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Zhou Y, Zhang Q, Zhao Z, Hu X, You Q, Jiang Z. Targeting kelch-like (KLHL) proteins: achievements, challenges and perspectives. Eur J Med Chem 2024; 269:116270. [PMID: 38490062 DOI: 10.1016/j.ejmech.2024.116270] [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: 01/02/2024] [Revised: 02/07/2024] [Accepted: 02/19/2024] [Indexed: 03/17/2024]
Abstract
Kelch-like proteins (KLHLs) are a large family of BTB-containing proteins. KLHLs function as the substrate adaptor of Cullin 3-RING ligases (CRL3) to recognize substrates. KLHLs play pivotal roles in regulating various physiological and pathological processes by modulating the ubiquitination of their respective substrates. Mounting evidence indicates that mutations or abnormal expression of KLHLs are associated with various human diseases. Targeting KLHLs is a viable strategy for deciphering the KLHLs-related pathways and devising therapies for associated diseases. Here, we comprehensively review the known KLHLs inhibitors to date and the brilliant ideas underlying their development.
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Affiliation(s)
- Yangguo Zhou
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Qiong Zhang
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Ziquan Zhao
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Xiuqi Hu
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Qidong You
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| | - Zhengyu Jiang
- Jiang Su Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
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Shim T, Kim JY, Kim W, Lee YI, Cho B, Moon C. Cullin-RING E3 ubiquitin ligase 4 regulates neurite morphogenesis during neurodevelopment. iScience 2024; 27:108933. [PMID: 38318354 PMCID: PMC10839267 DOI: 10.1016/j.isci.2024.108933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/30/2023] [Accepted: 01/12/2024] [Indexed: 02/07/2024] Open
Abstract
Neuritogenesis is crucial for establishing proper neuronal connections during brain development; its failure causes neurodevelopmental defects. Cullin-RING E3 ubiquitin ligase complexes participate in various neurodevelopmental processes by regulating protein stability. We demonstrated the regulatory function of Cullin-RING E3 ubiquitin ligase 4 (CRL4) in neurite morphogenesis during early neurodevelopment. Cul4a and Cul4b, the core scaffold proteins of CRL4, exhibit high expression and activation within the cytosol of developing neurons, regulated by neuronal stimulation through N-methyl D-aspartate (NMDA) receptor signaling. CRL4 also interacts with cytoskeleton-regulating proteins involved in neurite morphogenesis. Notably, genetic depletion and inhibition of cytosolic CRL4 enhance neurite extension and branching in developing neurons. Conversely, Cul4a overexpression suppresses basal and NMDA-enhanced neuritogenesis. Furthermore, CRL4 and its substrate adaptor regulate the polyubiquitination and proteasomal degradation of doublecortin protein. Collectively, our findings suggest that CRL4 ensures proper neurite morphogenesis in developing neurons by regulating cytoskeleton-regulating proteins.
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Affiliation(s)
- Tammy Shim
- Department of Brain Sciences, DGIST, Daegu 42988, Republic of Korea
- Convergence Research Advanced Centre for Olfaction, DGIST, Daegu 42988, Republic of Korea
| | - Jae Yeon Kim
- Department of Neurology, University of California, San Francisco, CA 94143, USA
| | - WonCheol Kim
- Department of Brain Sciences, DGIST, Daegu 42988, Republic of Korea
- Convergence Research Advanced Centre for Olfaction, DGIST, Daegu 42988, Republic of Korea
| | - Yun-Il Lee
- Division of Biotechnology, DGIST, Daegu 42988, Republic of Korea
| | - Bongki Cho
- Division of Biotechnology, DGIST, Daegu 42988, Republic of Korea
| | - Cheil Moon
- Department of Brain Sciences, DGIST, Daegu 42988, Republic of Korea
- Convergence Research Advanced Centre for Olfaction, DGIST, Daegu 42988, Republic of Korea
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Zhang Z, Sie B, Chang A, Leng Y, Nardone C, Timms RT, Elledge SJ. Elucidation of E3 ubiquitin ligase specificity through proteome-wide internal degron mapping. Mol Cell 2023; 83:3377-3392.e6. [PMID: 37738965 PMCID: PMC10594193 DOI: 10.1016/j.molcel.2023.08.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 06/07/2023] [Accepted: 08/17/2023] [Indexed: 09/24/2023]
Abstract
The ubiquitin-proteasome system plays a critical role in biology by regulating protein degradation. Despite their importance, precise recognition specificity is known for a few of the 600 E3s. Here, we establish a two-pronged strategy for identifying and mapping critical residues of internal degrons on a proteome-scale in HEK-293T cells. We employ global protein stability profiling combined with machine learning to identify 15,800 peptides likely to contain sequence-dependent degrons. We combine this with scanning mutagenesis to define critical residues for over 5,000 predicted degrons. Focusing on Cullin-RING ligase degrons, we generated mutational fingerprints for 219 degrons and developed DegronID, a computational algorithm enabling the clustering of degron peptides with similar motifs. CRISPR analysis enabled the discovery of E3-degron pairs, of which we uncovered 16 pairs that revealed extensive degron variability and structural determinants. We provide the visualization of these data on the public DegronID data browser as a resource for future exploration.
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Affiliation(s)
- Zhiqian Zhang
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Brandon Sie
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Aiquan Chang
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Yumei Leng
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Christopher Nardone
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Richard T Timms
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Stephen J Elledge
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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Ye G, Wang J, Yang W, Li J, Ye M, Jin X. The roles of KLHL family members in human cancers. Am J Cancer Res 2022; 12:5105-5139. [PMID: 36504893 PMCID: PMC9729911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/08/2022] [Indexed: 12/15/2022] Open
Abstract
The Kelch-like (KLHL) family members consist of three domains: bric-a-brac, tramtrack, broad complex/poxvirus and zinc finger domain, BACK domain and Kelch domain, which combine and interact with Cullin3 to form an E3 ubiquitin ligase. Research has indicated that KLHL family members ubiquitinate target substrates to regulate physiological and pathological processes, including tumorigenesis and progression. KLHL19, a member of the KLHL family, is associated with tumorigenesis and drug resistance. However, the regulation and cross talks of other KLHL family members, which also play roles in cancer, are still unclear. Our review mainly explores studies concerning the roles of other KLHL family members in tumor-related regulation to provide novel insights into KLHL family members.
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Affiliation(s)
- Ganghui Ye
- The Affiliated Hospital of Medical School, Ningbo UniversityNingbo 315020, Zhejiang, P. R. China,Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo UniversityNingbo 315211, Zhejiang, P. R. China
| | - Jie Wang
- The Affiliated Hospital of Medical School, Ningbo UniversityNingbo 315020, Zhejiang, P. R. China,Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo UniversityNingbo 315211, Zhejiang, P. R. China
| | - Weili Yang
- Yinzhou People’s Hospital of Medical School, Ningbo UniversityNingbo 315040, Zhejiang, P. R. China
| | - Jinyun Li
- The Affiliated Hospital of Medical School, Ningbo UniversityNingbo 315020, Zhejiang, P. R. China,Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo UniversityNingbo 315211, Zhejiang, P. R. China
| | - Meng Ye
- The Affiliated Hospital of Medical School, Ningbo UniversityNingbo 315020, Zhejiang, P. R. China,Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo UniversityNingbo 315211, Zhejiang, P. R. China
| | - Xiaofeng Jin
- The Affiliated Hospital of Medical School, Ningbo UniversityNingbo 315020, Zhejiang, P. R. China,Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo UniversityNingbo 315211, Zhejiang, P. R. China
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Chen J, Liao Y, Li R, Luo M, Wu G, Tan R, Xiao Z. Immunotherapeutic Significance of a Prognostic Alternative Splicing Signature in Bladder Cancer. Technol Cancer Res Treat 2022; 21:15330338221090093. [PMID: 35509211 PMCID: PMC9083046 DOI: 10.1177/15330338221090093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Objectives: Bladder cancer is the fourth most common malignancy in men in the United States. Aberrant alternative splicing (AS) events are involved in the carcinogenesis, but the association between AS and bladder cancer remains unclear. This study aimed to construct an AS-based prognostic signature and elucidate the role of the tumor immune microenvironment (TIME) and the response to immunotherapy and chemotherapy in bladder cancer. Methods: Univariate Cox regression analysis was performed to detect prognosis-related AS events. The least absolute shrinkage and selection operator (LASSO) and multivariate Cox analyses were employed to build prognostic signatures. Kaplan-Meier survival analysis, multivariate Cox regression analysis, and receiver operating characteristic (ROC) curves were conducted to validate the prognostic signatures. Then, the Estimation of Stromal and Immune cells in MAlignant Tumor tissues using Expression data (ESTIMATE) and tumor immune estimation resource (TIMER) databases were searched and the single-sample gene set enrichment analysis (ssGSEA) algorithm and CIBERSORT method were performed to uncover the context of TIME in bladder cancer. The Tumor Immune Dysfunction and Exclusion (TIDE) web tool and pRRophetic algorithm were used to predict the response to immunotherapy and chemotherapy. Finally, we constructed a correlation network between splicing factors (SFs) and survival-related AS events. Results: A total of 4684 AS events were significantly associated with overall survival in patients with bladder cancer. Eight prognostic signatures of bladder cancer were established, and a clinical survival prediction model was built. In addition, the consolidated prognostic signature was closely related to immune infiltration and the response to immunotherapy and chemotherapy. Furthermore, the correlation identified EIF3A, DDX21, SDE2, TNPO1, and RNF40 as hub SFs, and function analysis found ubiquitin-mediated proteolysis is correlated most significantly with survival-associated AS events. Conclusion: Our findings highlight the prognostic value of AS for patients with bladder cancer and reveal pivotal players of AS events in the context of TIME and the response to immunotherapy and chemotherapy, which may be important for patient management and treatment.
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Affiliation(s)
- Jiang Chen
- The Second Affiliated Hospital, Hengyang Medical School, 34706University of South China, Hengyang, China
| | - Yangjie Liao
- 504354The Third Xiangya Hospital of Central South University, Changsha, Hunan, PR China
| | - Rui Li
- 22494Cedars-Sinai Samuel Oschin Comprehensive Cancer Institute, Los Angeles, CA, USA.,Sichuan Cancer Center, School of Medicine, Sichuan Cancer Hospital and Institute, University of Electronic Science and Technology of China, Chengdu, China
| | - Mingjiang Luo
- The Second Affiliated Hospital, Hengyang Medical School, 34706University of South China, Hengyang, China
| | - Guanlin Wu
- School of Basic Medical Sciences, 58305Fudan University, Shanghai, China
| | - Ruirong Tan
- 22494Cedars-Sinai Samuel Oschin Comprehensive Cancer Institute, Los Angeles, CA, USA.,International Center for Translational Chinese Medicine, Sichuan Academy of Chinese Medicine Sciences, Chengdu, China
| | - Zhihong Xiao
- The Second Affiliated Hospital, Hengyang Medical School, 34706University of South China, Hengyang, China
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