including neurological and kidney diseases and, especially, in different types of cancer. The hallmark of this regulated cell death is the presence of iron-driven lipid peroxidation; the activation of key genes related to this process such as glutathione peroxidase-4 (gpx4), acyl-CoA synthetase long-chain family member-4 (acsl4), carbonyl reductase [NADPH] 3 (cbr3), and prostaglandin peroxidase synthase-2 (ptgs2); and morphological changes including shrunken and electron-dense mitochondria. Iron overload in the liver has long been recognized as both a major trigger of liver damage in different diseases, and it is also associated with liver fibrosis. New evidence suggests that ferroptosis might be a novel type of non-apoptotic cell death in several liver diseases including non-alcoholic steatohepatitis (NASH), alcoholic liver disease (ALD), drug-induced liver injury (DILI), viral hepatitis, and hemochromatosis. The interaction between iron-related lipid peroxidation, cellular stress signals, and antioxidant systems plays a pivotal role in the development of this novel type of cell death. In addition, integrated responses from lipidic mediators together with free iron from iron-containing enzymes are essential to understanding this process. The presence of ferroptosis and the exact mechanisms leading to this non-apoptotic type of cell death in the liver remain scarcely elucidated. Recognizing ferroptosis as a novel type of cell death in the liver could lead to the understanding of the complex interaction between different types of cell death, their role in progression of liver fibrosis, the development of new biomarkers, as well as the use of modulators of ferroptosis, allowing improved theranostic approaches in the clinic.
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23
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Poganik JR, Aye Y. Electrophile Signaling and Emerging Immuno- and Neuro-modulatory Electrophilic Pharmaceuticals. Front Aging Neurosci 2020; 12:1. [PMID: 32116644 PMCID: PMC7019031 DOI: 10.3389/fnagi.2020.00001] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 01/07/2020] [Indexed: 12/11/2022] Open
Abstract
With a lipid-rich environment and elevated oxygen consumption, the central nervous system (CNS) is subject to intricate regulation by lipid-derived electrophiles (LDEs). Investigations into oxidative damage and chronic LDE generation in neural disorders have spurred the development of tools that can detect and catalog the gamut of LDE-adducted proteins. Despite these advances, deconstructing the precise consequences of individual protein-specific LDE modifications remained largely impossible until recently. In this perspective, we first overview emerging toolsets that can decode electrophile-signaling events in a protein/context-specific manner, and how the accumulating mechanistic insights brought about by these tools have begun to offer new means to modulate pathways relevant to multiple sclerosis (MS). By surveying the latest data surrounding the blockbuster MS drug dimethyl fumarate that functions through LDE-signaling-like mechanisms, we further provide a vision for how chemical biology tools probing electrophile signaling may be leveraged toward novel interventions in CNS disease.
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Affiliation(s)
- Jesse R Poganik
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Yimon Aye
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
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24
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Chen Y, Fang R, Yue C, Chang G, Li P, Guo Q, Wang J, Zhou A, Zhang S, Fuller GN, Shi X, Huang S. Wnt-Induced Stabilization of KDM4C Is Required for Wnt/β-Catenin Target Gene Expression and Glioblastoma Tumorigenesis. Cancer Res 2019; 80:1049-1063. [PMID: 31888886 DOI: 10.1158/0008-5472.can-19-1229] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 11/14/2019] [Accepted: 12/23/2019] [Indexed: 12/14/2022]
Abstract
Wnt/β-catenin signaling activates the transcription of target genes to regulate stem cells and cancer development. However, the contribution of epigenetic regulation to this process is unknown. Here, we report that Wnt activation stabilizes the epigenetic regulator KDM4C that promotes tumorigenesis and survival of human glioblastoma cells by epigenetically activating the transcription of Wnt target genes. KDM4C protein expression was upregulated in human glioblastomas, and its expression directly correlated with Wnt activity and Wnt target gene expression. KDM4C was essential for Wnt-induced gene expression and tumorigenesis of glioblastoma cells. In the absence of Wnt3a, protein kinase R phosphorylated KDM4C at Ser918, inducing KDM4C ubiquitination and degradation. Wnt3a stabilized KDM4C through inhibition of GSK3-dependent protein kinase R activity. Stabilized KDM4C accumulated in the nucleus and bound to and demethylated TCF4-associated histone H3K9 by interacting with β-catenin, promoting HP1γ removal and transcriptional activation. These findings reveal that Wnt-KDM4C-β-catenin signaling represents a novel mechanism for the transcription of Wnt target genes and regulation of tumorigenesis, with important clinical implications. SIGNIFICANCE: These findings identify the Wnt-KDM4C-β-catenin signaling axis as a critical mechanism for glioma tumorigenesis that may serve as a new therapeutic target in glioblastoma.
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Affiliation(s)
- Yaohui Chen
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Runping Fang
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Human and Molecular Genetics, Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
| | - Chen Yue
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Guoqiang Chang
- Department of Human and Molecular Genetics, Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
| | - Peng Li
- Department of Human and Molecular Genetics, Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
| | - Qing Guo
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Aidong Zhou
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sicong Zhang
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gregory N Fuller
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, Texas
| | - Xiaobing Shi
- The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, Texas
- Department of Molecular Carcinogenesis, Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan
| | - Suyun Huang
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas.
- Department of Human and Molecular Genetics, Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia
- The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, Texas
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25
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Poganik JR, Long MJC, Disare MT, Liu X, Chang SH, Hla T, Aye Y. Post-transcriptional regulation of Nrf2-mRNA by the mRNA-binding proteins HuR and AUF1. FASEB J 2019; 33:14636-14652. [PMID: 31665914 DOI: 10.1096/fj.201901930r] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The nuclear factor erythroid 2-related factor 2 (Nrf2) signaling axis is a target of covalent drugs and bioactive native electrophiles. However, much of our understanding of Nrf2 regulation has been focused at the protein level. Here we report a post-transcriptional modality to directly regulate Nrf2-mRNA. Our initial studies focused on the effects of the key mRNA-binding protein (mRBP) HuR on global transcriptomic changes incurred upon oxidant or electrophile stimulation. These RNA-sequencing data and subsequent mechanistic analyses led us to discover a novel role of HuR in regulating Nrf2 activity, and in the process, we further identified the related mRBP AUF1 as an additional novel Nrf2 regulator. Both mRBPs regulate Nrf2 activity by direct interaction with the Nrf2 transcript. Our data showed that HuR enhances Nrf2-mRNA maturation and promotes its nuclear export, whereas AUF1 stabilizes Nrf2-mRNA. Both mRBPs target the 3'-UTR of Nrf2-mRNA. Using a Nrf2 activity-reporter zebrafish strain, we document that this post-transcriptional control of Nrf2 activity is conserved at the whole-vertebrate level.-Poganik, J. R., Long, M. J. C., Disare, M. T., Liu, X., Chang, S.-H., Hla, T., Aye, Y. Post-transcriptional regulation of Nrf2-mRNA by the mRNA-binding proteins HuR and AUF1.
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Affiliation(s)
- Jesse R Poganik
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.,Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Marcus J C Long
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Michael T Disare
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Xuyu Liu
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Sung-Hee Chang
- Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Timothy Hla
- Department of Surgery, Harvard Medical School, Boston, Massachusetts, USA; and.,Vascular Biology Program, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Yimon Aye
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
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26
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Qu J, Yue L, Gao J, Yao H. Perspectives on Wnt Signal Pathway in the Pathogenesis and Therapeutics of Chronic Obstructive Pulmonary Disease. J Pharmacol Exp Ther 2019; 369:473-480. [PMID: 30952680 DOI: 10.1124/jpet.118.256222] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 04/04/2019] [Indexed: 12/16/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a chronic lung disease with progressive airflow limitation and functional decline. The pathogenic mechanisms for this disease include oxidative stress, inflammatory responses, disturbed protease/antiprotease equilibrium, apoptosis/proliferation imbalance, senescence, autophagy, metabolic reprogramming, and mitochondrial dysfunction. The Wnt signaling pathway is an evolutionarily conserved signaling pathway that is abnormal in COPD, including chronic bronchitis and pulmonary emphysema. Furthermore, Wnt signaling has been shown to modulate aforementioned cellular processes involved in COPD. From this perspective, we provide an updated understanding of the crosstalk between Wnt signal and these cellular processes, and highlight the crucial role of the Wnt signal during the development of COPD. We also discuss the potential for targeting the Wnt signal in future translational and pharmacological therapeutics aimed at prevention and treatment of this disease.
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Affiliation(s)
- Jiao Qu
- The Second Affiliated Hospital, School of Pharmacy, Dalian Medical University, Dalian, Liaoning, China (J. Q., J. G.); The First Affiliated Hospital, School of Pharmacy, Anhui Medical University, Hefei, Anhui, China (J.Q., J.G.); Department of Orthopedics, Warren Alpert Medical School, Brown University/Rhode Island Hospital, Providence, Rhode Island (L.Y.); and Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Providence, Rhode Island (H.Y.)
| | - Li Yue
- The Second Affiliated Hospital, School of Pharmacy, Dalian Medical University, Dalian, Liaoning, China (J. Q., J. G.); The First Affiliated Hospital, School of Pharmacy, Anhui Medical University, Hefei, Anhui, China (J.Q., J.G.); Department of Orthopedics, Warren Alpert Medical School, Brown University/Rhode Island Hospital, Providence, Rhode Island (L.Y.); and Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Providence, Rhode Island (H.Y.)
| | - Jian Gao
- The Second Affiliated Hospital, School of Pharmacy, Dalian Medical University, Dalian, Liaoning, China (J. Q., J. G.); The First Affiliated Hospital, School of Pharmacy, Anhui Medical University, Hefei, Anhui, China (J.Q., J.G.); Department of Orthopedics, Warren Alpert Medical School, Brown University/Rhode Island Hospital, Providence, Rhode Island (L.Y.); and Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Providence, Rhode Island (H.Y.)
| | - Hongwei Yao
- The Second Affiliated Hospital, School of Pharmacy, Dalian Medical University, Dalian, Liaoning, China (J. Q., J. G.); The First Affiliated Hospital, School of Pharmacy, Anhui Medical University, Hefei, Anhui, China (J.Q., J.G.); Department of Orthopedics, Warren Alpert Medical School, Brown University/Rhode Island Hospital, Providence, Rhode Island (L.Y.); and Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Providence, Rhode Island (H.Y.)
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27
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Long MJ, Liu X, Aye Y. Genie in a bottle: controlled release helps tame natural polypharmacology? Curr Opin Chem Biol 2019; 51:48-56. [PMID: 30913473 DOI: 10.1016/j.cbpa.2019.02.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 02/02/2019] [Accepted: 02/12/2019] [Indexed: 02/06/2023]
Abstract
Ability to faithfully report drug-target interactions constitutes a major critical parameter in preclinical/clinical settings. Yet the assessment of target engagement remains challenging, particularly for promiscuous and/or polypharmacologic ligands. Drawing from our improved insights into native electrophile signaling and emerging technologies that profile and interrogate these non-enzyme-assisted signaling subsystems, we posit that 'trained' polypharmocologic covalent inhibitors can be designed. Accumulating evidence indicates that electrophile-modified states at fractional occupancy can alter cell fate. Thus, by understanding sensing preferences and ligandable regions favored by the natural electrophilic signals at individual protein-ligand resolution, we can better evaluate target engagement and develop a function-guided understanding of polypharmacology.
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Affiliation(s)
- Marcus Jc Long
- 47 Pudding Gate, Bishop Burton, Beverley East Riding of Yorkshire, HU17 8QH, UK
| | - Xuyu Liu
- École Polytechnique Fédérale de Lausanne, Institute of Chemical Sciences and Engineering, 1015, Lausanne, Switzerland
| | - Yimon Aye
- École Polytechnique Fédérale de Lausanne, Institute of Chemical Sciences and Engineering, 1015, Lausanne, Switzerland.
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28
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Long MJC, Liu X, Aye Y. Chemical Biology Gateways to Mapping Location, Association, and Pathway Responsivity. Front Chem 2019; 7:125. [PMID: 30949469 PMCID: PMC6437114 DOI: 10.3389/fchem.2019.00125] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 02/18/2019] [Indexed: 12/14/2022] Open
Abstract
Here we discuss, how by applying chemical concepts to biological problems, methods have been developed to map spatiotemporal regulation of proteins and small-molecule modulation of proteome signaling responses. We outline why chemical-biology platforms are ideal for such purposes. We further discuss strengths and weaknesses of chemical-biology protocols, contrasting them against classical genetic and biochemical approaches. We make these evaluations based on three parameters: occupancy; functional information; and spatial restriction. We demonstrate how the specific choice of chemical reagent and experimental set-up unite to resolve biological problems. Potential improvements/extensions as well as specific controls that in our opinion are often overlooked or employed incorrectly are also considered. Finally, we discuss some of the latest emerging methods to illuminate how chemical-biology innovations provide a gateway toward information hitherto inaccessible by conventional genetic/biochemical means. Finally, we also caution against solely relying on chemical-biology strategies and urge the field to undertake orthogonal validations to ensure robustness of results.
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Affiliation(s)
| | - Xuyu Liu
- École Polytechnique Fédérale de Lausanne, Institute of Chemical Sciences and Engineering, Lausanne, Switzerland
| | - Yimon Aye
- École Polytechnique Fédérale de Lausanne, Institute of Chemical Sciences and Engineering, Lausanne, Switzerland
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29
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Poganik JR, Long MJC, Aye Y. Interrogating Precision Electrophile Signaling. Trends Biochem Sci 2019; 44:380-381. [PMID: 30765181 DOI: 10.1016/j.tibs.2019.01.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 01/15/2019] [Indexed: 12/17/2022]
Abstract
Understanding the targets and signaling roles of reactive electrophilic species (RES) at a specific cellular space and time has long been hampered by the reliance of the field on the bulk administration of excess RES from outside of cells and/or animals. Uncontrolled bolus methods provide limited understanding of target engagement for these individual nonenzymatic RES-modification events. REX technologies [targetable reactive electrophiles and oxidants (T-REX) and its genome-wide variant (G-REX)] were developed as a gateway to address these limitations. These protocols offer a new ability to both profile kinetically privileged sensors (KPSs) of RES at a systems level (G-REX™ profiling) and monitor signaling responses at the sensor protein-of-interest (POI)-specific level (T-REX™ delivery) with high spatiotemporal resolution. REX technologies are compatible with several model systems and are built on a HaloTag-targetable small-molecule photocaged precursor to a native RES.
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Affiliation(s)
- Jesse R Poganik
- École Polytechnique Fédérale de Lausanne, Institute of Chemical Sciences and Engineering, 1015 Lausanne, Switzerland; Cornell University, Ithaca, NY 14850, USA
| | | | - Yimon Aye
- École Polytechnique Fédérale de Lausanne, Institute of Chemical Sciences and Engineering, 1015 Lausanne, Switzerland.
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30
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Tang L, Fang W, Lin J, Li J, Wu W, Xu J. Vitamin D protects human melanocytes against oxidative damage by activation of Wnt/β-catenin signaling. J Transl Med 2018; 98:1527-1537. [PMID: 30206310 DOI: 10.1038/s41374-018-0126-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 07/06/2018] [Accepted: 08/09/2018] [Indexed: 12/23/2022] Open
Abstract
Vitamin D analogs have been widely utilized for the treatment of vitiligo, but the molecular mechanism underlying their pharmacological effects (especially their antioxidant properties) has not yet been investigated. We evaluated the relationship between serum vitamin D level and oxidative damage severity in vitiligo patients, and investigated the molecular mechanism of vitamin D in protecting melanocytes against oxidative stress. Serum levels of 25-hydroxyvitamin D and malondialdehyde (MDA) were first measured in patients. A variety of in vitro experiments such as intracellular reactive oxygen species (ROS), cellular viability, migration, and apoptotic assays were then performed to detect the effects of vitamin D or β-catenin silencing on H2O2-treated melanocytes. Expression of Wnt/β-catenin, Nrf2, apoptotic, and MITF pathways was finally examined using quantitative real-time PCR and western blot. In this study, we initially found that vitamin D insufficiency was closely associated with the severity of oxidative stress in vitiligo patients. Using ex vivo cell models, we further showed that vitamin D positively modulated β-catenin signaling at both translational and posttranslational levels in melanocytes under oxidative stress. Like WNT agonists, vitamin D significantly inhibited ROS accumulation and cell apoptosis in H2O2-treated melanocytes and promoted their proliferative and migratory activity, while the protective effects of vitamin D against oxidative stress were abolished by β-catenin silencing in melanocytes. Furthermore, β-catenin deficiency also blocked the activation of Nrf2 and MITF as well as the inhibition of apoptosis induced by vitamin D. Taken together, vitamin D insufficiency was associated with severity of oxidative stress in vitiligo patients. Our work also provides new insights into the mechanism of vitamin D against vitiligo, in which vitamin D protects melanocytes against oxidative stress by activating Wnt/β-catenin signaling.
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Affiliation(s)
- Luyan Tang
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China.,The Shanghai Institute of Dermatology, Shanghai, China
| | - Wei Fang
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology and Venereology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Jinran Lin
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China.,The Shanghai Institute of Dermatology, Shanghai, China
| | - Jian Li
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China.,The Shanghai Institute of Dermatology, Shanghai, China
| | - Wenyu Wu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China. .,The Shanghai Institute of Dermatology, Shanghai, China.
| | - Jinhua Xu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China. .,The Shanghai Institute of Dermatology, Shanghai, China.
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31
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Proteomics and Beyond: Cell Decision-Making Shaped by Reactive Electrophiles. Trends Biochem Sci 2018; 44:75-89. [PMID: 30327250 DOI: 10.1016/j.tibs.2018.09.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/21/2018] [Accepted: 09/19/2018] [Indexed: 12/11/2022]
Abstract
Revolutionary proteomic strategies have enabled rapid profiling of the cellular targets of electrophilic small molecules. However, precise means to directly interrogate how these individual electrophilic modifications at low occupancy functionally reshape signaling networks have until recently been largely limited. We highlight here new methods that transcend proteomic platforms to forge a quantitative link between protein target-selective engagement and downstream signaling. We focus on recent progress in the study of non-enzyme-assisted signaling mechanisms and crosstalk choreographed by native reactive electrophilic species (RES). Using this as a model, we offer a long-term vision of how these toolsets together with fundamental biochemical knowledge of precision electrophile signaling may be harnessed to assist covalent ligand-target matching and ultimately amend disease-specific signaling dysfunction.
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32
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Abstract
The concept of cell signaling in the context of nonenzyme-assisted protein modifications by reactive electrophilic and oxidative species, broadly known as redox signaling, is a uniquely complex topic that has been approached from numerous different and multidisciplinary angles. Our Review reflects on five aspects critical for understanding how nature harnesses these noncanonical post-translational modifications to coordinate distinct cellular activities: (1) specific players and their generation, (2) physicochemical properties, (3) mechanisms of action, (4) methods of interrogation, and (5) functional roles in health and disease. Emphasis is primarily placed on the latest progress in the field, but several aspects of classical work likely forgotten/lost are also recollected. For researchers with interests in getting into the field, our Review is anticipated to function as a primer. For the expert, we aim to stimulate thought and discussion about fundamentals of redox signaling mechanisms and nuances of specificity/selectivity and timing in this sophisticated yet fascinating arena at the crossroads of chemistry and biology.
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Affiliation(s)
- Saba Parvez
- Department of Pharmacology and Toxicology, College of
Pharmacy, University of Utah, Salt Lake City, Utah, 84112, USA
- Department of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York, 14853, USA
| | - Marcus J. C. Long
- Department of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York, 14853, USA
| | - Jesse R. Poganik
- Ecole Polytechnique Fédérale de Lausanne,
Institute of Chemical Sciences and Engineering, 1015, Lausanne, Switzerland
- Department of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York, 14853, USA
| | - Yimon Aye
- Ecole Polytechnique Fédérale de Lausanne,
Institute of Chemical Sciences and Engineering, 1015, Lausanne, Switzerland
- Department of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York, 14853, USA
- Department of Biochemistry, Weill Cornell Medicine, New
York, New York, 10065, USA
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33
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Van Hall-Beauvais A, Zhao Y, Urul DA, Long MJC, Aye Y. Single-Protein-Specific Redox Targeting in Live Mammalian Cells and C. elegans. CURRENT PROTOCOLS IN CHEMICAL BIOLOGY 2018; 10:e43. [PMID: 30085412 PMCID: PMC6125161 DOI: 10.1002/cpch.43] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
T-REX (targetable reactive electrophiles and oxidants) enables electrophile targeting in living systems with high spatiotemporal precision and at single-protein-target resolution. T-REX allows functional consequences of individual electrophile signaling events to be directly linked to on-target modifications. T-REX is accomplished by expressing a HaloTagged protein of interest (POI) and introducing a Halo-targetable bioinert photocaged precursor to a reactive electrophilic signal (RES). Light exposure releases the unfettered RES on demand, enabling precision modification of the POI due to proximity. Using alkyne-functionalized 4-hydroxynonenal (HNE) as a representative RES, this protocol delineates optimized strategies to (1) execute T-REX in live human cells and C. elegans, (2) quantitate the POI's RES-sensitivity by either azido-fluorescent-dye conjugation or (3) enrich using biotin-azide/streptavidin pulldown procedure in both model systems, and (4) identify the site of RES-labeling on the POI using proteomics. Built-in T-REX controls that allow users to directly confirm on-target/on-site specificity of RES-sensing are also described. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
| | - Yi Zhao
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
| | - Daniel A. Urul
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
| | - Marcus J. C. Long
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
| | - Yimon Aye
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
- Department of Biochemistry, Weill Cornell Medicine, New York, NY 10065
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34
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Surya SL, Long MJC, Urul DA, Zhao Y, Mercer EJ, EIsaid IM, Evans T, Aye Y. Cardiovascular Small Heat Shock Protein HSPB7 Is a Kinetically Privileged Reactive Electrophilic Species (RES) Sensor. ACS Chem Biol 2018; 13:1824-1831. [PMID: 29397684 PMCID: PMC6260788 DOI: 10.1021/acschembio.7b00925] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Small heat shock protein (sHSP)-B7 (HSPB7) is a muscle-specific member of the non-ATP-dependent sHSPs. The precise role of HSPB7 is enigmatic. Here, we disclose that zebrafish Hspb7 is a kinetically privileged sensor that is able to react rapidly with native reactive electrophilic species (RES), when only substoichiometric amounts of RES are available in proximity to Hspb7 expressed in living cells. Among the two Hspb7-cysteines, this RES sensing is fulfilled by a single cysteine (C117). Purification and characterizations in vitro reveal that the rate for RES adduction is among the most efficient reported for protein-cysteines with native carbonyl-based RES. Covalent-ligand binding is accompanied by structural changes (increase in β-sheet-content), based on circular dichroism analysis. Among the two cysteines, only C117 is conserved across vertebrates; we show that the human ortholog is also capable of RES sensing in cells. Furthermore, a cancer-relevant missense mutation reduces this RES-sensing property. This evolutionarily conserved cysteine-biosensor may play a redox-regulatory role in cardioprotection.
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Affiliation(s)
- Sanjna L. Surya
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Marcus J. C. Long
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Daniel A. Urul
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Yi Zhao
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Emily J. Mercer
- Department of Surgery, Weill Cornell Medicine, New York, New York 10065, United States
| | - Islam M. EIsaid
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Todd Evans
- Department of Surgery, Weill Cornell Medicine, New York, New York 10065, United States
| | - Yimon Aye
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Department of Biochemistry, Weill Cornell Medicine, New York, New York 10065, United States
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35
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Poganik JR, Long MJC, Aye Y. Getting the Message? Native Reactive Electrophiles Pass Two Out of Three Thresholds to be Bona Fide Signaling Mediators. Bioessays 2018; 40:e1700240. [PMID: 29603288 PMCID: PMC6488019 DOI: 10.1002/bies.201700240] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 02/24/2018] [Indexed: 12/11/2022]
Abstract
Precision cell signaling activities of reactive electrophilic species (RES) are arguably among the most poorly-understood means to transmit biological messages. Latest research implicates native RES to be a chemically-distinct subset of endogenous redox signals that influence cell decision making through non-enzyme-assisted modifications of specific proteins. Yet, fundamental questions remain regarding the role of RES as bona fide second messengers. Here, we lay out three sets of criteria we feel need to be met for RES to be considered as true cellular signals that directly mediate information transfer by modifying "first-responding" sensor proteins. We critically assess the available evidence and define the extent to which each criterion has been fulfilled. Finally, we offer some ideas on the future trajectories of the electrophile signaling field taking inspiration from work that has been done to understand canonical signaling mediators. Also see the video abstract here: https://youtu.be/rG7o0clVP0c.
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Affiliation(s)
- Jesse R. Poganik
- Department of Chemistry and Chemical Biology Cornell University Ithaca, NY 14853, USA
| | - Marcus J. C. Long
- Department of Chemistry and Chemical Biology Cornell University Ithaca, NY 14853, USA
| | - Yimon Aye
- Department of Chemistry and Chemical Biology Cornell University Ithaca, NY 14853, USA
- Department of Biochemistry Weill Cornell Medicine New York, NY 10065, USA
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36
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Long MC, Urul DA, Chawla S, Lin HY, Zhao Y, Haegele JA, Wang Y, Aye Y. Precision Electrophile Tagging in Caenorhabditis elegans. Biochemistry 2018; 57:216-220. [PMID: 28857552 PMCID: PMC5770885 DOI: 10.1021/acs.biochem.7b00642] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 08/30/2017] [Indexed: 11/30/2022]
Abstract
Adduction of an electrophile to privileged sensor proteins and the resulting phenotypically dominant responses are increasingly appreciated as being essential for metazoan health. Functional similarities between the biological electrophiles and electrophilic pharmacophores commonly found in covalent drugs further fortify the translational relevance of these small-molecule signals. Genetically encodable or small-molecule-based fluorescent reporters and redox proteomics have revolutionized the observation and profiling of cellular redox states and electrophile-sensor proteins, respectively. However, precision mapping between specific redox-modified targets and specific responses has only recently begun to be addressed, and systems tractable to both genetic manipulation and on-target redox signaling in vivo remain largely limited. Here we engineer transgenic Caenorhabditis elegans expressing functional HaloTagged fusion proteins and use this system to develop a generalizable light-controlled approach to tagging a prototypical electrophile-sensor protein with native electrophiles in vivo. The method circumvents issues associated with low uptake/distribution and toxicity/promiscuity. Given the validated success of C. elegans in aging studies, this optimized platform offers a new lens with which to scrutinize how on-target electrophile signaling influences redox-dependent life span regulation.
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Affiliation(s)
- Marcus
J. C. Long
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
| | - Daniel A. Urul
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
| | - Shivansh Chawla
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
| | - Hong-Yu Lin
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
| | - Yi Zhao
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
| | - Joseph A. Haegele
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
| | - Yiran Wang
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
| | - Yimon Aye
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
- Department
of Biochemistry, Weill Cornell Medicine, New York, New York 10065, United States
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37
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Affiliation(s)
- Hope A. Flaxman
- Department of Chemistry and
Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Christina M. Woo
- Department of Chemistry and
Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
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