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Tsai JM, Nowak RP, Ebert BL, Fischer ES. Targeted protein degradation: from mechanisms to clinic. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00729-9. [PMID: 38684868 DOI: 10.1038/s41580-024-00729-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2024] [Indexed: 05/02/2024]
Abstract
Targeted protein degradation refers to the use of small molecules to induce the selective degradation of proteins. In its most common form, this degradation is achieved through ligand-mediated neo-interactions between ubiquitin E3 ligases - the principal waste disposal machines of a cell - and the protein targets of interest, resulting in ubiquitylation and subsequent proteasomal degradation. Notable advances have been made in biological and mechanistic understanding of serendipitously discovered degraders. This improved understanding and novel chemistry has not only provided clinical proof of concept for targeted protein degradation but has also led to rapid growth of the field, with dozens of investigational drugs in active clinical trials. Two distinct classes of protein degradation therapeutics are being widely explored: bifunctional PROTACs and molecular glue degraders, both of which have their unique advantages and challenges. Here, we review the current landscape of targeted protein degradation approaches and how they have parallels in biological processes. We also outline the ongoing clinical exploration of novel degraders and provide some perspectives on the directions the field might take.
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Affiliation(s)
- Jonathan M Tsai
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Radosław P Nowak
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Institute of Structural Biology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Boston, MA, USA.
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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2
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Miao M, Yu F, Wang D, Tong Y, Yang L, Xu J, Qiu Y, Zhou X, Zhao X. Proteomics Profiling of Host Cell Response via Protein Expression and Phosphorylation upon Dengue Virus Infection. Virol Sin 2019; 34:549-562. [PMID: 31134586 DOI: 10.1007/s12250-019-00131-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 04/08/2019] [Indexed: 12/26/2022] Open
Abstract
Dengue virus (DENV) infection is a worldwide public health threat. To date, the knowledge about the pathogenesis and progression of DENV infection is still limited. Combining global profiling based on proteomic analysis together with functional verification analysis is a powerful strategy to investigate the interplay between the virus and host cells. In the present study, quantitative proteomics has been applied to evaluate host responses (as indicated by altered proteins and modifications) in human cells (using K562 cell line) upon DENV-2 infection, as DENV-2 spreads most widely among all DENV serotypes. Comparative analysis was performed to define differentially expressed proteins in the infected cells compared to the mock-control, and it revealed critical pathogen-induced changes covering a broad spectrum of host cellular compartments and processes. We also discovered more dramatic changes (> 20%, 160 regulated phosphoproteins) in protein phosphorylation compared to protein expression (14%, 321 regulated proteins). Most of these proteins/phosphoproteins were involved in transcription regulation, RNA splicing and processing, immune system, cellular response to stimulus, and macromolecule biosynthesis. Western blot analysis was also performed to confirm the proteomic data. Potential roles of these altered proteins were discussed. The present study provides valuable large-scale protein-related information for elucidating the functional emphasis of host cell proteins and their post-translational modifications in virus infection, and also provides insight and protein evidence for understanding the general pathogenesis and pathology of DENV.
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Affiliation(s)
- Meng Miao
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Fei Yu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China.,Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Danya Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China.,Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yongjia Tong
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China.,Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Liuting Yang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China.,Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jiuyue Xu
- Laboratory of RNA Virology, Wuhan Institute of Virology, Chinese Academy of Science, Wuhan, 430071, China
| | - Yang Qiu
- Laboratory of RNA Virology, Wuhan Institute of Virology, Chinese Academy of Science, Wuhan, 430071, China
| | - Xi Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China. .,Laboratory of RNA Virology, Wuhan Institute of Virology, Chinese Academy of Science, Wuhan, 430071, China.
| | - Xiaolu Zhao
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China. .,Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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3
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Nguyen DQ, Hoang DH, Nguyen Vo TT, Huynh V, Ghoda L, Marcucci G, Nguyen LXT. The role of ErbB3 binding protein 1 in cancer: Friend or foe? J Cell Physiol 2018; 233:9110-9120. [PMID: 30076717 DOI: 10.1002/jcp.26951] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 06/12/2018] [Indexed: 12/20/2022]
Abstract
ErbB3, a member of the epidermal growth factor receptor family, reportedly plays an essential role in the regulation of cancer progression and therapeutic resistance. Numerous studies have indicated that ErbB3 binding protein 1 (Ebp1), a binding partner for ErbB3, plays an important regulatory role in the expression and function of ErbB3, but there is no agreement as to whether Ebp1 also has an ErbB3-independent function in cancer and how it might contribute to tumorigenesis. In this review, we will discuss the different functions of the two Ebp1 isoforms, p48 and p42, that may be responsible for the potentially dual role of Ebp1 in cancer growth.
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Affiliation(s)
- Dang Quan Nguyen
- Department of Medical Biotechnology, Biotechnology Center of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Dinh Hoa Hoang
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, California
| | - Thanh Thao Nguyen Vo
- Department of Medical Biotechnology, Biotechnology Center of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Vu Huynh
- Department of Medical Biotechnology, Biotechnology Center of Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Lucy Ghoda
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, California
| | - Guido Marcucci
- Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, California
| | - Le Xuan Truong Nguyen
- Department of Medical Biotechnology, Biotechnology Center of Ho Chi Minh City, Ho Chi Minh City, Vietnam.,Gehr Family Center for Leukemia Research, Hematology Malignancies and Stem Cell Transplantation Institute, City of Hope Medical Center, Duarte, California
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4
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Wu J, Zhou SL, Pi LH, Shi XJ, Ma LR, Chen Z, Qu ML, Li X, Nie SD, Liao DF, Pei JJ, Wang S. High glucose induces formation of tau hyperphosphorylation via Cav-1-mTOR pathway: A potential molecular mechanism for diabetes-induced cognitive dysfunction. Oncotarget 2018; 8:40843-40856. [PMID: 28489581 PMCID: PMC5522306 DOI: 10.18632/oncotarget.17257] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 04/07/2017] [Indexed: 12/31/2022] Open
Abstract
The abnormally hyperphosphorylated tau is thought to be implicated in diabetes-associated cognitive deficits. The role of mammalian target of rapamycin (mTOR) / S6 kinase (S6K) signalling in the formation of tau hyperphosphorylation has been previously studied. Caveolin-1 (Cav-1), the essential structure protein of caveolae, promotes neuronal survival and growth, and inhibits glucose metabolism. In this study, we aimed to investigate the role of Cav-1 in the formation of tau hyperphosphorylation under chronic hyperglycemic condition (HGC). Diabetic rats were induced by streptozotocin (STZ). Primary hippocampal neurons with or without molecular intervention such as the transient over-expression or knock-down were subjected to HGC. The obtained experimental samples were analyzed by real time quantitative RT-PCR, Western blot, immunofluorescence or immunohistochemisty. We found: 1) that a chronic HGC directly decreases Cav-1 expression, increases tau phosphorylation and activates mTOR/S6K signalling in the brain neurons of diabetic rats, 2) that overexpression of Cav-1 attenuates tau hyperphosphorylation induced by chronic HGC in primary hippocampal neurons, whereas down-regulation of Cav-1 using Cav-1 siRNA dramatically worsens tau hyperphosphorylation via mTOR/S6K signalling pathway, and 3) that the down-regulation of Cav-1 induced by HGC is independent of mTOR signalling. Our results suggest that tau hyperphosphorylation and the sustained over-activated mTOR signalling under hyperglycemia may be due to the suppression of Cav-1. Therefore, Cav-1 is a potential therapeutic target for diabetes-induced cognitive dysfunction.
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Affiliation(s)
- Jing Wu
- Department of Endocrinology, Xiang-Ya Hospital, Central South University, Changsha, China
| | - Shan-Lei Zhou
- Department of Endocrinology, Xiang-Ya Hospital, Central South University, Changsha, China
| | - Lin-Hua Pi
- Department of Endocrinology, Xiang-Ya Hospital, Central South University, Changsha, China
| | - Xia-Jie Shi
- Department of Endocrinology, Xiang-Ya Hospital, Central South University, Changsha, China
| | - Ling-Ran Ma
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, China
| | - Zi Chen
- Department of Endocrinology, Xiang-Ya Hospital, Central South University, Changsha, China
| | - Min-Li Qu
- Department of Endocrinology, Xiang-Ya Hospital, Central South University, Changsha, China
| | - Xin Li
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, China
| | - Sheng-Dan Nie
- Institute of Clinical Medicine, People's Hospital of Hunan province, The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Duan-Fang Liao
- Division of Stem Cell Regulation and Application, School of Pharmacy, Hunan University of Traditional Chinese Medicine, Changsha, Hunan, China
| | - Jin-Jing Pei
- KI-Alzheimer's Disease Research Center, Karolinska Institutet, Novum, Stockholm, Sweden.,Department of Neurology, Xuan Wu Hospital, Capital Medical University, China.,Center of Alzheimer's Disease, Beijing Institute for Brain Disorders, Beijing, China
| | - Shan Wang
- Department of Endocrinology, Xiang-Ya Hospital, Central South University, Changsha, China.,Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha, China
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5
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López SN, Rodríguez-Valentín M, Rivera M, Rodríguez M, Babu M, Cubano LA, Xiong H, Wang G, Kucheryavykh L, Boukli NM. HIV-1 Gp120 clade B/C induces a GRP78 driven cytoprotective mechanism in astrocytoma. Oncotarget 2017; 8:68415-68438. [PMID: 28978127 PMCID: PMC5620267 DOI: 10.18632/oncotarget.19474] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 06/28/2017] [Indexed: 01/20/2023] Open
Abstract
HIV-1 clades are known to be one of the key factors implicated in modulating HIV-associated neurocognitive disorders. HIV-1 B and C clades account for the majority of HIV-1 infections, clade B being the most neuropathogenic. The mechanisms behind HIV-mediated neuropathogenesis remain the subject of active research. We hypothesized that HIV-1 gp120 clade B and C proteins may exert differential proliferation, cell survival and NeuroAIDS effects in human astrocytoma cells via the Unfolded Protein Response, an endoplasmic reticulum- based cytoprotective mechanism. The differential effect of gp120 clade B and C was evaluated using for the first time a Tandem Mass Tag isobaric labeling quantitative proteomic approach. Flow cytometry analyses were performed for cell cycle and cell death identification. Among the proteins differentiated by HIV-1 gp120 proteins figure cytoskeleton, oxidative stress, UPR markers and numerous glycolytic metabolism enzymes. Our results demonstrate that HIV-1 gp120 B induced migration, proliferative and protective responses granted by the expression of GRP78, while HIV-1 gp120 C induced the expression of key inflammatory and pro-apoptotic markers. These novel findings put forward the first evidence that GRP78 is a key player in HIV-1 clade B and C neuropathogenic discrepancies and can be used as a novel target for immunotherapies.
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Affiliation(s)
- Sheila N López
- Biomedical Proteomics Facility, Department of Microbiology and Immunology, Universidad Central del Caribe, School of Medicine, Bayamón, PR, USA
| | - Madeline Rodríguez-Valentín
- Biomedical Proteomics Facility, Department of Microbiology and Immunology, Universidad Central del Caribe, School of Medicine, Bayamón, PR, USA
| | - Mariela Rivera
- Biomedical Proteomics Facility, Department of Microbiology and Immunology, Universidad Central del Caribe, School of Medicine, Bayamón, PR, USA
| | - Maridaliz Rodríguez
- Biomedical Proteomics Facility, Department of Microbiology and Immunology, Universidad Central del Caribe, School of Medicine, Bayamón, PR, USA
| | - Mohan Babu
- Department of Biochemistry, Research and Innovation Center, University of Regina, Saskatchewan, Canada
| | - Luis A Cubano
- Biomedical Proteomics Facility, Department of Microbiology and Immunology, Universidad Central del Caribe, School of Medicine, Bayamón, PR, USA
| | - Huangui Xiong
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, USA
| | - Guangdi Wang
- RCMI Cancer Research Center, Xavier University of Louisiana, New Orleans, LA, USA
| | - Lilia Kucheryavykh
- Department of Biochemistry, Universidad Central del Caribe, School of Medicine, Bayamón, PR, USA
| | - Nawal M Boukli
- Biomedical Proteomics Facility, Department of Microbiology and Immunology, Universidad Central del Caribe, School of Medicine, Bayamón, PR, USA
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Mishra P, Dixit U, Pandey AK, Upadhyay A, Pandey VN. Modulation of HCV replication and translation by ErbB3 binding protein1 isoforms. Virology 2016; 500:35-49. [PMID: 27770702 DOI: 10.1016/j.virol.2016.10.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/30/2016] [Accepted: 10/06/2016] [Indexed: 01/01/2023]
Abstract
We recently identified a cell-factor, ErbB3 binding protein 1 (Ebp-1), which specifically interacts with the viral RNA genome and modulates HCV replication and translation. Ebp1 has two isoforms, p48, and p42, that result from differential splicing. We found that both isoforms interact with HCV proteins NS5A and NS5B, as well as cell-factor PKR. The p48 isoform, which localizes in the cytoplasm and nuclei, promoted HCV replication, whereas the shorter p42 isoform, which resides exclusively in the cytoplasm, strongly inhibited HCV replication. Transient expression of individual isoforms in Ebp1-knockdown MH14 cells confirmed that the p48 isoform promotes HCV replication, while the p42 isoform inhibits it. We found that Ebp1-p42 significantly enhanced autophosphorylation of PKR, while Ebp1-p48 isoform strongly inhibited it. We propose that modulation of autophosphorylation of PKR by p48 isoform is an important mechanism whereby the HCV virus escapes innate antiviral immune responses by circumventing p42-mediated inhibition of its replication.
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Affiliation(s)
- Priya Mishra
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
| | - Updesh Dixit
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
| | - Ashutosh K Pandey
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
| | - Alok Upadhyay
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
| | - Virendra N Pandey
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA.
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7
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Hou H, Wang JZ, Liu BG, Zhang T. Pin1 liberates the human immunodeficiency virus type-1 (HIV-1): Must we stop it? Gene 2015; 565:9-14. [PMID: 25913034 DOI: 10.1016/j.gene.2015.04.049] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Revised: 03/07/2015] [Accepted: 04/20/2015] [Indexed: 11/16/2022]
Abstract
Acquired immune deficiency syndrome (AIDS) is mainly caused by the human immunodeficiency virus type-1 (HIV-1). To our knowledge, this is the first review focusing on the vital role of Pin1 in the infection of HIV-1 and the development of AIDS. We and others have demonstrated that Pin1, the only known cis-to-trans isomerase recognizing the pThr/pSer-Pro motifs in proteins, plays striking roles in several human diseases. Interestingly, recent evidence gradually indicates that Pin1 regulates several key steps of the life cycle of HIV-1, including the uncoating of the HIV-1 core, the reverse transcription of the RNA genome of HIV-1, and the integration of the HIV-1 cDNA into human chromosomes. Whereas inhibiting Pin1 suppresses all of these key steps and attenuates the replication of HIV-1, at the same time different PIN1 gene variants are correlated with the susceptibility to HIV-1 infection. Furthermore, Pin1 potentially promotes HIV-1 infection by activating multiple oncogenes and inactivating multiple tumor suppressors, extending the life span of HIV-infected cells. These descriptions suggest Pin1 as a promising therapeutic target for the prevention of HIV-1 and highlight the possibility of blocking the development of AIDS by Pin1 inhibitors.
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Affiliation(s)
- Hai Hou
- Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China
| | - Jing-Zhang Wang
- Affiliated Hospital, College of Medicine, Hebei University of Engineering, Handan 056002, Hebei, PR China.
| | - Bao-Guo Liu
- Affiliated Hospital, College of Medicine, Hebei University of Engineering, Handan 056002, Hebei, PR China
| | - Ting Zhang
- Affiliated Hospital, College of Medicine, Hebei University of Engineering, Handan 056002, Hebei, PR China
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Cullin E3 ligases and their rewiring by viral factors. Biomolecules 2014; 4:897-930. [PMID: 25314029 PMCID: PMC4279162 DOI: 10.3390/biom4040897] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Revised: 08/20/2014] [Accepted: 09/15/2014] [Indexed: 02/06/2023] Open
Abstract
The ability of viruses to subvert host pathways is central in disease pathogenesis. Over the past decade, a critical role for the Ubiquitin Proteasome System (UPS) in counteracting host immune factors during viral infection has emerged. This counteraction is commonly achieved by the expression of viral proteins capable of sequestering host ubiquitin E3 ligases and their regulators. In particular, many viruses hijack members of the Cullin-RING E3 Ligase (CRL) family. Viruses interact in many ways with CRLs in order to impact their ligase activity; one key recurring interaction involves re-directing CRL complexes to degrade host targets that are otherwise not degraded within host cells. Removal of host immune factors by this mechanism creates a more amenable cellular environment for viral propagation. To date, a small number of target host factors have been identified, many of which are degraded via a CRL-proteasome pathway. Substantial effort within the field is ongoing to uncover the identities of further host proteins targeted in this fashion and the underlying mechanisms driving their turnover by the UPS. Elucidation of these targets and mechanisms will provide appealing anti-viral therapeutic opportunities. This review is focused on the many methods used by viruses to perturb host CRLs, focusing on substrate sequestration and viral regulation of E3 activity.
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