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Kim S, Yeo H, Lee BI. Structural analysis of EPOP BC-box binding to the elongin BC complex. Biochem Biophys Res Commun 2025; 759:151691. [PMID: 40153999 DOI: 10.1016/j.bbrc.2025.151691] [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: 03/17/2025] [Accepted: 03/23/2025] [Indexed: 04/01/2025]
Abstract
The elongin BC complex (ELOBC) interacts with BC-box-containing proteins and plays a role in various cellular processes, including transcriptional regulation and ubiquitination. Elongin BC and polycomb repressive complex 2-associated protein (EPOP) contains a BC-box motif in its N-terminal region and influences cancer cell proliferation and differentiation. A previous study showed that a BC-box containing an EPOP-derived peptide suppresses cancer cell growth and induces apoptosis by disrupting the interaction between the ELOBC and its partner proteins. Here, we report the crystal structure of the EPOP BC-box peptide bound to the ELOBC and compare it with the structures of other BC-box-containing proteins in complex with the ELOBC. The overall structure of interactions between the BC-box and the ELOC was similar across different complexes, indicating a conserved binding mode. Our structural analysis revealed that the strictly conserved leucine residue (Leu40) within the BC-box of EPOP, which was previously suggested to be critical for interactions between the BC-box and the ELOC, was deeply embedded in the hydrophobic pocket of the ELOC protein. This study provided structural insights into BC-box-mediated protein-protein interactions and may serve as a fundamental resource for developing small molecules that modulate the interactions between ELOBC and BC-box-containing proteins.
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Affiliation(s)
- Soeun Kim
- Research Institute, National Cancer Center, Goyang-si, Gyeonggi-do, 10408, Republic of Korea; Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang-si, Gyeonggi-do, 10408, Republic of Korea
| | - HyunKu Yeo
- Research Institute, National Cancer Center, Goyang-si, Gyeonggi-do, 10408, Republic of Korea.
| | - Byung Il Lee
- Research Institute, National Cancer Center, Goyang-si, Gyeonggi-do, 10408, Republic of Korea; Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang-si, Gyeonggi-do, 10408, Republic of Korea.
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2
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Chatterjee S, Paul N, Das A, Bank S, Bankura B, Yadav RP, Sarkar K, Saha S, Malakar S, Choudhury S, Ghosh S, Das M. Molecular dynamics reveal potential effects of novel VHL variants on VHL-Elongin C binding in ccRCC patients from Eastern India. Sci Rep 2025; 15:13022. [PMID: 40234555 PMCID: PMC12000512 DOI: 10.1038/s41598-025-95875-1] [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: 06/05/2024] [Accepted: 03/24/2025] [Indexed: 04/17/2025] Open
Abstract
Renal cell carcinoma (RCC) is the one of the most fatal and frequent form of urological malignancy worldwide. The von Hippel-Lindau (VHL) tumour suppressor gene is a critical component of the VHL-Cullin2-ElonginB/C (VCB) complex that regulates the ubiquitin-mediated proteasomal degradation of proteins with mutations consistently associated with the development of clear cell renal cell carcinoma (ccRCC). Despite extensive investigations conducted worldwide, there is a notable lack of data concerning VHL mutations in sporadic ccRCC patients from India. Our study aimed to investigate the sporadic VHL mutations within the tumours of 210 ccRCC patients without a familial history of VHL disease. We extracted genomic DNA from tumour and adjacent normal tissues, PCR amplified and sequenced the VHL gene. In silico tools were used assess the damaging potential of missense variants on pVHL structure and stability. Protein-protein docking and protein flexibility molecular docking simulation study were employed to study the interaction between wild-type and mutated VHL models with Elongin C. Sequence analysis revealed seven novel missense mutations in patient tumour tissues p.(Val170Phe), p.(Arg69Cys), p.(Phe76Leu), p.(Glu173Asp), p.(Leu201Val), p.(His208Leu), p.(Arg205Pro). I-Mutant 2.0 indicated these mutations reduced pVHL stability (ΔΔG < -0.5 kcal/mol). Protein Flexibility-Molecular Dynamic (MD) Simulation study indicated that mutations weaken the interaction of VHL with Elongin C, with V170F showing the most significant reduction in binding quality and stability. In conclusion, this study introduces novel genetic data from an understudied population and highlights the impact of VHL mutations on its interaction with Elongin C. These findings contribute to our understanding of the molecular basis of VHL-related pathologies and may guide future therapeutic strategies targeting these interactions.
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Affiliation(s)
- Srilagna Chatterjee
- Department of Zoology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Nirvika Paul
- Department of Zoology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Anwesha Das
- Department of Zoology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Sarbashri Bank
- Department of Zoology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Biswabandhu Bankura
- Multidisciplinary Research Unit, Calcutta Medical College and Hospital, Kolkata, West Bengal, India
| | - Ravi Prakash Yadav
- Department of Zoology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Kunal Sarkar
- Department of Zoology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Soumen Saha
- Department of Urology, Calcutta Medical College and Hospital, Kolkata, West Bengal, India
| | - Subhajit Malakar
- Department of Urology, Institute of Postgraduate Medical Education and Research, Kolkata, West Bengal, India
| | - Sunirmal Choudhury
- Department of Urology, Calcutta Medical College and Hospital, Kolkata, West Bengal, India
| | - Sudakshina Ghosh
- Department of Zoology, Vidyasagar College for Women, 39 Sankar Ghosh Lane, Kolkata, 700006, India
| | - Madhusudan Das
- Department of Zoology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India.
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3
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Lucas SCC, Xu Y, Hewitt S, Collie GW, Fusani L, Kadamur G, Hadfield TE, Su N, Truman C, Demanze S, Hao H, Phillips C. Discovery of a Series of Covalent Ligands That Bind to Cys77 of the Von Hippel-Lindau Tumor Suppressor Protein (VHL). ACS Med Chem Lett 2025; 16:693-699. [PMID: 40236540 PMCID: PMC11995237 DOI: 10.1021/acsmedchemlett.4c00582] [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: 12/04/2024] [Revised: 02/01/2025] [Accepted: 03/13/2025] [Indexed: 04/17/2025] Open
Abstract
Most ligands for the Von Hippel-Lindau tumor suppressor (VHL) bind at the HIF-1α binding site. Ligands that bind to allosteric sites on VHL could be highly valuable for the field of protein degradation, therefore, a covalent hit identification campaign was run targeting Cys77 on VHL. Hit 2 bound selectively to Cys77 on VHL and did not alkylate the reactive Cys89 on Elongin B. It showed time- and concentration-dependent labeling, with a k inact/K I of 0.30 M-1 s-1, and does not affect binding at the HIF-1α site. This hit ligand was optimized to afford compound 15 which showed improved potency and labeling of VHL. An X-ray structure of a close analogue was determined revealing the compound binding in a shallow groove on the surface of VHL. These are the first small molecules that bind covalently to an allosteric site on VHL and provide a suitable starting point for further optimization.
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Affiliation(s)
- Simon C. C. Lucas
- Hit
Discovery, Discovery Sciences, R&D,
AstraZeneca, Cambridge, CB2 0AA, U.K.
| | - Yong Xu
- Assays,
Profiling and Cell Sciences, Discovery Sciences, R&D, AstraZeneca, Cambridge, CB2 0AA, U.K.
| | - Sarah Hewitt
- Assays,
Profiling and Cell Sciences, Discovery Sciences, R&D, AstraZeneca, Cambridge, CB2 0AA, U.K.
| | - Gavin W. Collie
- Protein,
Structure and Biophysics, Discovery Sciences, R&D, AstraZeneca, Cambridge, CB2 0AA, U.K.
| | - Lucia Fusani
- Hit
Discovery, Discovery Sciences, R&D,
AstraZeneca, Cambridge, CB2 0AA, U.K.
| | - Ganesh Kadamur
- Assays,
Profiling and Cell Sciences, Discovery Sciences, R&D, AstraZeneca, Cambridge, CB2 0AA, U.K.
| | - Thomas E. Hadfield
- Hit
Discovery, Discovery Sciences, R&D,
AstraZeneca, Cambridge, CB2 0AA, U.K.
| | - Nancy Su
- Assays,
Profiling and Cell Sciences, Discovery Sciences, R&D, AstraZeneca, Waltham, Massachusetts 02451, United States
| | - Caroline Truman
- Assays,
Profiling and Cell Sciences, Discovery Sciences, R&D, AstraZeneca, Cambridge, CB2 0AA, U.K.
| | - Sylvain Demanze
- Medicinal
Chemistry, Oncology R&D, AstraZeneca, Cambridge, CB2 0AA, U.K.
| | - Haie Hao
- Pharmaron
Beijing Co. Ltd., Beijing, 100176, P. R.
China
| | - Christopher Phillips
- Protein,
Structure and Biophysics, Discovery Sciences, R&D, AstraZeneca, Cambridge, CB2 0AA, U.K.
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4
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Braganca Xavier C, Guardia GDA, Alves JPB, Lopes CDH, Awni BM, Campos EF, Jardim DL, Galante PAF. Identifying predictors of overall survival among patients with TMB-low metastatic cancer treated with immune checkpoint inhibitors. Oncologist 2025; 30:oyaf078. [PMID: 40285678 PMCID: PMC12032576 DOI: 10.1093/oncolo/oyaf078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2024] [Accepted: 03/25/2025] [Indexed: 04/29/2025] Open
Abstract
BACKGROUND Immune checkpoint inhibitors (ICIs) have significantly advanced cancer therapy, yet their efficacy in tumors with low tumor mutational burden (TMB) remains suboptimal. In this study, we aimed to elucidate the impact of somatic mutations on overall survival (OS) in TMB-low patients treated with ICIs and to explore the potential for personalized treatment selection through machine learning. METHODS We conducted a comprehensive analysis of 1172 TMB-low (TMB < 10 mutations per megabase) patients with cancer receiving ICIs, examining the association between specific gene mutations and OS. Additionally, we developed a decision tree model (DTM) to predict OS based on clinical features and tumor mutational profiles. RESULTS Our findings reveal that mutations in DAXX, HLA-A, H3C2, IGF1R, CTNNB1, SMARCA4, KMT2D, and TP53 are significantly associated with poorer survival outcomes in the multivariate analysis. Remarkably, for renal cell carcinoma (RCC) patients, VHL mutations predicted improved OS following ICI even when adjusted for age, sex, and microsatellite instability (MSI) status in both multivariate analysis and the DTM model. CONCLUSIONS These results reinforce the prevailing notion that TMB alone does not predict ICI response, highlighting the critical role of individual gene mutations in TMB-low tumors under ICI therapy. Furthermore, our study demonstrates the promise of machine learning models in optimizing ICI treatment decisions, paving the way for more precise and effective therapeutic strategies in this patient population.
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Affiliation(s)
- Camila Braganca Xavier
- MD Anderson Cancer Center, Houston, TX, 77030, United States
- Hospital Sírio-Libanês, São Paulo, SP, 01308-050, Brazil
| | | | | | | | - Beatriz M Awni
- Hospital Sírio-Libanês, São Paulo, SP, 01308-050, Brazil
| | | | - Denis L Jardim
- Hospital Sírio-Libanês, São Paulo, SP, 01308-050, Brazil
- Oncoclínicas&CO - Medica Scientia Innovation Research (MedSir), São Paulo, SP, 04538-132, Brazil
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5
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Zhuang X, Gao F, Xuan Y, Sun Z, Ye X, Huang X, Jiang R, Wu J, Wang M, Chang Q, Xu G, Liu W. Novel OCT Angiography Features, von Hippel-Lindau Disease Association, and Genetic Characterization of Juxtapapillary Retinal Capillary Hemangiomas. Invest Ophthalmol Vis Sci 2025; 66:34. [PMID: 40232713 PMCID: PMC12007667 DOI: 10.1167/iovs.66.4.34] [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: 10/14/2024] [Accepted: 03/13/2025] [Indexed: 04/16/2025] Open
Abstract
Purpose To present new clinical features of juxtapapillary retinal capillary hemangiomas (JRCHs), assess the risk of von Hippel-Lindau (VHL) disease, and explore the genotype-phenotype correlations in patients with JRCH. Methods Fifty patients with JRCH were included. Multimodal retinal imaging including optical coherence tomography angiography (OCTA), visual acuity, presence of peripheral RCHs, affected lateralities, systemic evaluation for VHL disease, and underlying VHL variants were reviewed. Results Of 59 eyes, 48 had classic JRCHs, whereas 11 had atypical JRCHs (type B, if it broke through the inner limiting membrane: 3 eyes; type A, if not: 8 eyes). Compared with atypical type A, which was indolent, type B might warrant surgical interventions. Better final visual acuity (P < 0.0001), fewer peripheral RCHs (P = 0.02), and lower prevalence of large peripheral RCHs (>1.5 mm) (P = 0.027) were observed in eyes with atypical JRCHs than classic JRCHs. VHL was diagnosed clinically in 72% of patients, and 22 VHL variants were identified, including 5 novel variants. Patients with truncating variants had a higher prevalence of atypical JRCHs than those with single amino acid substitution/deletion variants (P = 0.009). Patients with bilateral VHL-JRCHs were more likely to have large peripheral RCHs (P = 0.02) and less likely to harbor β-domain single amino acid substitution/deletion variants (P = 0.066) than those with unilateral VHL-JRCHs. Conclusions Atypical JRCHs, with distinctive OCTA characteristics and favorable visual outcomes, are less complicated by peripheral RCHs and more relevant to truncating variant genotypes. JRCH monitoring should incorporate OCTA classification and genotype analysis.
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Affiliation(s)
- Xiaonan Zhuang
- Eye Institute and Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
- NHC Key Laboratory of Myopia and Related Eye Diseases, Chinese Academy of Medical Sciences, Shanghai, China
| | - Fengjuan Gao
- Eye Institute and Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
- NHC Key Laboratory of Myopia and Related Eye Diseases, Chinese Academy of Medical Sciences, Shanghai, China
| | - Yi Xuan
- Eye Institute and Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
- NHC Key Laboratory of Myopia and Related Eye Diseases, Chinese Academy of Medical Sciences, Shanghai, China
| | - Zhongcui Sun
- Eye Institute and Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
- NHC Key Laboratory of Myopia and Related Eye Diseases, Chinese Academy of Medical Sciences, Shanghai, China
| | - Xiaofeng Ye
- Eye Institute and Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
- NHC Key Laboratory of Myopia and Related Eye Diseases, Chinese Academy of Medical Sciences, Shanghai, China
| | - Xin Huang
- Eye Institute and Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
- NHC Key Laboratory of Myopia and Related Eye Diseases, Chinese Academy of Medical Sciences, Shanghai, China
| | - Rui Jiang
- Eye Institute and Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
- NHC Key Laboratory of Myopia and Related Eye Diseases, Chinese Academy of Medical Sciences, Shanghai, China
| | - Jihong Wu
- Eye Institute and Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
- NHC Key Laboratory of Myopia and Related Eye Diseases, Chinese Academy of Medical Sciences, Shanghai, China
| | - Min Wang
- Eye Institute and Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
- NHC Key Laboratory of Myopia and Related Eye Diseases, Chinese Academy of Medical Sciences, Shanghai, China
| | - Qing Chang
- Eye Institute and Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
- NHC Key Laboratory of Myopia and Related Eye Diseases, Chinese Academy of Medical Sciences, Shanghai, China
| | - Gezhi Xu
- Eye Institute and Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
- NHC Key Laboratory of Myopia and Related Eye Diseases, Chinese Academy of Medical Sciences, Shanghai, China
| | - Wei Liu
- Eye Institute and Department of Ophthalmology, Eye and ENT Hospital, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
- NHC Key Laboratory of Myopia and Related Eye Diseases, Chinese Academy of Medical Sciences, Shanghai, China
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6
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Li S, Wang X, Huang J, Cao X, Liu Y, Bai S, Zeng T, Chen Q, Li C, Lu C, Yang H. Decoy-PROTAC for specific degradation of "Undruggable" STAT3 transcription factor. Cell Death Dis 2025; 16:197. [PMID: 40118821 PMCID: PMC11928565 DOI: 10.1038/s41419-025-07535-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2024] [Revised: 02/18/2025] [Accepted: 03/12/2025] [Indexed: 03/24/2025]
Abstract
Signal transducer and activator of transcription 3 (STAT3) is widely recognized as an attractive target for cancer therapy due to its significant role in the initiation and progression of tumorigenesis. However, existing STAT3 inhibitors have suffered from drawbacks including poor efficacy, limited specificity, and undesirable off-target effects, due to the challenging nature of identifying active sites or allosteric regulatory pockets on STAT3 amenable to small-molecule inhibition. In response to these obstacles, we utilize the innovative proteolysis targeting chimera (PROTAC) technology to create a highly specific decoy-targeted protein degradation system for STAT3 protein, termed D-PROTAC. This system fuses DNA decoy that targets STAT3 with an E3 ligase ligand, utilizing a click chemistry approach. Experimental results demonstrate that D-PROTAC efficiently mediates the degradation of the STAT3 protein across various cancer cell types, leading to the downregulation of crucial downstream STAT3 targets, inhibiting tumor cell growth, triggering cell cycle arrest and apoptosis, and suppressing tumor immune evasion. Furthermore, D-PROTAC is capable of achieving significant tumor suppression in xenograft models. Overall, our research validates that D-PROTAC can successfully target and eliminate the "undruggable" STAT3, showcasing specificity and potent antitumor effects. This strategy will suggest a promising avenue for the development of targeted therapies against the critical functions of STAT3 in human cancers and potentially other diseases.
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Affiliation(s)
- Shiqing Li
- New Cornerstone Science Laboratory, MOE Key Laboratory for Analytical Science of Food Safety and Biology, College of Chemistry, Fuzhou University, Fuzhou, People's Republic of China
| | - Xin Wang
- New Cornerstone Science Laboratory, MOE Key Laboratory for Analytical Science of Food Safety and Biology, College of Chemistry, Fuzhou University, Fuzhou, People's Republic of China
| | - Jiabao Huang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, People's Republic of China
| | - Xiuping Cao
- New Cornerstone Science Laboratory, MOE Key Laboratory for Analytical Science of Food Safety and Biology, College of Chemistry, Fuzhou University, Fuzhou, People's Republic of China
| | - Yana Liu
- New Cornerstone Science Laboratory, MOE Key Laboratory for Analytical Science of Food Safety and Biology, College of Chemistry, Fuzhou University, Fuzhou, People's Republic of China
| | - Shiyan Bai
- New Cornerstone Science Laboratory, MOE Key Laboratory for Analytical Science of Food Safety and Biology, College of Chemistry, Fuzhou University, Fuzhou, People's Republic of China
| | - Tao Zeng
- New Cornerstone Science Laboratory, MOE Key Laboratory for Analytical Science of Food Safety and Biology, College of Chemistry, Fuzhou University, Fuzhou, People's Republic of China
| | - Qi Chen
- Interdisciplinary Institute for Medical Engineering, Fuzhou University, Fuzhou, People's Republic of China
| | - Chunsen Li
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, People's Republic of China
| | - Chunhua Lu
- New Cornerstone Science Laboratory, MOE Key Laboratory for Analytical Science of Food Safety and Biology, College of Chemistry, Fuzhou University, Fuzhou, People's Republic of China.
| | - Huanghao Yang
- New Cornerstone Science Laboratory, MOE Key Laboratory for Analytical Science of Food Safety and Biology, College of Chemistry, Fuzhou University, Fuzhou, People's Republic of China.
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7
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Li T, Cui Y, Zhou Y, Zhou T, Chen S, Lu L, Zhang Y, Tong A. Pheochromocytoma in von Hippel-Lindau Disease: Clinical Features and Comparison With Sporadic Pheochromocytoma. Clin Endocrinol (Oxf) 2025; 102:355-361. [PMID: 39722564 DOI: 10.1111/cen.15190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2024] [Revised: 12/08/2024] [Accepted: 12/19/2024] [Indexed: 12/28/2024]
Abstract
OBJECTIVES Pheochromocytomas and paragangliomas (PPGLs) are manifestations of von Hippel-Lindau (VHL) disease. This study aims to describe the clinical features of PPGLs in VHL patients and the distinctions between VHL disease-related PPGLs and sporadic PPGLs. DESIGN, PATIENTS AND MEASUREMENTS The study included all patients with VHL disease and PPGLs treated in a single centre from 2007 to 2023. A total of 145 patients were included in the sporadic PPGLs group. Their clinical data were retrospectively reviewed. Genetic testing for VHL mutation was conducted using Sanger sequencing. Statistical analysis was performed using SPSS 22. RESULTS Fifty-nine (65.6%) of the 90 VHL disease patients had PPGLs (male: female, 38:21; age at diagnosis, 25.0 ± 13.3 years). 42 (71.2%) patients had lesions only in the adrenal gland, and 16 (27.1%) patients had lesions both in and out of the adrenal gland. 45 (76.3%) patients had multiple lesions. Eighteen (45.0%) patients developed recurrence after surgery. Fifty-eight patients with PPGLs underwent genetic testing and had pathogenic or likely pathogenic mutations in the VHL gene. Fifty-three (91.4%) patients had missense mutations, 34 of which were located in the Elongin-C binding domain. The hotspot mutation sites were codon 161 and codon 167. Five novel mutations were identified. The clinical characteristics showed no significant differences between groups with different mutation sites. Compared to sporadic PPGLs, VHL disease-related PPGLs were more frequently located in the adrenal gland (71.2% vs. 49.0%, p < 0.001), had a higher prevalence of multiple lesions (76.3% vs. 11.0%, p < 0.001), and secreted noradrenaline (80.4% vs. 43.2%, p < 0.001). They were also more likely to relapse after surgery (45.0% vs. 15.3%, p < 0.001). CONCLUSION VHL disease-related PPGLs were often multifocal and noradrenergic, and more likely to relapse compared with sporadic PPGLs. No relationships were identified between the mutation sites and the clinical characteristics of PPGLs.
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Affiliation(s)
- Tianyi Li
- Department of Endocrinology, Key Laboratory of Endocrinology, National Health Commission of the People's Republic of China, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yunying Cui
- Department of Endocrinology, Key Laboratory of Endocrinology, National Health Commission of the People's Republic of China, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yue Zhou
- Department of Endocrinology, Key Laboratory of Endocrinology, National Health Commission of the People's Republic of China, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ting Zhou
- Department of Endocrinology, Key Laboratory of Endocrinology, National Health Commission of the People's Republic of China, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shi Chen
- Department of Endocrinology, Key Laboratory of Endocrinology, National Health Commission of the People's Republic of China, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lin Lu
- Department of Endocrinology, Key Laboratory of Endocrinology, National Health Commission of the People's Republic of China, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yushi Zhang
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Anli Tong
- Department of Endocrinology, Key Laboratory of Endocrinology, National Health Commission of the People's Republic of China, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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8
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Gupta S, Cheville JC. Renal Neoplasia: Rare Subtypes and Uncommon Clinical Presentations. Surg Pathol Clin 2025; 18:157-174. [PMID: 39890302 DOI: 10.1016/j.path.2024.09.001] [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] [Indexed: 02/03/2025]
Abstract
Herein, the authors have discussed a series of uncommon familial kidney cancer syndromes (including hyperparathyroidism-jaw tumor syndrome and PTEN hamartoma tumor syndrome), sporadically occurring tumors (BRAF and MTOR pathway-mutated tumors, and juxtaglomerular cell tumors), and uncommon patterns of well-established subtypes of kidney cancer (mucinous tubular spindle cell carcinoma, fumarate hydratase-deficient, and TFE3-rearranged renal cell carcinoma). The rarity of these tumors often leads to diagnostic odysseys for pathologists and patients. Appropriate classification of these rare tumors has implications for screening at-risk family members in the case of hereditary tumor predisposition syndromes, accurate prognostication, and appropriate patient selection for clinical trials.
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Affiliation(s)
- Sounak Gupta
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
| | - John C Cheville
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
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9
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Kim Y, Baek SJ, Yoon EK, Choi M, Kim JH, Kim K, Park CH, Lee BI. Identification of novel 7-hydroxycoumarin derivatives as ELOC binders with potential to modulate CRL2 complex formation. Sci Rep 2025; 15:3622. [PMID: 39881207 PMCID: PMC11779939 DOI: 10.1038/s41598-025-88166-2] [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: 10/10/2024] [Accepted: 01/24/2025] [Indexed: 01/31/2025] Open
Abstract
The VHL-containing cullin-RING E3 ubiquitin ligase (CRL2VHL) complex is an E3 ligase commonly used in targeted protein degradation (TPD). Hydroxyproline-based ligands that mimic VHL substrates have been developed as anchor molecules for proteolysis-targeting chimeras (PROTACs) in TPD. To expand the chemical space for VHL ligands, we conducted fragment screening using VHL-ELOB-ELOC (VBC) proteins. We found that certain 7-hydroxycoumarin derivatives (7HCs), rather than VHL, would bind to the ELOC component of the VBC complex. The 7HC binding site overlapped with the CUL2 binding interface on ELOC but did not overlap with the CUL5 binding interface, suggesting that 7HCs may influence the formation of CRL2 but not CRL5. Although the binding affinities of these 7HCs to the VBC complex were relatively low, they represent novel and promising foundational agents for the development of chemical probes or inhibitors that target ELOC-containing CRLs.
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Affiliation(s)
- Yonghyeok Kim
- Research Institute, National Cancer Center, Goyang-si, 10408, Gyeonggi, Republic of Korea
| | - Seon Jeong Baek
- Research Institute, National Cancer Center, Goyang-si, 10408, Gyeonggi, Republic of Korea
- Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang-si, 10408, Gyeonggi, Republic of Korea
| | - Eun-Kyung Yoon
- Research Institute, National Cancer Center, Goyang-si, 10408, Gyeonggi, Republic of Korea
| | - Minhee Choi
- Research Institute, National Cancer Center, Goyang-si, 10408, Gyeonggi, Republic of Korea
| | - Jung-Hoon Kim
- Research Institute, National Cancer Center, Goyang-si, 10408, Gyeonggi, Republic of Korea
- Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang-si, 10408, Gyeonggi, Republic of Korea
| | - Kyungtae Kim
- Research Institute, National Cancer Center, Goyang-si, 10408, Gyeonggi, Republic of Korea
| | - Chi Hoon Park
- Department of Medicinal Chemistry and Pharmacology, University of Science and Technology, Daejeon, 34113, Republic of Korea
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon, 34114, Republic of Korea
| | - Byung Il Lee
- Research Institute, National Cancer Center, Goyang-si, 10408, Gyeonggi, Republic of Korea.
- Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang-si, 10408, Gyeonggi, Republic of Korea.
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10
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Li H, Wu M, Chao H, Yin Y, Xia Y, Cheng X, Chen K, Yan S, Wang X, Xiong Y, He J, Fan S, Ding Y, Zhang L, Jia H, Zhang C, Li M. A rare dominant allele DYSOC1 determines seed coat color and improves seed oil content in Brassica napus. SCIENCE ADVANCES 2025; 11:eads7620. [PMID: 39752491 PMCID: PMC11698099 DOI: 10.1126/sciadv.ads7620] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2024] [Accepted: 11/27/2024] [Indexed: 01/06/2025]
Abstract
Yellow seed coat color (SCC) is a valuable trait in Brassica napus, which is significantly correlated to high seed oil content (SOC) and low seed lignocellulose content (SLC). However, no dominant yellow SCC genes were identified in B. napus. In this study, a dominant yellow SCC B. napus N53-2 was verified, and then 58,981 eQTLs and 25 trans-eQTL hotspots were identified in a double haploid population derived from N53-2 and black SCC material Ken-C8. A rare dominant allele DYSOC1 (dominant gene of yellow seed coat color and improved seed oil content 1) was subsequently cloned in a trans-eQTL hotspot that colocated with SCC, SOC, and SLC QTL hotspot on ChrA09 through QTL fine mapping and multi-omics analysis. Transgenic experiments revealed that the expression of DYSOC1 produced yellow SCC seeds with significantly increased SOC and decreased SLC. Our result provides a rare dominant yellow SCC allele in B. napus, which has excellent potential for yellow SCC and high SOC rapeseed breeding.
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Affiliation(s)
- Huaixin Li
- College of Life Science and Technology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Mingli Wu
- College of Life Science and Technology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Hongbo Chao
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yongtai Yin
- College of Life Science and Technology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan 430074, China
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
| | - Yutian Xia
- College of Life Science and Technology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xin Cheng
- College of Life Science and Technology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Kang Chen
- College of Life Science and Technology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Shuxiang Yan
- College of Life Science and Technology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xiaodong Wang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing 210014, China
| | - Yiyi Xiong
- College of Life Science and Technology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Jianjie He
- College of Life Science and Technology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Shipeng Fan
- College of Life Science and Technology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yiran Ding
- College of Life Science and Technology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Libin Zhang
- College of Life Science and Technology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan 430074, China
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, Wuhan 430074, China
| | - Haibo Jia
- College of Life Science and Technology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Chunyu Zhang
- National Key Lab of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Maoteng Li
- College of Life Science and Technology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan 430074, China
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11
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Nishizawa H, Funasaki S, Ma W, Kubota Y, Watanabe K, Arima Y, Kuroda S, Ito T, Furuya M, Motoshima T, Nishiyama A, Mehanna S, Satou Y, Hasumi H, Jikuya R, Makiyama K, Tamura T, Oike Y, Tanaka Y, Suda T, Schmidt LS, Linehan WM, Baba M, Kamba T. HIF1α Plays a Crucial Role in the Development of TFE3-Rearranged Renal Cell Carcinoma by Orchestrating a Metabolic Shift Toward Fatty Acid Synthesis. Genes Cells 2025; 30:e13195. [PMID: 39807625 PMCID: PMC11729263 DOI: 10.1111/gtc.13195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2024] [Revised: 01/05/2025] [Accepted: 01/06/2025] [Indexed: 01/30/2025]
Abstract
Tumor development often requires cellular adaptation to a unique, high metabolic state; however, the molecular mechanisms that drive such metabolic changes in TFE3-rearranged renal cell carcinoma (TFE3-RCC) remain poorly understood. TFE3-RCC, a rare subtype of RCC, is defined by the formation of chimeric proteins involving the transcription factor TFE3. In this study, we analyzed cell lines and genetically engineered mice, demonstrating that the expression of the chimeric protein PRCC-TFE3 induced a hypoxia-related signature by transcriptionally upregulating HIF1α and HIF2α. The upregulation of HIF1α by PRCC-TFE3 led to increased cellular ATP production by enhancing glycolysis, which also supplied substrates for the TCA cycle while maintaining mitochondrial oxidative phosphorylation. We crossed TFE3-RCC mouse models with Hif1α and/or Hif2α knockout mice and found that Hif1α, rather than Hif2α, is essential for tumor development in vivo. RNA-seq and metabolomic analyses of the kidney tissues from these mice revealed that ketone body production is inversely correlated with tumor development, whereas de novo lipid synthesis is upregulated through the HIF1α/SREBP1-dependent mechanism in TFE3-RCC. Our data suggest that the coordinated metabolic shift via the PRCC-TFE3/HIF1α/SREBP1 axis is a key mechanism by which PRCC-TFE3 enhances cancer cell metabolism, promoting tumor development in TFE3-RCC.
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Grants
- JP21K19721 Japan Society for the Promotion of Science
- HHSN261201500003C NCI NIH HHS
- JP24K09315 Japan Society for the Promotion of Science
- JP 24K02578 Japan Society for the Promotion of Science
- JPMXP0618217493 Ministry of Education, Culture, Sports, Science and Technology
- JP20K09560 Japan Society for the Promotion of Science
- JPMXP0622717006 Ministry of Education, Culture, Sports, Science and Technology
- JP21K09374 Japan Society for the Promotion of Science
- JP23K24474 Japan Society for the Promotion of Science
- JP21K06000 Japan Society for the Promotion of Science
- HHSN261201500003I NCI NIH HHS
- JP23K27589 Japan Society for the Promotion of Science
- JPMXP0723833149 Ministry of Education, Culture, Sports, Science and Technology
- Japan Society for the Promotion of Science
- Ministry of Education, Culture, Sports, Science and Technology
- National Cancer Institute
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Affiliation(s)
- Hidekazu Nishizawa
- Department of Urology, Graduate School of Medical SciencesKumamoto UniversityKumamotoJapan
| | - Shintaro Funasaki
- Divison of Molecular and Vascular Biology, IRDAKumamoto UniversityKumamotoJapan
| | - Wenjuan Ma
- Cambridge Stem Cell Institute, University of CambridgeCambridgeUK
| | - Yoshiaki Kubota
- Department of AnatomyInstitute for Advanced Medical Research and Keio University School of MedicineTokyoJapan
| | | | - Yuichiro Arima
- Developmental Cardiology Laboratory, International Research Center for Medical Science (IRCMS)Kumamoto UniversityKumamotoJapan
| | - Shoichiro Kuroda
- Department of Urology, Graduate School of Medical SciencesKumamoto UniversityKumamotoJapan
| | - Takaaki Ito
- Department of Medical TechnologyKumamoto Health Science University Faculty of Health SciencesKumamotoJapan
| | - Mitsuko Furuya
- Department of Surgical PathologyHokkaido University HospitalSapporoJapan
| | - Takanobu Motoshima
- Department of Urology, Graduate School of Medical SciencesKumamoto UniversityKumamotoJapan
| | - Akira Nishiyama
- Department of ImmunologyYokohama City University Graduate School of MedicineKanagawaJapan
| | - Sally Mehanna
- Biotechnology Department, Faculty of Nanotechnology for Postgraduate Studies, Cairo UniversityAd DoqiEgypt
| | - Yorifumi Satou
- Division of Genomics and Transcriptomics, Joint Research Center for Human Retrovirus InfectionKumamoto UniversityKumamotoJapan
| | - Hisashi Hasumi
- Department of UrologyYokohama City University Graduate School of MedicineKanagawaJapan
| | - Ryosuke Jikuya
- Department of UrologyYokohama City University Graduate School of MedicineKanagawaJapan
| | - Kazuhide Makiyama
- Department of UrologyYokohama City University Graduate School of MedicineKanagawaJapan
| | - Tomohiko Tamura
- Department of ImmunologyYokohama City University Graduate School of MedicineKanagawaJapan
- Advanced Medical Research CenterYokohama City UniversityKanagawaJapan
| | - Yuichi Oike
- Department of Molecular Genetics, Graduate School of Medical SciencesKumamoto UniversityKumamotoJapan
| | - Yasuhito Tanaka
- Department of Gastroenterology and Hepatology, Graduate School of Medical SciencesKumamoto UniversityKumamotoJapan
| | - Toshio Suda
- Laboratory of Stem Cell Regulation, International Research Center for Medical Science (IRCMS)Kumamoto UniversityKumamotoJapan
| | - Laura S. Schmidt
- Urologic Oncology BranchNational Cancer Institute, National Institutes of HealthBethesdaMarylandUSA
- Basic Science Program, Frederick National Laboratory for Cancer ResearchNational Cancer InstituteFrederickMarylandUSA
| | - W. Marston Linehan
- Urologic Oncology BranchNational Cancer Institute, National Institutes of HealthBethesdaMarylandUSA
| | - Masaya Baba
- Department of Urology, Graduate School of Medical SciencesKumamoto UniversityKumamotoJapan
| | - Tomomi Kamba
- Department of Urology, Graduate School of Medical SciencesKumamoto UniversityKumamotoJapan
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12
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You H, Zhang H, Jin X, Yan Z. Dysregulation of ubiquitination modification in renal cell carcinoma. Front Genet 2024; 15:1453191. [PMID: 39748950 PMCID: PMC11693700 DOI: 10.3389/fgene.2024.1453191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Accepted: 11/26/2024] [Indexed: 01/04/2025] Open
Abstract
Renal cell carcinoma (RCC) is a malignant tumor of the renal tubular epithelial cells with a relatively high incidence rate worldwide. A large number of studies have indicated that dysregulation of the ubiquitination, including ubiquitination and dysregulation, is associated with the occurrence and development of RCC. This review focuses on several abnormal signaling pathways caused by E3 ligases and deubiquitinases. Additionally, we discuss research progress in RCC treatment by targeting key enzymes related to ubiquitination modifications.
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Affiliation(s)
| | | | - Xiaofeng Jin
- Department of Urology, The First Affiliated Hospital of Ningbo University, Ningbo University, Ningbo, Zhejiang, China
| | - Zejun Yan
- Department of Urology, The First Affiliated Hospital of Ningbo University, Ningbo University, Ningbo, Zhejiang, China
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13
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Greco F, Panunzio A, Cerroni L, Cea L, Bernetti C, Tafuri A, Beomonte Zobel B, Mallio CA. CT Characterization of Lipid Metabolism in Clear Cell Renal Cell Carcinoma: Relationship Between Liver Hounsfield Unit Values and Adipose Differentiation-Related Protein Gene Expression. Int J Mol Sci 2024; 25:12587. [PMID: 39684299 DOI: 10.3390/ijms252312587] [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: 11/01/2024] [Revised: 11/16/2024] [Accepted: 11/21/2024] [Indexed: 12/18/2024] Open
Abstract
Radiogenomics is an emerging field that links imaging features with molecular characteristics of diseases. In clear cell renal cell carcinoma (ccRCC), metabolic reprogramming leads to lipid accumulation, influenced by the adipose differentiation-related protein (ADFP). This study aimed to investigate whether hepatic and tumoral Hounsfield Unit (HU) values could serve as noninvasive radiogenomic biomarkers for ADFP expression in ccRCC. We analyzed CT images of 185 ccRCC patients, comparing lipid-associated HU values in the liver and tumor across ADFP expression statuses. Patients with low-grade ccRCC expressing ADFP showed significantly lower minimum HU values in both liver and tumor tissue, indicating greater lipid accumulation. Additionally, ADFP expression correlated negatively with abdominal adipose tissue compartments and positively with minimum tumoral HU values, linking systemic lipid metabolism to tumor biology. These findings suggest that hepatic and tumoral HU measurements may serve as noninvasive markers of lipid accumulation related to ADFP, providing insight into metabolic alterations in ccRCC. While promising, these results require validation in larger, controlled studies due to sample size and variability limitations. This approach could enhance the radiogenomic assessment of ccRCC, supporting noninvasive insights into tumor metabolism and progression.
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Affiliation(s)
- Federico Greco
- Department of Radiology, Cittadella della Salute, Azienda Sanitaria Locale di Lecce, Piazza Filippo Bottazzi, 2, 73100 Lecce, Italy
- Research Unit of Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Roma, Italy
| | - Andrea Panunzio
- Department of Urology, "Vito Fazzi" Hospital, Piazza Filippo Muratore, 1, 73100 Lecce, Italy
| | - Laura Cerroni
- Research Unit of Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Roma, Italy
- Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Roma, Italy
| | - Laura Cea
- Research Unit of Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Roma, Italy
- Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Roma, Italy
| | - Caterina Bernetti
- Research Unit of Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Roma, Italy
- Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Roma, Italy
| | - Alessandro Tafuri
- Department of Urology, "Vito Fazzi" Hospital, Piazza Filippo Muratore, 1, 73100 Lecce, Italy
| | - Bruno Beomonte Zobel
- Research Unit of Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Roma, Italy
- Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Roma, Italy
| | - Carlo Augusto Mallio
- Research Unit of Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Roma, Italy
- Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Roma, Italy
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14
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Qiu Y, Wiewiora RP, Izaguirre JA, Xu H, Sherman W, Tang W, Huang X. Non-Markovian Dynamic Models Identify Non-Canonical KRAS-VHL Encounter Complex Conformations for Novel PROTAC Design. JACS AU 2024; 4:3857-3868. [PMID: 39483225 PMCID: PMC11522902 DOI: 10.1021/jacsau.4c00503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 08/26/2024] [Accepted: 09/16/2024] [Indexed: 11/03/2024]
Abstract
Targeted protein degradation (TPD) is emerging as a promising therapeutic approach for cancer and other diseases, with an increasing number of programs demonstrating its efficacy in human clinical trials. One notable method for TPD is Proteolysis Targeting Chimeras (PROTACs) that selectively degrade a protein of interest (POI) through E3-ligase induced ubiquitination followed by proteasomal degradation. PROTACs utilize a warhead-linker-ligand architecture to bring the POI (bound to the warhead) and the E3 ligase (bound to the ligand) into proximity. The resulting non-native protein-protein interactions (PPIs) formed between the POI and E3 ligase lead to the formation of a stable ternary complex, enhancing cooperativity for TPD. A significant challenge in PROTAC design is the screening of the linkers to induce favorable non-native PPIs between POI and E3 ligase. Here, we present a physics-based computational protocol to predict noncanonical and metastable PPI interfaces between an E3 ligase and a given POI, aiding in the design of linkers to stabilize the ternary complex and enhance degradation. Specifically, we build the non-Markovian dynamic model using the Integrative Generalized Master equation (IGME) method from ∼1.5 ms all-atom molecular dynamics simulations of linker-less encounter complex, to systematically explore the inherent PPIs between the oncogene homologue protein and the von Hippel-Lindau E3 ligase. Our protocol revealed six metastable states each containing a different PPI interface. We selected three of these metastable states containing promising PPIs for linker design. Our selection criterion included thermodynamic and kinetic stabilities of PPIs and the accessibility between the solvent-exposed sites on the warheads and E3 ligand. One selected PPIs closely matches a recent cocrystal PPI interface structure induced by an experimentally designed PROTAC with potent degradation efficacy. We anticipate that our protocol has significant potential for widespread application in predicting metastable POI-ligase interfaces that can enable rational design of PROTACs.
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Affiliation(s)
- Yunrui Qiu
- Department
of Chemistry, Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Data
Science Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | | | | | - Huafeng Xu
- Atommap
Corporation, NY, New York 10013, United
States
| | - Woody Sherman
- Psivant
Therapeutics, Boston, Massachusetts 02210, United States
| | - Weiping Tang
- Lachman
Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Xuhui Huang
- Department
of Chemistry, Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Data
Science Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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15
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Xu F, Li J, Ai M, Zhang T, Ming Y, Li C, Pu W, Yang Y, Li Z, Qi Y, Xu X, Sun Q, Yuan Z, Xia Y, Peng Y. Penfluridol inhibits melanoma growth and metastasis through enhancing von Hippel‒Lindau tumor suppressor-mediated cancerous inhibitor of protein phosphatase 2A (CIP2A) degradation. MedComm (Beijing) 2024; 5:e758. [PMID: 39399646 PMCID: PMC11470999 DOI: 10.1002/mco2.758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2024] [Revised: 08/25/2024] [Accepted: 08/28/2024] [Indexed: 10/15/2024] Open
Abstract
Melanoma's high metastatic potential, especially to the brain, poses significant challenges to patient survival. The blood‒brain barrier (BBB) is a major obstacle to the effective treatment of melanoma brain metastases. We screened antipsychotic drugs capable of crossing the BBB and identified penfluridol (PF) as the most active candidate. PF reduced melanoma cell viability and induced apoptosis. In animal models, PF effectively inhibited melanoma growth and metastasis to the lung and brain. Using immunoprecipitation combined with high-resolution mass spectrometry, and other techniques such as drug affinity responsive target stability, we identified CIP2A as a direct binding protein of PF. CIP2A is highly expressed in melanoma and its metastases, and is linked to poor prognosis. PF can restore Protein Phosphatase 2A activity by promoting CIP2A degradation, thereby inhibiting several key oncogenic pathways, including AKT and c-Myc. Additionally, von Hippel‒Lindau (VHL) is the endogenous E3 ligase for CIP2A, and PF enhances the interaction between VHL and CIP2A, promoting the ubiquitin‒proteasome degradation of CIP2A, thereby inhibiting melanoma growth and metastasis. Overall, this study not only suggests PF's potential in treating melanoma and its brain metastases but also highlights CIP2A degradation as a therapeutic strategy for melanoma.
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Affiliation(s)
- Fuyan Xu
- Laboratory of Molecular OncologyFrontiers Science Center for Disease‐Related Molecular NetworkState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Jiao Li
- Laboratory of Molecular OncologyFrontiers Science Center for Disease‐Related Molecular NetworkState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Min Ai
- Laboratory of Molecular OncologyFrontiers Science Center for Disease‐Related Molecular NetworkState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Tingting Zhang
- Laboratory of Molecular OncologyFrontiers Science Center for Disease‐Related Molecular NetworkState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Yue Ming
- Laboratory of Molecular OncologyFrontiers Science Center for Disease‐Related Molecular NetworkState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Cong Li
- Department of BiotherapyCancer Center and State Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Wenchen Pu
- Laboratory of Molecular OncologyFrontiers Science Center for Disease‐Related Molecular NetworkState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Yang Yang
- Laboratory of Molecular OncologyFrontiers Science Center for Disease‐Related Molecular NetworkState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Zhang Li
- Laboratory of Molecular OncologyFrontiers Science Center for Disease‐Related Molecular NetworkState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Yucheng Qi
- Laboratory of Molecular OncologyFrontiers Science Center for Disease‐Related Molecular NetworkState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Xiaomin Xu
- Laboratory of Molecular OncologyFrontiers Science Center for Disease‐Related Molecular NetworkState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Qingxiang Sun
- Department of BiotherapyCancer Center and State Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Zhu Yuan
- Department of BiotherapyCancer Center and State Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Yong Xia
- Rehabilitation Medicine CenterState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Yong Peng
- Laboratory of Molecular OncologyFrontiers Science Center for Disease‐Related Molecular NetworkState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
- Frontier Medical CenterTianfu Jincheng LaboratoryChengduChina
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16
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Suzuki Y, Iemura R, Sutani A, Mizuno Y, Adachi E, Ushiama M, Yoshida T, Hirata M, Hoshino A, Yamomoto K, Akashi T, Nakano Y, Isoda T, Takasawa K, Kato M, Takagi M, Okamoto K, Morio T, Kashimada K. Familial and early recurrent pheochromocytoma in a child with a novel in-frame duplication variant of VHL. Clin Pediatr Endocrinol 2024; 33:229-237. [PMID: 39359666 PMCID: PMC11442702 DOI: 10.1297/cpe.2024-0020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 07/16/2024] [Indexed: 10/04/2024] Open
Abstract
Pheochromocytomas and paragangliomas (PPGLs) are rare neuroendocrine tumors often linked to underlying genetic variants. Genetic analysis can promote gene-adjusted, specific follow-up, and surveillance protocols for both patients and their families at risk. We report the case of a 7-yr-old boy with bilateral pheochromocytoma, which recurred a year after partial adrenalectomy. The patient's father developed bilateral pheochromocytomas at 25 yr of age. Both individuals possessed a novel heterogeneous in-frame duplication germline variant of VHL, yet neither exhibited other clinical manifestations of von Hippel-Lindau disease (VHL). Traditionally, VHL missense mutations have been associated with a higher risk of PPGL development, whereas truncating mutations typically confer a lower risk. In-frame duplication variants are rarely observed in patients with VHL but may lead to changes in the three-dimensional structure of the translated protein, similar to truncating variants. Our analysis suggests that these in-frame duplications of amino acids in specific regions may cause pheochromocytomas in a manner similar to missense variants. Further accumulation of VHL cases with various genotypes and standardized open-access worldwide databases, including longitudinal and specific clinical data linked to genotypes, is required. It is crucial to consider genetic analyses for pediatricians who may diagnose childhood-onset PPGL.
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Affiliation(s)
- Yuri Suzuki
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ryosei Iemura
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Akito Sutani
- Department of Pediatrics, Kawaguchi Municipal Medical Center, Saitama, Japan
| | - Yuki Mizuno
- Department of Pediatric Surgery, Tokyo Medical and Dental University Hospital, Tokyo, Japan
| | - Eriko Adachi
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Mineko Ushiama
- Department of Clinical Genomics, National Cancer Center Research Institute, Tokyo, Japan
- Department of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
| | - Teruhiko Yoshida
- Department of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
| | - Makoto Hirata
- Department of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
| | - Akihiro Hoshino
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kurara Yamomoto
- Department of Human Pathology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takumi Akashi
- Department of Diagnostic Pathology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yoshiko Nakano
- Department of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
- Department of Pediatrics, The University of Tokyo Hospital, Tokyo, Japan
| | - Takeshi Isoda
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kei Takasawa
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Motohiro Kato
- Department of Pediatrics, The University of Tokyo Hospital, Tokyo, Japan
| | - Masatoshi Takagi
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kentaro Okamoto
- Department of Pediatric Surgery, Tokyo Medical and Dental University Hospital, Tokyo, Japan
| | - Tomohiro Morio
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kenichi Kashimada
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University, Tokyo, Japan
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17
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Yu Z, Ran G, Chai J, Zhang EE. A nature-inspired HIF stabilizer derived from a highland-adaptation insertion of plateau pika Epas1 protein. Cell Rep 2024; 43:114727. [PMID: 39269902 DOI: 10.1016/j.celrep.2024.114727] [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: 04/29/2024] [Revised: 08/06/2024] [Accepted: 08/22/2024] [Indexed: 09/15/2024] Open
Abstract
Hypoxia-inducible factors (HIFs) play pivotal roles in numerous diseases and high-altitude adaptation, and HIF stabilizers have emerged as valuable therapeutic tools. In our prior investigation, we identified a highland-adaptation 24-amino-acid insertion within the Epas1 protein. This insertion enhances the protein stability of Epas1, and mice engineered with this insertion display enhanced resilience to hypoxic conditions. In the current study, we delved into the biochemical mechanisms underlying the protein-stabilizing effects of this insertion. Our findings unveiled that the last 11 amino acids within this insertion adopt a helical conformation and interact with the α-domain of the von Hippel-Lindau tumor suppressor protein (pVHL), thereby disrupting the Eloc-pVHL interaction and impeding the ubiquitination of Epas1. Utilizing a synthesized peptide, E14-24, we demonstrated its favorable membrane permeability and ability to stabilize endogenous HIF-α proteins, inducing the expression of hypoxia-responsive element (HRE) genes. Furthermore, the administration of E14-24 to mice subjected to hypoxic conditions mitigated body weight loss, suggesting its potential to enhance hypoxia adaptation.
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Affiliation(s)
- Ziqing Yu
- Graduate School of Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100006, China; National Institute of Biological Sciences, Beijing 102206, China.
| | - Guangdi Ran
- National Institute of Biological Sciences, Beijing 102206, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
| | - Juan Chai
- National Institute of Biological Sciences, Beijing 102206, China
| | - Eric Erquan Zhang
- National Institute of Biological Sciences, Beijing 102206, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China.
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18
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Greco F, Panunzio A, D’Andrea V, Vescovo M, Tafuri A, Carotti S, Beomonte Zobel B, Mallio CA. Exploring Tumor Heterogeneity: Radiogenomic Assessment of ADFP in Low WHO/ISUP Grade Clear Cell Renal Cell Carcinoma. Cancers (Basel) 2024; 16:3164. [PMID: 39335136 PMCID: PMC11430299 DOI: 10.3390/cancers16183164] [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: 08/22/2024] [Revised: 09/11/2024] [Accepted: 09/14/2024] [Indexed: 09/30/2024] Open
Abstract
This study aimed to investigate the association between metabolic lipid computed tomography (CT) features and adipose differentiation-related protein (ADFP) expression in clear cell renal cell carcinoma (ccRCC), providing insights into non-invasive methods for assessing ADFP expression and tumor characteristics. This study utilized data from The Cancer Genome Atlas and the Cancer Imaging Archive to analyze genetic alterations and imaging characteristics in ccRCC patients. Tumoral Hounsfield units (HU) analysis and quantification of abdominal adipose tissue compartments were performed using CT images. Statistical analyses were conducted to compare tumoral HU values according to ADFP gene expression and World Health Organization/International Society of Urological Pathology (WHO/ISUP) tumor grade, as well as to explore correlations between tumoral HU values and adipose tissue quantification. Among the 174 identified patients, those with ADFP gene expression showed significantly lower minimum tumoral HU values in low-grade cancers compared to high-grade cancers. Similarly, patients with low-grade cancers expressing ADFP exhibited lower minimum tumoral HU values compared to those without ADFP expression. Negative correlations were observed between minimum tumoral HU values and visceral adipose tissue, subcutaneous adipose tissue, and total adipose tissue in both ccRCC patients with and without ADFP expression. This study reveals a significant association between metabolic lipid CT features and ADFP expression in ccRCC patients. Lower minimum tumoral HU values, suggestive of higher intracellular lipid accumulation, were observed in tumors with low WHO/ISUP grade and ADFP expression.
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Affiliation(s)
- Federico Greco
- Department of Radiology, Cittadella della Salute, Azienda Sanitaria Locale di Lecce, Piazza Filippo Bottazzi, 2, 73100 Lecce, Italy
- Research Unit of Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Roma, Italy; (V.D.); (B.B.Z.); (C.A.M.)
| | - Andrea Panunzio
- Department of Urology, “Vito Fazzi” Hospital, Piazza Filippo Muratore, 1, 73100 Lecce, Italy; (A.P.); (A.T.)
| | - Valerio D’Andrea
- Research Unit of Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Roma, Italy; (V.D.); (B.B.Z.); (C.A.M.)
- Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Roma, Italy
| | - Mariavittoria Vescovo
- Anatomical Pathology Operative Research Unit, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Roma, Italy;
| | - Alessandro Tafuri
- Department of Urology, “Vito Fazzi” Hospital, Piazza Filippo Muratore, 1, 73100 Lecce, Italy; (A.P.); (A.T.)
| | - Simone Carotti
- Microscopic and Ultrastructural Anatomy Research Unit, Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Roma, Italy;
- Predictive Molecular Diagnostics, Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Roma, Italy
| | - Bruno Beomonte Zobel
- Research Unit of Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Roma, Italy; (V.D.); (B.B.Z.); (C.A.M.)
- Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Roma, Italy
| | - Carlo Augusto Mallio
- Research Unit of Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Roma, Italy; (V.D.); (B.B.Z.); (C.A.M.)
- Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Roma, Italy
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19
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Gómez-Virgilio L, Velazquez-Paniagua M, Cuazozon-Ferrer L, Silva-Lucero MDC, Gutierrez-Malacara AI, Padilla-Mendoza JR, Borbolla-Vázquez J, Díaz-Hernández JA, Jiménez-Orozco FA, Cardenas-Aguayo MDC. Genetics, Pathophysiology, and Current Challenges in Von Hippel-Lindau Disease Therapeutics. Diagnostics (Basel) 2024; 14:1909. [PMID: 39272694 PMCID: PMC11393980 DOI: 10.3390/diagnostics14171909] [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: 06/14/2024] [Revised: 08/12/2024] [Accepted: 08/23/2024] [Indexed: 09/15/2024] Open
Abstract
This review article focuses on von Hippel-Lindau (VHL) disease, a rare genetic disorder characterized by the development of tumors and cysts throughout the body. It discusses the following aspects of the disease. GENETICS VHL disease is caused by mutations in the VHL tumor suppressor gene located on chromosome 3. These mutations can be inherited or occur spontaneously. This article details the different types of mutations and their associated clinical features. PATHOPHYSIOLOGY The underlying cause of VHL disease is the loss of function of the VHL protein (pVHL). This protein normally regulates hypoxia-inducible factors (HIFs), which are involved in cell growth and survival. When pVHL is dysfunctional, HIF levels become elevated, leading to uncontrolled cell growth and tumor formation. CLINICAL MANIFESTATIONS VHL disease can affect various organs, including the brain, spinal cord, retina, kidneys, pancreas, and adrenal glands. Symptoms depend on the location and size of the tumors. DIAGNOSIS Diagnosis of VHL disease involves a combination of clinical criteria, imaging studies, and genetic testing. TREATMENT Treatment options for VHL disease depend on the type and location of the tumors. Surgery is the mainstay of treatment, but other options like radiation therapy may also be used. CHALLENGES This article highlights the challenges in VHL disease management, including the lack of effective therapies for some tumor types and the need for better methods to monitor disease progression. In conclusion, we emphasize the importance of ongoing research to develop new and improved treatments for VHL disease.
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Affiliation(s)
- Laura Gómez-Virgilio
- Laboratory of Cellular Reprogramming, Department of Physiology, Facultad de Medicina, Universidad Nacional Autónoma de México, Av. Universidad No. 3000, Coyoacan CDMX 04510, Mexico
| | - Mireya Velazquez-Paniagua
- Laboratory of Cellular Reprogramming, Department of Physiology, Facultad de Medicina, Universidad Nacional Autónoma de México, Av. Universidad No. 3000, Coyoacan CDMX 04510, Mexico
| | - Lucero Cuazozon-Ferrer
- Laboratory of Cellular Reprogramming, Department of Physiology, Facultad de Medicina, Universidad Nacional Autónoma de México, Av. Universidad No. 3000, Coyoacan CDMX 04510, Mexico
- Ingenieria en Biotecnología, Universidad Politécnica de Quintana Roo, Av. Arco Bicentenario, MZ. 11, Lote 1119-33 SM 255, Cancún Quintana Roo 77500, Mexico
| | - Maria-Del-Carmen Silva-Lucero
- Laboratory of Cellular Reprogramming, Department of Physiology, Facultad de Medicina, Universidad Nacional Autónoma de México, Av. Universidad No. 3000, Coyoacan CDMX 04510, Mexico
| | - Andres-Ivan Gutierrez-Malacara
- Laboratory of Cellular Reprogramming, Department of Physiology, Facultad de Medicina, Universidad Nacional Autónoma de México, Av. Universidad No. 3000, Coyoacan CDMX 04510, Mexico
| | - Juan-Ramón Padilla-Mendoza
- Laboratory of Cellular Reprogramming, Department of Physiology, Facultad de Medicina, Universidad Nacional Autónoma de México, Av. Universidad No. 3000, Coyoacan CDMX 04510, Mexico
| | - Jessica Borbolla-Vázquez
- Ingenieria en Biotecnología, Universidad Politécnica de Quintana Roo, Av. Arco Bicentenario, MZ. 11, Lote 1119-33 SM 255, Cancún Quintana Roo 77500, Mexico
| | - Job-Alí Díaz-Hernández
- Ingenieria en Biotecnología, Universidad Politécnica de Quintana Roo, Av. Arco Bicentenario, MZ. 11, Lote 1119-33 SM 255, Cancún Quintana Roo 77500, Mexico
| | | | - Maria-Del-Carmen Cardenas-Aguayo
- Laboratory of Cellular Reprogramming, Department of Physiology, Facultad de Medicina, Universidad Nacional Autónoma de México, Av. Universidad No. 3000, Coyoacan CDMX 04510, Mexico
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20
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Greco F, Panunzio A, Bernetti C, Tafuri A, Beomonte Zobel B, Mallio CA. The Radiogenomic Landscape of Clear Cell Renal Cell Carcinoma: Insights into Lipid Metabolism through Evaluation of ADFP Expression. Diagnostics (Basel) 2024; 14:1667. [PMID: 39125543 PMCID: PMC11311402 DOI: 10.3390/diagnostics14151667] [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: 06/27/2024] [Revised: 07/28/2024] [Accepted: 07/30/2024] [Indexed: 08/12/2024] Open
Abstract
This study aims to explore the relationship between radiological imaging and genomic characteristics in clear cell renal cell carcinoma (ccRCC), focusing on the expression of adipose differentiation-related protein (ADFP) detected through computed tomography (CT). The goal is to establish a radiogenomic lipid profile and understand its association with tumor characteristics. Data from The Cancer Genome Atlas (TCGA) and the Cancer Imaging Archive (TCIA) were utilized to correlate imaging features with adipose differentiation-related protein (ADFP) expression in ccRCC. CT scans assessed various tumor features, including size, composition, margin, necrosis, and growth pattern, alongside measurements of tumoral Hounsfield units (HU) and abdominal adipose tissue compartments. Statistical analyses compared demographics, clinical-pathological features, adipose tissue quantification, and tumoral HU between groups. Among 197 patients, 22.8% exhibited ADFP expression significantly associated with hydronephrosis. Low-grade ccRCC patients expressing ADFP had higher quantities of visceral and subcutaneous adipose tissue and lower tumoral HU values compared to their high-grade counterparts. Similar trends were observed in low-grade ccRCC patients without ADFP expression. ADFP expression in ccRCC correlates with specific imaging features such as hydronephrosis and altered adipose tissue distribution. Low-grade ccRCC patients with ADFP expression display a distinct lipid metabolic profile, emphasizing the relationship between radiological features, genomic expression, and tumor metabolism. These findings suggest potential for personalized diagnostic and therapeutic strategies targeting tumor lipid metabolism.
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Affiliation(s)
- Federico Greco
- Department of Radiology, Cittadella della Salute, Azienda Sanitaria Locale di Lecce, Piazza Filippo Bottazzi, 2, 73100 Lecce, Italy
- Research Unit of Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Roma, Italy; (C.B.); (B.B.Z.); (C.A.M.)
| | - Andrea Panunzio
- Department of Urology, “Vito Fazzi” Hospital, Piazza Filippo Muratore, 1, 73100 Lecce, Italy; (A.P.); (A.T.)
| | - Caterina Bernetti
- Research Unit of Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Roma, Italy; (C.B.); (B.B.Z.); (C.A.M.)
- Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Roma, Italy
| | - Alessandro Tafuri
- Department of Urology, “Vito Fazzi” Hospital, Piazza Filippo Muratore, 1, 73100 Lecce, Italy; (A.P.); (A.T.)
| | - Bruno Beomonte Zobel
- Research Unit of Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Roma, Italy; (C.B.); (B.B.Z.); (C.A.M.)
- Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Roma, Italy
| | - Carlo Augusto Mallio
- Research Unit of Radiology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, 21, 00128 Roma, Italy; (C.B.); (B.B.Z.); (C.A.M.)
- Fondazione Policlinico Universitario Campus Bio-Medico, Via Alvaro del Portillo, 200, 00128 Roma, Italy
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21
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Buckley M, Terwagne C, Ganner A, Cubitt L, Brewer R, Kim DK, Kajba CM, Forrester N, Dace P, De Jonghe J, Shepherd STC, Sawyer C, McEwen M, Diederichs S, Neumann-Haefelin E, Turajlic S, Ivakine EA, Findlay GM. Saturation genome editing maps the functional spectrum of pathogenic VHL alleles. Nat Genet 2024; 56:1446-1455. [PMID: 38969834 PMCID: PMC11250436 DOI: 10.1038/s41588-024-01800-z] [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: 05/11/2023] [Accepted: 05/13/2024] [Indexed: 07/07/2024]
Abstract
To maximize the impact of precision medicine approaches, it is critical to identify genetic variants underlying disease and to accurately quantify their functional effects. A gene exemplifying the challenge of variant interpretation is the von Hippel-Lindautumor suppressor (VHL). VHL encodes an E3 ubiquitin ligase that regulates the cellular response to hypoxia. Germline pathogenic variants in VHL predispose patients to tumors including clear cell renal cell carcinoma (ccRCC) and pheochromocytoma, and somatic VHL mutations are frequently observed in sporadic renal cancer. Here we optimize and apply saturation genome editing to assay nearly all possible single-nucleotide variants (SNVs) across VHL's coding sequence. To delineate mechanisms, we quantify mRNA dosage effects and compare functional effects in isogenic cell lines. Function scores for 2,268 VHL SNVs identify a core set of pathogenic alleles driving ccRCC with perfect accuracy, inform differential risk across tumor types and reveal new mechanisms by which variants impact function. These results have immediate utility for classifying VHL variants encountered clinically and illustrate how precise functional measurements can resolve pleiotropic and dosage-dependent genotype-phenotype relationships across complete genes.
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Affiliation(s)
- Megan Buckley
- The Genome Function Laboratory, The Francis Crick Institute, London, UK
| | - Chloé Terwagne
- The Genome Function Laboratory, The Francis Crick Institute, London, UK
| | - Athina Ganner
- Renal Division, Department of Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Laura Cubitt
- The Genome Function Laboratory, The Francis Crick Institute, London, UK
| | - Reid Brewer
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Dong-Kyu Kim
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Christina M Kajba
- The Genome Function Laboratory, The Francis Crick Institute, London, UK
| | - Nicole Forrester
- The Genome Function Laboratory, The Francis Crick Institute, London, UK
| | - Phoebe Dace
- The Genome Function Laboratory, The Francis Crick Institute, London, UK
| | - Joachim De Jonghe
- The Genome Function Laboratory, The Francis Crick Institute, London, UK
| | - Scott T C Shepherd
- The Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
- Renal and Skin Units, The Royal Marsden Hospital, London, UK
- Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London, UK
| | - Chelsea Sawyer
- Scientific Computing, The Francis Crick Institute, London, UK
| | - Mairead McEwen
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Sven Diederichs
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center-University of Freiburg, Faculty of Medicine, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg, A Partnership Between DKFZ and University Medical Center Freiburg, Freiburg, Germany
| | - Elke Neumann-Haefelin
- Renal Division, Department of Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Samra Turajlic
- The Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
- Renal and Skin Units, The Royal Marsden Hospital, London, UK
- Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London, UK
| | - Evgueni A Ivakine
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
| | - Gregory M Findlay
- The Genome Function Laboratory, The Francis Crick Institute, London, UK.
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22
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Liu X, Li Y, Castro L, Yu Z, Cheng Y, Daugherty MD, Gross JD. Structure of the E3 ligase CRL2-ZYG11B with substrates reveals the molecular basis for N-degron recognition and ubiquitination. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.24.600508. [PMID: 38979164 PMCID: PMC11230176 DOI: 10.1101/2024.06.24.600508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
ZYG11B is a substrate specificity factor for Cullin-RING ubiquitin ligase (CRL2) involved in many biological processes, including Gly/N-degron pathways. Yet how the binding of ZYG11B with CRL2 is coupled to substrate recognition and ubiquitination is unknown. We present the Cryo-EM structures of the CRL2-ZYG11B holoenzyme alone and in complex with a Gly/N-peptide from the inflammasome-forming pathogen sensor NLRP1. The structures indicate ZYG11B folds into a Leucine-Rich Repeat followed by two armadillo repeat domains that promote assembly with CRL2 and recognition of NLRP1 Gly/N-degron. ZYG11B promotes activation of the NLRP1 inflammasome through recognition and subsequent ubiquitination of the NLRP1 Gly/N-degron revealed by viral protease cleavage. Our structural and functional data indicate that blocking ZYG11B recognition of the NLRP1 Gly/N-degron inhibits NLRP1 inflammasome activation by a viral protease. Overall, we show how the CRL2-ZYG11B E3 ligase complex recognizes Gly/N-degron substrates, including those that are involved in viral protease-mediated activation of the NLRP1 inflammasome.
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23
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Wang S, Li H, Liu X, Yin T, Li T, Zheng M, Liu M, Meng X, Zhou J, Wang Y, Chen Y. VHL suppresses UBE3B-mediated breast tumor growth and metastasis. Cell Death Dis 2024; 15:446. [PMID: 38914543 PMCID: PMC11196597 DOI: 10.1038/s41419-024-06844-x] [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: 01/07/2024] [Revised: 06/15/2024] [Accepted: 06/18/2024] [Indexed: 06/26/2024]
Abstract
Protein homeostasis is predominantly governed through post-translational modification (PTM). UBE3B, identified as an oncoprotein, exhibits elevated protein levels in breast cancer. However, the impact of PTM on UBE3B remains unexplored. In this study, we show that VHL is a bona fide E3 ligase for UBE3B. Mechanistically, VHL directly binds to UBE3B, facilitating its lysine 48 (K48)-linked polyubiquitination at K286 and K427 in a prolyl hydroxylase (PHD)-independent manner. Consequently, this promotes the proteasomal degradation of UBE3B. The K286/427R mutation of UBE3B dramatically abolishes the inhibitory effect of VHL on breast tumor growth and lung metastasis. Additionally, the protein levels of UBE3B and VHL exhibit a negative correlation in breast cancer tissues. These findings delineate an important layer of UBE3B regulation by VHL.
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Affiliation(s)
- Shuo Wang
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Center for Cell Structure and Function, Institute of Biomedical Science, College of Life Sciences, Shandong Normal University, Jinan, Shandong, 250014, China
| | - Huiyan Li
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Center for Cell Structure and Function, Institute of Biomedical Science, College of Life Sciences, Shandong Normal University, Jinan, Shandong, 250014, China
| | - Xiong Liu
- School of Medicine, Jinan University, Guangzhou, Guangdong, 510632, China
| | - Tingting Yin
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Center for Cell Structure and Function, Institute of Biomedical Science, College of Life Sciences, Shandong Normal University, Jinan, Shandong, 250014, China
| | - Tingru Li
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Center for Cell Structure and Function, Institute of Biomedical Science, College of Life Sciences, Shandong Normal University, Jinan, Shandong, 250014, China
| | - Miaomiao Zheng
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Center for Cell Structure and Function, Institute of Biomedical Science, College of Life Sciences, Shandong Normal University, Jinan, Shandong, 250014, China
| | - Min Liu
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Center for Cell Structure and Function, Institute of Biomedical Science, College of Life Sciences, Shandong Normal University, Jinan, Shandong, 250014, China
| | - Xiaoqian Meng
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Center for Cell Structure and Function, Institute of Biomedical Science, College of Life Sciences, Shandong Normal University, Jinan, Shandong, 250014, China
| | - Jun Zhou
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Center for Cell Structure and Function, Institute of Biomedical Science, College of Life Sciences, Shandong Normal University, Jinan, Shandong, 250014, China
| | - Yijie Wang
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Center for Cell Structure and Function, Institute of Biomedical Science, College of Life Sciences, Shandong Normal University, Jinan, Shandong, 250014, China.
| | - Yan Chen
- Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, Center for Cell Structure and Function, Institute of Biomedical Science, College of Life Sciences, Shandong Normal University, Jinan, Shandong, 250014, China.
- School of Medicine, Jinan University, Guangzhou, Guangdong, 510632, China.
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24
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Kurlekar S, Lima JDCC, Li R, Lombardi O, Masson N, Barros AB, Pontecorvi V, Mole DR, Pugh CW, Adam J, Ratcliffe PJ. Oncogenic Cell Tagging and Single-Cell Transcriptomics Reveal Cell Type-Specific and Time-Resolved Responses to Vhl Inactivation in the Kidney. Cancer Res 2024; 84:1799-1816. [PMID: 38502859 PMCID: PMC11148546 DOI: 10.1158/0008-5472.can-23-3248] [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: 10/17/2023] [Revised: 01/16/2024] [Accepted: 03/13/2024] [Indexed: 03/21/2024]
Abstract
Defining the initial events in oncogenesis and the cellular responses they entrain, even in advance of morphologic abnormality, is a fundamental challenge in understanding cancer initiation. As a paradigm to address this, we longitudinally studied the changes induced by loss of the tumor suppressor gene von Hippel Lindau (VHL), which ultimately drives clear cell renal cell carcinoma. Vhl inactivation was directly coupled to expression of a tdTomato reporter within a single allele, allowing accurate visualization of affected cells in their native context and retrieval from the kidney for single-cell RNA sequencing. This strategy uncovered cell type-specific responses to Vhl inactivation, defined a proximal tubular cell class with oncogenic potential, and revealed longer term adaptive changes in the renal epithelium and the interstitium. Oncogenic cell tagging also revealed markedly heterogeneous cellular effects including time-limited proliferation and elimination of specific cell types. Overall, this study reports an experimental strategy for understanding oncogenic processes in which cells bearing genetic alterations can be generated in their native context, marked, and analyzed over time. The observed effects of loss of Vhl in kidney cells provide insights into VHL tumor suppressor action and development of renal cell carcinoma. SIGNIFICANCE Single-cell analysis of heterogeneous and dynamic responses to Vhl inactivation in the kidney suggests that early events shape the cell type specificity of oncogenesis, providing a focus for mechanistic understanding and therapeutic targeting.
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Affiliation(s)
- Samvid Kurlekar
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Joanna D C C Lima
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Ran Li
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Olivia Lombardi
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Norma Masson
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Ayslan B Barros
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Virginia Pontecorvi
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - David R Mole
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Christopher W Pugh
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Julie Adam
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Peter J Ratcliffe
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- The Francis Crick Institute, 1 Midland Road, London, United Kingdom
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25
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Wu Z, Huang Y, Liu K, Min J. N/C-degron pathways and inhibitor development for PROTAC applications. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:194952. [PMID: 37263341 DOI: 10.1016/j.bbagrm.2023.194952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/03/2023]
Abstract
Ubiquitination is a fascinating post-translational modification that has received continuous attention since its discovery. In this review, we first provide a concise overview of the E3 ubiquitin ligases, delving into classification, characteristics and mechanisms of ubiquitination. We then specifically examine the ubiquitination pathways mediated by the N/C-degrons, discussing their unique features and substrate recognition mechanisms. Finally, we offer insights into the current state of development pertaining to inhibitors that target the N/C-degron pathways, as well as the promising advances in the field of PROTAC (PROteolysis TArgeting Chimeras). Overall, this review offers a comprehensive understanding of the rapidly-evolving field of ubiquitin biology.
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Affiliation(s)
- Zhibin Wu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Yunyuan Huang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Ke Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China.
| | - Jinrong Min
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China.
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26
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Setia N, Almuqdadi HTA, Abid M. Journey of Von Hippel-Lindau (VHL) E3 ligase in PROTACs design: From VHL ligands to VHL-based degraders. Eur J Med Chem 2024; 265:116041. [PMID: 38199162 DOI: 10.1016/j.ejmech.2023.116041] [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: 10/02/2023] [Revised: 12/08/2023] [Accepted: 12/08/2023] [Indexed: 01/12/2024]
Abstract
The scientific community has shown considerable interest in proteolysis-targeting chimeras (PROTACs) in the last decade, indicating their remarkable potential as a means of achieving targeted protein degradation (TPD). Not only are PROTACs seen as valuable tools in molecular biology but their emergence as a modality for drug discovery has also garnered significant attention. PROTACs bind to E3 ligases and target proteins through respective ligands connected via a linker to induce proteasome-mediated protein degradation. The discovery of small molecule ligands for E3 ligases has led to the prevalent use of various E3 ligases in PROTAC design. Furthermore, the incorporation of different types of linkers has proven beneficial in enhancing the efficacy of PROTACs. By far more than 3300 PROTACs have been reported in the literature. Notably, Von Hippel-Lindau (VHL)-based PROTACs have surfaced as a propitious strategy for targeting proteins, even encompassing those that were previously considered non-druggable. VHL is extensively utilized as an E3 ligase in the advancement of PROTACs owing to its widespread expression in various tissues and well-documented binders. Here, we review the discovery of VHL ligands, the types of linkers employed to develop VHL-based PROTACs, and their subsequent modulation to design advanced non-conventional degraders to target various disease-causing proteins. Furthermore, we provide an overview of other E3 ligases recruited in the field of PROTAC technology.
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Affiliation(s)
- Nisha Setia
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | | | - Mohammad Abid
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India.
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Mason JW, Chow YT, Hudson L, Tutter A, Michaud G, Westphal MV, Shu W, Ma X, Tan ZY, Coley CW, Clemons PA, Bonazzi S, Berst F, Briner K, Liu S, Zécri FJ, Schreiber SL. DNA-encoded library-enabled discovery of proximity-inducing small molecules. Nat Chem Biol 2024; 20:170-179. [PMID: 37919549 PMCID: PMC10917151 DOI: 10.1038/s41589-023-01458-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 09/24/2023] [Indexed: 11/04/2023]
Abstract
Small molecules that induce protein-protein associations represent powerful tools to modulate cell circuitry. We sought to develop a platform for the direct discovery of compounds able to induce association of any two preselected proteins, using the E3 ligase von Hippel-Lindau (VHL) and bromodomains as test systems. Leveraging the screening power of DNA-encoded libraries (DELs), we synthesized ~1 million DNA-encoded compounds that possess a VHL-targeting ligand, a variety of connectors and a diversity element generated by split-and-pool combinatorial chemistry. By screening our DEL against bromodomains in the presence and absence of VHL, we could identify VHL-bound molecules that simultaneously bind bromodomains. For highly barcode-enriched library members, ternary complex formation leading to bromodomain degradation was confirmed in cells. Furthermore, a ternary complex crystal structure was obtained for our most enriched library member with BRD4BD1 and a VHL complex. Our work provides a foundation for adapting DEL screening to the discovery of proximity-inducing small molecules.
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Affiliation(s)
- Jeremy W Mason
- Chemical Biology and Therapeutics Science, Broad Institute, Cambridge, MA, USA
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Yuen Ting Chow
- Chemical Biology and Therapeutics Science, Broad Institute, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Liam Hudson
- Chemical Biology and Therapeutics Science, Broad Institute, Cambridge, MA, USA
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Antonin Tutter
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Gregory Michaud
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Matthias V Westphal
- Chemical Biology and Therapeutics Science, Broad Institute, Cambridge, MA, USA
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Wei Shu
- Structural and Biophysical Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Xiaolei Ma
- Structural and Biophysical Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, USA
| | - Zher Yin Tan
- Chemical Biology and Therapeutics Science, Broad Institute, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Connor W Coley
- Chemical Biology and Therapeutics Science, Broad Institute, Cambridge, MA, USA
| | - Paul A Clemons
- Chemical Biology and Therapeutics Science, Broad Institute, Cambridge, MA, USA
| | - Simone Bonazzi
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Frédéric Berst
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, Basel, Switzerland
| | - Karin Briner
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Shuang Liu
- Chemical Biology and Therapeutics Science, Broad Institute, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
| | - Frédéric J Zécri
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Cambridge, MA, USA.
| | - Stuart L Schreiber
- Chemical Biology and Therapeutics Science, Broad Institute, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
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28
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Serghini A, Portelli S, Troadec G, Song C, Pan Q, Pires DEV, Ascher DB. Characterizing and predicting ccRCC-causing missense mutations in Von Hippel-Lindau disease. Hum Mol Genet 2024; 33:224-232. [PMID: 37883464 PMCID: PMC10800015 DOI: 10.1093/hmg/ddad181] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Mutations within the Von Hippel-Lindau (VHL) tumor suppressor gene are known to cause VHL disease, which is characterized by the formation of cysts and tumors in multiple organs of the body, particularly clear cell renal cell carcinoma (ccRCC). A major challenge in clinical practice is determining tumor risk from a given mutation in the VHL gene. Previous efforts have been hindered by limited available clinical data and technological constraints. METHODS To overcome this, we initially manually curated the largest set of clinically validated VHL mutations to date, enabling a robust assessment of existing predictive tools on an independent test set. Additionally, we comprehensively characterized the effects of mutations within VHL using in silico biophysical tools describing changes in protein stability, dynamics and affinity to binding partners to provide insights into the structure-phenotype relationship. These descriptive properties were used as molecular features for the construction of a machine learning model, designed to predict the risk of ccRCC development as a result of a VHL missense mutation. RESULTS Analysis of our model showed an accuracy of 0.81 in the identification of ccRCC-causing missense mutations, and a Matthew's Correlation Coefficient of 0.44 on a non-redundant blind test, a significant improvement in comparison to the previous available approaches. CONCLUSION This work highlights the power of using protein 3D structure to fully explore the range of molecular and functional consequences of genomic variants. We believe this optimized model will better enable its clinical implementation and assist guiding patient risk stratification and management.
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Affiliation(s)
- Adam Serghini
- School of Chemistry and Molecular Biosciences, Chemistry Building 68, Cooper Road, The University of Queensland, St Lucia, QLD 4072, Queensland, Australia
| | - Stephanie Portelli
- School of Chemistry and Molecular Biosciences, Chemistry Building 68, Cooper Road, The University of Queensland, St Lucia, QLD 4072, Queensland, Australia
| | - Guillaume Troadec
- School of Computing and Information Systems, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Catherine Song
- School of Computing and Information Systems, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Qisheng Pan
- School of Chemistry and Molecular Biosciences, Chemistry Building 68, Cooper Road, The University of Queensland, St Lucia, QLD 4072, Queensland, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, 75 Commercial Road, Melbourne, VIC 3004, Australia
| | - Douglas E V Pires
- School of Computing and Information Systems, University of Melbourne, Melbourne, VIC 3010, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, 75 Commercial Road, Melbourne, VIC 3004, Australia
| | - David B Ascher
- School of Chemistry and Molecular Biosciences, Chemistry Building 68, Cooper Road, The University of Queensland, St Lucia, QLD 4072, Queensland, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, 75 Commercial Road, Melbourne, VIC 3004, Australia
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29
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Purser N, Tripathi-Giesgen I, Li J, Scott DC, Horn-Ghetko D, Baek K, Schulman BA, Alpi AF, Kleiger G. Catalysis of non-canonical protein ubiquitylation by the ARIH1 ubiquitin ligase. Biochem J 2023; 480:1817-1831. [PMID: 37870100 PMCID: PMC10657180 DOI: 10.1042/bcj20230373] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 10/24/2023]
Abstract
Protein ubiquitylation typically involves isopeptide bond formation between the C-terminus of ubiquitin to the side-chain amino group on Lys residues. However, several ubiquitin ligases (E3s) have recently been identified that ubiquitylate proteins on non-Lys residues. For instance, HOIL-1 belongs to the RING-in-between RING (RBR) class of E3s and has an established role in Ser ubiquitylation. Given the homology between HOIL-1 and ARIH1, an RBR E3 that functions with the large superfamily of cullin-RING E3 ligases (CRLs), a biochemical investigation was undertaken, showing ARIH1 catalyzes Ser ubiquitylation to CRL-bound substrates. However, the efficiency of ubiquitylation was exquisitely dependent on the location and chemical environment of the Ser residue within the primary structure of the substrate. Comprehensive mutagenesis of the ARIH1 Rcat domain identified residues whose mutation severely impacted both oxyester and isopeptide bond formation at the preferred site for Ser ubiquitylation while only modestly affecting Lys ubiquitylation at the physiological site. The results reveal dual isopeptide and oxyester protein ubiquitylation activities of ARIH1 and set the stage for physiological investigations into this function of emerging importance.
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Affiliation(s)
- Nicholas Purser
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, U.S.A
| | - Ishita Tripathi-Giesgen
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jerry Li
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, U.S.A
| | - Daniel C. Scott
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, U.S.A
| | - Daniel Horn-Ghetko
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Kheewoong Baek
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Brenda A. Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, U.S.A
| | - Arno F. Alpi
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Gary Kleiger
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, U.S.A
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30
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Ding X, Liang T, Li B, Liang B, Li J, Wang F, Chen S, Wang S, Zheng X, Wang T, Feng E. A nonsense mutation in VHL causing Von Hippel-Lindau syndrome in a large Chinese family-a genetic study of familial neoplastic disease. Int J Neurosci 2023:1-8. [PMID: 38014447 DOI: 10.1080/00207454.2023.2286210] [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: 05/29/2022] [Accepted: 11/15/2023] [Indexed: 11/29/2023]
Abstract
Von Hippel-Lindau (VHL) syndrome is a multi-organ neoplastic disease characterized by highly vascular and cystic tumors in the central nervous system (CNS), retina, and visceral lesions, which are mainly caused by germline mutations in VHL. We aimed to detect novel mutations in VHL gene in families with VHL. Here, a large consanguineous four-generation family with variant phenotypes of VHL syndrome was recruited, and its molecular genetics were tested via Sanger sequencing. And various tools and databases were used to predict the variant pathogenicity, frequency, and protein function. Genetic investigation detected a c.351G > A nonsense mutation in VHL that altered the downstream reading frame and created a premature TGA stop signal, resulting in severely truncated pVHL (p.Trp117Ter). This mutation is absent from most public databases, and functional prediction bioinformatic tools demonstrated that this residue is conserved and that this variant is highly likely to be deleterious. The c.315G > A nonsense mutation in VHL is the causal mutation of this kindred that may lead to clear familial aggregation of VHL syndrome because of the dysfunction of the truncated pVHL.
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Affiliation(s)
- Xinghuan Ding
- Department of Neurosurgery, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Tingyu Liang
- Department of Neurosurgery, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Ben Li
- Department of Neurosurgery, Weifang Yidu Central Hospital, Qingzhou, Shandong, China
| | - Bo Liang
- Department of Neurosurgery, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Jingjing Li
- Department of Radiology, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Fang Wang
- Department of Neurosurgery, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Shichao Chen
- Department of Neurosurgery, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Shanjun Wang
- Department of Neurosurgery, Weifang Yidu Central Hospital, Qingzhou, Shandong, China
| | - Xinmei Zheng
- Department of Neurosurgery, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Tongxin Wang
- Department of Neurosurgery, Weifang Yidu Central Hospital, Qingzhou, Shandong, China
| | - Enshan Feng
- Department of Neurosurgery, Beijing Ditan Hospital, Capital Medical University, Beijing, China
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31
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Park S, Cho JH, Kim JH, Park M, Park S, Kim SY, Kim SK, Kim K, Park S, Park B, Moon J, Lee G, Kim S, Kim JA, Kim JH. Hypoxia stabilizes SETDB1 to maintain genome stability. Nucleic Acids Res 2023; 51:11178-11196. [PMID: 37850636 PMCID: PMC10639076 DOI: 10.1093/nar/gkad796] [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: 10/01/2022] [Revised: 08/17/2023] [Accepted: 09/25/2023] [Indexed: 10/19/2023] Open
Abstract
Von Hippel-Lindau (VHL) is a tumor suppressor that functions as the substrate recognition subunit of the CRL2VHL E3 complex. While substrates of VHL have been identified, its tumor suppressive role remains to be fully understood. For further determination of VHL substrates, we analyzed the physical interactome of VHL and identified the histone H3K9 methyltransferase SETBD1 as a novel target. SETDB1 undergoes oxygen-dependent hydroxylation by prolyl hydroxylase domain proteins and the CRL2VHL complex recognizes hydroxylated SETDB1 for ubiquitin-mediated degradation. Under hypoxic conditions, SETDB1 accumulates by escaping CRL2VHL activity. Loss of SETDB1 in hypoxia compared with that in normoxia escalates the production of transposable element-derived double-stranded RNAs, thereby hyperactivating the immune-inflammatory response. In addition, strong derepression of TEs in hypoxic cells lacking SETDB1 triggers DNA damage-induced death. Our collective results support a molecular mechanism of oxygen-dependent SETDB1 degradation by the CRL2VHL E3 complex and reveal a role of SETDB1 in genome stability under hypoxia.
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Affiliation(s)
- Sungryul Park
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Jin Hwa Cho
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Jong-Hwan Kim
- Korea Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Mijin Park
- Aging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
- Department of Bioscience, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Seulki Park
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Seon-Young Kim
- Korea Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
- Department of Bioscience, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Seon-Kyu Kim
- Aging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
- Department of Bioscience, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Kidae Kim
- R&D Center, PharmAbcine Inc., Daejeon 34047, Republic of Korea
| | - Sung Goo Park
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
- Department of Bioscience, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Byoung Chul Park
- Department of Bioscience, University of Science and Technology, Daejeon 34113, Republic of Korea
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Jeong Hee Moon
- Core Research Facility & Analysis Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Gaseul Lee
- Core Research Facility & Analysis Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
- College of Pharmacy, Chungbuk National University, Cheongju, Chungbuk 28160, Republic of Korea
| | - Sunhong Kim
- Drug Discovery Center, LG Chem Ltd., Seoul 07796, Republic of Korea
| | - Jung-Ae Kim
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
- Aging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
- Department of Bioscience, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Jeong-Hoon Kim
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
- Department of Bioscience, University of Science and Technology, Daejeon 34113, Republic of Korea
- Graduate School of New Drug Discovery and Development, Chungnam National University, Daejeon 34134, Republic of Korea
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32
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Figg WD, Fiorini G, Chowdhury R, Nakashima Y, Tumber A, McDonough MA, Schofield CJ. Structural basis for binding of the renal carcinoma target hypoxia-inducible factor 2α to prolyl hydroxylase domain 2. Proteins 2023; 91:1510-1524. [PMID: 37449559 PMCID: PMC10952196 DOI: 10.1002/prot.26541] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/08/2023] [Accepted: 06/08/2023] [Indexed: 07/18/2023]
Abstract
The hypoxia-inducible factor (HIF) prolyl-hydroxylases (human PHD1-3) catalyze prolyl hydroxylation in oxygen-dependent degradation (ODD) domains of HIFα isoforms, modifications that signal for HIFα proteasomal degradation in an oxygen-dependent manner. PHD inhibitors are used for treatment of anemia in kidney disease. Increased erythropoietin (EPO) in patients with familial/idiopathic erythrocytosis and pulmonary hypertension is associated with mutations in EGLN1 (PHD2) and EPAS1 (HIF2α); a drug inhibiting HIF2α activity is used for clear cell renal cell carcinoma (ccRCC) treatment. We report crystal structures of PHD2 complexed with the C-terminal HIF2α-ODD in the presence of its 2-oxoglutarate cosubstrate or N-oxalylglycine inhibitor. Combined with the reported PHD2.HIFα-ODD structures and biochemical studies, the results inform on the different PHD.HIFα-ODD binding modes and the potential effects of clinically observed mutations in HIFα and PHD2 genes. They may help enable new therapeutic avenues, including PHD isoform-selective inhibitors and sequestration of HIF2α by the PHDs for ccRCC treatment.
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Affiliation(s)
- William D. Figg
- Chemistry Research Laboratory, Department of Chemistry and the Ineos OxfordInstitute for Antimicrobial Research, University of OxfordOxfordUK
| | - Giorgia Fiorini
- Chemistry Research Laboratory, Department of Chemistry and the Ineos OxfordInstitute for Antimicrobial Research, University of OxfordOxfordUK
| | - Rasheduzzaman Chowdhury
- Chemistry Research Laboratory, Department of Chemistry and the Ineos OxfordInstitute for Antimicrobial Research, University of OxfordOxfordUK
| | - Yu Nakashima
- Chemistry Research Laboratory, Department of Chemistry and the Ineos OxfordInstitute for Antimicrobial Research, University of OxfordOxfordUK
- Institute of Natural Medicine, University of ToyamaToyamaJapan
| | - Anthony Tumber
- Chemistry Research Laboratory, Department of Chemistry and the Ineos OxfordInstitute for Antimicrobial Research, University of OxfordOxfordUK
| | - Michael A. McDonough
- Chemistry Research Laboratory, Department of Chemistry and the Ineos OxfordInstitute for Antimicrobial Research, University of OxfordOxfordUK
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos OxfordInstitute for Antimicrobial Research, University of OxfordOxfordUK
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33
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Shirole NH, Kaelin WG. von-Hippel Lindau and Hypoxia-Inducible Factor at the Center of Renal Cell Carcinoma Biology. Hematol Oncol Clin North Am 2023; 37:809-825. [PMID: 37270382 PMCID: PMC11315268 DOI: 10.1016/j.hoc.2023.04.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The most common form of kidney cancer is clear cell renal cell carcinoma (ccRCC). Biallelic VHL tumor suppressor gene inactivation is the usual initiating event in both hereditary (VHL Disease) and sporadic ccRCCs. The VHL protein, pVHL, earmarks the alpha subunits of the HIF transcription factor for destruction in an oxygen-dependent manner. Deregulation of HIF2 drives ccRCC pathogenesis. Drugs inhibiting the HIF2-responsive growth factor VEGF are now mainstays of ccRCC treatment. A first-in-class allosteric HIF2 inhibitor was recently approved for treating VHL Disease-associated neoplasms and appears active against sporadic ccRCC in early clinical trials.
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Affiliation(s)
- Nitin H Shirole
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - William G Kaelin
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Brigham and Women's Hospital, Harvard Medical School; Howard Hughes Medical Institute.
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34
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Hu J, Smith DJ, Wu L. VHL L169P Variant Does Not Alter Cellular Hypoxia Tension in Clear Cell Renal Cell Carcinoma. Int J Mol Sci 2023; 24:14075. [PMID: 37762376 PMCID: PMC10530985 DOI: 10.3390/ijms241814075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/09/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
In the current era of tumor genome sequencing, single amino acid missense variants in the von Hippel-Lindau (VHL) tumor suppressor gene are frequently identified in clear cell renal carcinoma (ccRCC). Due to the incomplete knowledge of the structural architecture of VHL protein, the functional significance of many missense mutations cannot be assigned. L169P is one such missense mutation identified in the case of aggressive, metastatic ccRCC. Here, we characterized the biochemical activity, transcriptomic hypoxia signature and biological functions of the L169P variant. Lentiviral vector expressing either wildtype (WT) or L169P VHL were used to transduce two VHL-deficient human ccRCC cell lines, 786-O and RCC4. The stability of the VHL protein and the expression level of VHL, HIF1α and HIF2α were analyzed. The impact of restoring L169P or WT VHL on the hypoxia gene expression program in 786-O cells was assessed by mRNA sequencing (RNAseq) and computed hypoxic scores. The impact of restoring VHL expression on the growth of ccRCC models was assessed in cell cultures and in chorioallantoic membrane (CAM) xenografts. In the 786-O cells, the protein stability of L169P VHL was comparable to WT VHL. No obvious difference in the capability of degrading HIF1α and HIF2α was observed between WT and L169P VHL in the 786-O or RCC4 cells. The hypoxic scores were not significantly different in the 786-O cells expressing either wildtype or L169P VHL. From the cellular function perspective, both WT and L169P VHL slowed cell proliferation in vitro and in vivo. The L169P VHL variant is comparable to WT VHL in terms of protein stability, ability to degrade HIF1α factors and ability to regulate hypoxia gene expression, as well as in the suppression of ccRCC tumor cell growth. Taken together, our data indicate that the L169P VHL variant alone is unlikely to drive the oncogenesis of sporadic ccRCC.
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Affiliation(s)
- Junhui Hu
- Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA;
- Institute of Urologic Oncology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Desmond J. Smith
- Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA;
- Brain Research Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Lily Wu
- Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA;
- Institute of Urologic Oncology, University of California Los Angeles, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA 90095, USA
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Batavia AA, Rutishauser D, Sobottka B, Schraml P, Beerenwinkel N, Moch H. Biallelic ELOC-Inactivated Renal Cell Carcinoma: Molecular Features Supporting Classification as a Distinct Entity. Mod Pathol 2023; 36:100194. [PMID: 37088333 DOI: 10.1016/j.modpat.2023.100194] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/28/2023] [Accepted: 04/16/2023] [Indexed: 04/25/2023]
Abstract
Approximately 70% of clear cell renal cell carcinoma (ccRCC) is characterized by the biallelic inactivation of von Hippel-Lindau (VHL) on chromosome 3p. ELOC-mutated (Elongin C-mutated) renal cell carcinoma containing biallelic ELOC inactivations with chromosome 8q deletions is considered a novel subtype of renal cancer possessing a morphologic overlap with ccRCC, renal cell carcinoma (RCC) with fibromyomatous stroma exhibiting Tuberous Sclerosis Complex (TSC)/mammalian Target of Rapamycin (mTOR) mutations, and clear cell papillary tumor. However, the frequency and consequences of ELOC alterations in wild-type VHL and mutated VHL RCC are unclear. In this study, we characterize 123 renal tumors with clear cell morphology and known VHL mutation status to assess the morphologic and molecular consequences of ELOC inactivation. Using OncoScan and whole-exome sequencing, we identify 18 ELOC-deleted RCCs, 3 of which contain ELOC mutations resulting in the biallelic inactivation of ELOC. Biallelic ELOC and biallelic VHL aberrations were mutually exclusive; however, 2 ELOC-mutated RCCs showed monoallelic VHL alterations. Furthermore, no mutations in TSC1, TSC2, or mTOR were identified in ELOC-mutated RCC with biallelic ELOC inactivation. Using High Ambiguity Driven biomolecular DOCKing, we report a novel ELOC variant containing a duplication event disrupting ELOC-VHL interaction alongside the frequently seen Y79C alteration. Using hyper reaction monitoring mass spectrometry, we show RCCs with biallelic ELOC alterations have significantly reduced ELOC expression but similar carbonic anhydrase 9 and vascular endothelial growth factor A expression compared with classical ccRCC with biallelic VHL inactivation. The absence of biallelic VHL and TSC1, TSC2, or mTOR inactivation in RCC with biallelic ELOC inactivation (ELOC mutation in combination with ELOC deletions on chromosome 8q) supports the notion of a novel, molecularly defined tumor entity.
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Affiliation(s)
- Aashil A Batavia
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland; Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Dorothea Rutishauser
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Bettina Sobottka
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Peter Schraml
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zürich, Basel, Switzerland; Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.
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Stampone E, Bencivenga D, Capellupo MC, Roberti D, Tartaglione I, Perrotta S, Della Ragione F, Borriello A. Genome editing and cancer therapy: handling the hypoxia-responsive pathway as a promising strategy. Cell Mol Life Sci 2023; 80:220. [PMID: 37477829 PMCID: PMC10361942 DOI: 10.1007/s00018-023-04852-2] [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: 05/02/2023] [Revised: 06/14/2023] [Accepted: 06/29/2023] [Indexed: 07/22/2023]
Abstract
The precise characterization of oxygen-sensing pathways and the identification of pO2-regulated gene expression are both issues of critical importance. The O2-sensing system plays crucial roles in almost all the pivotal human processes, including the stem cell specification, the growth and development of tissues (such as embryogenesis), the modulation of intermediate metabolism (including the shift of the glucose metabolism from oxidative to anaerobic ATP production and vice versa), and the control of blood pressure. The solid cancer microenvironment is characterized by low oxygen levels and by the consequent activation of the hypoxia response that, in turn, allows a complex adaptive response characterized mainly by neoangiogenesis and metabolic reprogramming. Recently, incredible advances in molecular genetic methodologies allowed the genome editing with high efficiency and, above all, the precise identification of target cells/tissues. These new possibilities and the knowledge of the mechanisms of adaptation to hypoxia suggest the effective development of new therapeutic approaches based on the manipulation, targeting, and exploitation of the oxygen-sensor system molecular mechanisms.
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Affiliation(s)
- Emanuela Stampone
- Department of Precision Medicine, University of Campania "L. Vanvitelli", Via Luigi De Crecchio, 7, 80138, Naples, Italy
| | - Debora Bencivenga
- Department of Precision Medicine, University of Campania "L. Vanvitelli", Via Luigi De Crecchio, 7, 80138, Naples, Italy
| | - Maria Chiara Capellupo
- Department of Precision Medicine, University of Campania "L. Vanvitelli", Via Luigi De Crecchio, 7, 80138, Naples, Italy
| | - Domenico Roberti
- Department of the Woman, the Child and of the General and Specialty Surgery, University of Campania "L. Vanvitelli", Via Luigi De Crecchio, 2, 80138, Naples, Italy
| | - Immacolata Tartaglione
- Department of the Woman, the Child and of the General and Specialty Surgery, University of Campania "L. Vanvitelli", Via Luigi De Crecchio, 2, 80138, Naples, Italy
| | - Silverio Perrotta
- Department of the Woman, the Child and of the General and Specialty Surgery, University of Campania "L. Vanvitelli", Via Luigi De Crecchio, 2, 80138, Naples, Italy
| | - Fulvio Della Ragione
- Department of Precision Medicine, University of Campania "L. Vanvitelli", Via Luigi De Crecchio, 7, 80138, Naples, Italy.
| | - Adriana Borriello
- Department of Precision Medicine, University of Campania "L. Vanvitelli", Via Luigi De Crecchio, 7, 80138, Naples, Italy.
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37
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Fischer S, Trinh VT, Simon C, Weber LM, Forné I, Nist A, Bange G, Abendroth F, Stiewe T, Steinchen W, Liefke R, Vázquez O. Peptide-mediated inhibition of the transcriptional regulator Elongin BC induces apoptosis in cancer cells. Cell Chem Biol 2023:S2451-9456(23)00155-1. [PMID: 37354906 DOI: 10.1016/j.chembiol.2023.05.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 04/12/2023] [Accepted: 05/30/2023] [Indexed: 06/26/2023]
Abstract
Inhibition of protein-protein interactions (PPIs) via designed peptides is an effective strategy to perturb their biological functions. The Elongin BC heterodimer (ELOB/C) binds to a BC-box motif and is essential for cancer cell growth. Here, we report a peptide that mimics the high-affinity BC-box of the PRC2-associated protein EPOP. This peptide tightly binds to the ELOB/C dimer (kD = 0.46 ± 0.02 nM) and blocks the association of ELOB/C with its interaction partners, both in vitro and in the cellular environment. Cancer cells treated with our peptide inhibitor showed decreased cell viability, increased apoptosis, and perturbed gene expression. Therefore, our work proposes that blocking the BC-box-binding pocket of ELOB/C is a feasible strategy to impair its function and inhibit cancer cell growth. Our peptide inhibitor promises novel mechanistic insights into the biological function of the ELOB/C dimer and offers a starting point for therapeutics linked to ELOB/C dysfunction.
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Affiliation(s)
- Sabrina Fischer
- Institute of Molecular Biology and Tumor Research (IMT), University of Marburg, 35043 Marburg, Germany
| | - Van Tuan Trinh
- Department of Chemistry, University of Marburg, 35043 Marburg, Germany
| | - Clara Simon
- Institute of Molecular Biology and Tumor Research (IMT), University of Marburg, 35043 Marburg, Germany
| | - Lisa M Weber
- Institute of Molecular Biology and Tumor Research (IMT), University of Marburg, 35043 Marburg, Germany
| | - Ignasi Forné
- Protein Analysis Unit, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-University (LMU) Munich, 82152 Martinsried, Germany
| | - Andrea Nist
- Genomics Core Facility, Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), University of Marburg, 35043 Marburg, Germany
| | - Gert Bange
- Department of Chemistry, University of Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, 35043 Marburg, Germany
| | - Frank Abendroth
- Department of Chemistry, University of Marburg, 35043 Marburg, Germany
| | - Thorsten Stiewe
- Genomics Core Facility, Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), University of Marburg, 35043 Marburg, Germany
| | - Wieland Steinchen
- Department of Chemistry, University of Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, 35043 Marburg, Germany
| | - Robert Liefke
- Institute of Molecular Biology and Tumor Research (IMT), University of Marburg, 35043 Marburg, Germany; Department of Hematology, Oncology, and Immunology, University Hospital Giessen and Marburg, 35043 Marburg, Germany.
| | - Olalla Vázquez
- Department of Chemistry, University of Marburg, 35043 Marburg, Germany; Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, 35043 Marburg, Germany.
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Schwalm MP, Krämer A, Dölle A, Weckesser J, Yu X, Jin J, Saxena K, Knapp S. Tracking the PROTAC degradation pathway in living cells highlights the importance of ternary complex measurement for PROTAC optimization. Cell Chem Biol 2023:S2451-9456(23)00157-5. [PMID: 37354907 DOI: 10.1016/j.chembiol.2023.06.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 04/03/2023] [Accepted: 06/01/2023] [Indexed: 06/26/2023]
Abstract
The multi-step degradation process of PROteolysis TArgeting Chimeras (PROTACs) poses a challenge for their rational development, as the rate-limiting steps that determine PROTACs efficiency remain largely unknown. Moreover, the slow throughput of currently used endpoint assays does not allow the comprehensive analysis of larger series of PROTACs. Here, we developed cell-based assays using the NanoLuciferase and HaloTag that allow measuring PROTAC-induced degradation and ternary complex formation kinetics and stability in cells. Using PROTACs developed for the degradation of WD40 repeat domain protein 5 (WDR5), the characterization of the mode of action of these PROTACs in the early degradation cascade revealed a key role of ternary complex formation and stability. Comparing a series of ternary complex crystal structures highlighted the importance of an efficient E3-target interface for ternary complex stability. The developed assays outline a strategy for the rational optimization of PROTACs using a series of live cell assays monitoring key steps of the early PROTAC-induced degradation pathway.
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Affiliation(s)
- Martin P Schwalm
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Andreas Krämer
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Anja Dölle
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Janik Weckesser
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Xufen Yu
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Krishna Saxena
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Stefan Knapp
- Institut für Pharmazeutische Chemie, Goethe-University Frankfurt, Biozentrum, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Structural Genomics Consortium, Goethe-University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany; German Cancer Consortium (DKTK)/German Cancer Research Center (DKFZ), DKTK site Frankfurt-Mainz, 69120 Heidelberg, Germany.
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Ray S, Dason S, Singer EA. Integrating Surgery in the Multidisciplinary Care of Advanced Renal Cell Carcinoma. Urol Clin North Am 2023; 50:311-323. [PMID: 36948674 DOI: 10.1016/j.ucl.2023.01.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
The role of surgery for patients with locally advanced and metastatic renal cell carcinoma (RCC) is not precisely defined in our contemporary era of systemic therapies. Research in this field is focused on the role of regional lymphadenectomy, along with indications and timing of cytoreductive nephrectomy and metastasectomy. As our understanding of the molecular and immunological basis of RCC continues to develop along with the advent of novel systemic therapies, prospective clinical trials will be critical in defining how surgery should be integrated into the treatment paradigm of advanced RCC.
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Affiliation(s)
- Shagnik Ray
- Division of Urologic Oncology, The Ohio State University Comprehensive Cancer Center, 915 Olentangy River Road, 3rd Floor, Urology Suite 3100, Columbus, OH 43212, USA
| | - Shawn Dason
- Division of Urologic Oncology, The Ohio State University Comprehensive Cancer Center, 915 Olentangy River Road, 3rd Floor, Urology Suite 3100, Columbus, OH 43212, USA
| | - Eric A Singer
- Division of Urologic Oncology, The Ohio State University Comprehensive Cancer Center, 915 Olentangy River Road, 3rd Floor, Urology Suite 3100, Columbus, OH 43212, USA.
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40
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Kelm JM, Pandey DS, Malin E, Kansou H, Arora S, Kumar R, Gavande NS. PROTAC'ing oncoproteins: targeted protein degradation for cancer therapy. Mol Cancer 2023; 22:62. [PMID: 36991452 PMCID: PMC10061819 DOI: 10.1186/s12943-022-01707-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 12/23/2022] [Indexed: 03/31/2023] Open
Abstract
Molecularly targeted cancer therapies substantially improve patient outcomes, although the durability of their effectiveness can be limited. Resistance to these therapies is often related to adaptive changes in the target oncoprotein which reduce binding affinity. The arsenal of targeted cancer therapies, moreover, lacks coverage of several notorious oncoproteins with challenging features for inhibitor development. Degraders are a relatively new therapeutic modality which deplete the target protein by hijacking the cellular protein destruction machinery. Degraders offer several advantages for cancer therapy including resiliency to acquired mutations in the target protein, enhanced selectivity, lower dosing requirements, and the potential to abrogate oncogenic transcription factors and scaffolding proteins. Herein, we review the development of proteolysis targeting chimeras (PROTACs) for selected cancer therapy targets and their reported biological activities. The medicinal chemistry of PROTAC design has been a challenging area of active research, but the recent advances in the field will usher in an era of rational degrader design.
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Affiliation(s)
- Jeremy M Kelm
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences (EACPHS), Wayne State University, Detroit, MI, 48201, USA
| | - Deepti S Pandey
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences (EACPHS), Wayne State University, Detroit, MI, 48201, USA
| | - Evan Malin
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences (EACPHS), Wayne State University, Detroit, MI, 48201, USA
| | - Hussein Kansou
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences (EACPHS), Wayne State University, Detroit, MI, 48201, USA
| | - Sahil Arora
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, 151401, India
| | - Raj Kumar
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda, 151401, India
| | - Navnath S Gavande
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences (EACPHS), Wayne State University, Detroit, MI, 48201, USA.
- Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, 48201, USA.
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41
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Scott DC, King MT, Baek K, Gee CT, Kalathur R, Li J, Purser N, Nourse A, Chai SC, Vaithiyalingam S, Chen T, Lee RE, Elledge SJ, Kleiger G, Schulman BA. E3 ligase autoinhibition by C-degron mimicry maintains C-degron substrate fidelity. Mol Cell 2023; 83:770-786.e9. [PMID: 36805027 PMCID: PMC10080726 DOI: 10.1016/j.molcel.2023.01.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/19/2022] [Accepted: 01/18/2023] [Indexed: 02/18/2023]
Abstract
E3 ligase recruitment of proteins containing terminal destabilizing motifs (degrons) is emerging as a major form of regulation. How those E3s discriminate bona fide substrates from other proteins with terminal degron-like sequences remains unclear. Here, we report that human KLHDC2, a CRL2 substrate receptor targeting C-terminal Gly-Gly degrons, is regulated through interconversion between two assemblies. In the self-inactivated homotetramer, KLHDC2's C-terminal Gly-Ser motif mimics a degron and engages the substrate-binding domain of another protomer. True substrates capture the monomeric CRL2KLHDC2, driving E3 activation by neddylation and subsequent substrate ubiquitylation. Non-substrates such as NEDD8 bind KLHDC2 with high affinity, but its slow on rate prevents productive association with CRL2KLHDC2. Without substrate, neddylated CRL2KLHDC2 assemblies are deactivated via distinct mechanisms: the monomer by deneddylation and the tetramer by auto-ubiquitylation. Thus, substrate specificity is amplified by KLHDC2 self-assembly acting like a molecular timer, where only bona fide substrates may bind before E3 ligase inactivation.
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Affiliation(s)
- Daniel C Scott
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Moeko T King
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kheewoong Baek
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Clifford T Gee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ravi Kalathur
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Protein Technologies Center, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jerry Li
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Nicholas Purser
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Amanda Nourse
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Protein Technologies Center, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sergio C Chai
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sivaraja Vaithiyalingam
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Protein Technologies Center, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Richard E Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stephen J Elledge
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Gary Kleiger
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Brenda A Schulman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
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Ferro M, Musi G, Marchioni M, Maggi M, Veccia A, Del Giudice F, Barone B, Crocetto F, Lasorsa F, Antonelli A, Schips L, Autorino R, Busetto GM, Terracciano D, Lucarelli G, Tataru OS. Radiogenomics in Renal Cancer Management-Current Evidence and Future Prospects. Int J Mol Sci 2023; 24:4615. [PMID: 36902045 PMCID: PMC10003020 DOI: 10.3390/ijms24054615] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Abstract
Renal cancer management is challenging from diagnosis to treatment and follow-up. In cases of small renal masses and cystic lesions the differential diagnosis of benign or malignant tissues has potential pitfalls when imaging or even renal biopsy is applied. The recent artificial intelligence, imaging techniques, and genomics advancements have the ability to help clinicians set the stratification risk, treatment selection, follow-up strategy, and prognosis of the disease. The combination of radiomics features and genomics data has achieved good results but is currently limited by the retrospective design and the small number of patients included in clinical trials. The road ahead for radiogenomics is open to new, well-designed prospective studies, with large cohorts of patients required to validate previously obtained results and enter clinical practice.
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Affiliation(s)
- Matteo Ferro
- Department of Urology, European Institute of Oncology (IEO) IRCCS, 20141 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy
| | - Gennaro Musi
- Department of Urology, European Institute of Oncology (IEO) IRCCS, 20141 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy
| | - Michele Marchioni
- Department of Medical, Oral and Biotechnological Sciences, G. d’Annunzio, University of Chieti, 66100 Chieti, Italy
- Urology Unit, SS. Annunziata Hospital, 66100 Chieti, Italy
- Department of Urology, ASL Abruzzo 2, 66100 Chieti, Italy
| | - Martina Maggi
- Department of Maternal Infant and Urologic Sciences, Policlinico Umberto I Hospital, University of Rome, 00161 Rome, Italy
| | - Alessandro Veccia
- Department of Urology, Azienda Ospedaliera Universitaria Integrata of Verona, University of Verona, 37126 Verona, Italy
| | - Francesco Del Giudice
- Department of Maternal Infant and Urologic Sciences, Policlinico Umberto I Hospital, University of Rome, 00161 Rome, Italy
| | - Biagio Barone
- Department of Neurosciences and Reproductive Sciences and Odontostomatology, University of Naples Federico II, 80131 Naples, Italy
| | - Felice Crocetto
- Department of Neurosciences and Reproductive Sciences and Odontostomatology, University of Naples Federico II, 80131 Naples, Italy
| | - Francesco Lasorsa
- Urology, Andrology and Kidney Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari Aldo Moro, 70124 Bari, Italy
| | - Alessandro Antonelli
- Department of Urology, Azienda Ospedaliera Universitaria Integrata of Verona, University of Verona, 37126 Verona, Italy
| | - Luigi Schips
- Department of Medical, Oral and Biotechnological Sciences, G. d’Annunzio, University of Chieti, 66100 Chieti, Italy
- Urology Unit, SS. Annunziata Hospital, 66100 Chieti, Italy
- Department of Urology, ASL Abruzzo 2, 66100 Chieti, Italy
| | | | - Gian Maria Busetto
- Department of Urology and Renal Transplantation, University of Foggia, 71122 Foggia, Italy
| | - Daniela Terracciano
- Department of Translational Medical Sciences, University of Naples Federico II, 80131 Naples, Italy
| | - Giuseppe Lucarelli
- Urology, Andrology and Kidney Transplantation Unit, Department of Precision and Regenerative Medicine and Ionian Area, University of Bari Aldo Moro, 70124 Bari, Italy
| | - Octavian Sabin Tataru
- Department of Simulation Applied in Medicine, The Institution Organizing University Doctoral Studies (I.O.S.U.D.), George Emil Palade University of Medicine, Pharmacy, Sciences, and Technology of Târgu Mureș, 540142 Târgu Mureș, Romania
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Downstream Targets of VHL/HIF-α Signaling in Renal Clear Cell Carcinoma Progression: Mechanisms and Therapeutic Relevance. Cancers (Basel) 2023; 15:cancers15041316. [PMID: 36831657 PMCID: PMC9953937 DOI: 10.3390/cancers15041316] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/09/2023] [Accepted: 02/11/2023] [Indexed: 02/22/2023] Open
Abstract
The clear cell variant of renal cell carcinoma (ccRCC) is the most common renal epithelial malignancy and responsible for most of the deaths from kidney cancer. Patients carrying inactivating mutations in the Von Hippel-Lindau (VHL) gene have an increased proclivity to develop several types of tumors including ccRCC. Normally, the Hypoxia Inducible Factor alpha (HIF-α) subunits of the HIF heterodimeric transcription factor complex are regulated by oxygen-dependent prolyl-hydroxylation, VHL-mediated ubiquitination and proteasomal degradation. Loss of pVHL function results in elevated levels of HIF-α due to increased stability, leading to RCC progression. While HIF-1α acts as a tumor suppressor, HIF-2α promotes oncogenic potential by driving tumor progression and metastasis through activation of hypoxia-sensitive signaling pathways and overexpression of HIF-2α target genes. One strategy to suppress ccRCC aggressiveness is directed at inhibition of HIF-2α and the associated molecular pathways leading to cell proliferation, angiogenesis, and metastasis. Indeed, clinical and pre-clinical data demonstrated the effectiveness of HIF-2α targeted therapy in attenuating ccRCC progression. This review focuses on the signaling pathways and the involved genes (cyclin D, c-Myc, VEGF-a, EGFR, TGF-α, GLUT-1) that confer oncogenic potential downstream of the VHL-HIF-2α signaling axis in ccRCC. Discussed as well are current treatment options (including receptor tyrosine kinase inhibitors such as sunitinib), the medical challenges (high prevalence of metastasis at the time of diagnosis, refractory nature of advanced disease to current treatment options), scientific challenges and future directions.
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Kanno H, Matsumoto S, Yoshizumi T, Nakahara K, Kubo A, Murata H, Shuin T, U HS. Role of SOCS and VHL Proteins in Neuronal Differentiation and Development. Int J Mol Sci 2023; 24:ijms24043880. [PMID: 36835292 PMCID: PMC9960776 DOI: 10.3390/ijms24043880] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
The basic helix-loop-helix factors play a central role in neuronal differentiation and nervous system development, which involve the Notch and signal transducer and activator of transcription (STAT)/small mother against decapentaplegic signaling pathways. Neural stem cells differentiate into three nervous system lineages, and the suppressor of cytokine signaling (SOCS) and von Hippel-Lindau (VHL) proteins are involved in this neuronal differentiation. The SOCS and VHL proteins both contain homologous structures comprising the BC-box motif. SOCSs recruit Elongin C, Elongin B, Cullin5(Cul5), and Rbx2, whereas VHL recruits Elongin C, Elongin B, Cul2, and Rbx1. SOCSs form SBC-Cul5/E3 complexes, and VHL forms a VBC-Cul2/E3 complex. These complexes degrade the target protein and suppress its downstream transduction pathway by acting as E3 ligases via the ubiquitin-proteasome system. The Janus kinase (JAK) is the main target protein of the E3 ligase SBC-Cul5, whereas hypoxia-inducible factor is the primary target protein of the E3 ligase VBC-Cul2; nonetheless, VBC-Cul2 also targets the JAK. SOCSs not only act on the ubiquitin-proteasome system but also act directly on JAKs to suppress the Janus kinase-signal transduction and activator of transcription (JAK-STAT) pathway. Both SOCS and VHL are expressed in the nervous system, predominantly in brain neurons in the embryonic stage. Both SOCS and VHL induce neuronal differentiation. SOCS is involved in differentiation into neurons, whereas VHL is involved in differentiation into neurons and oligodendrocytes; both proteins promote neurite outgrowth. It has also been suggested that the inactivation of these proteins may lead to the development of nervous system malignancies and that these proteins may function as tumor suppressors. The mechanism of action of SOCS and VHL involved in neuronal differentiation and nervous system development is thought to be mediated through the inhibition of downstream signaling pathways, JAK-STAT, and hypoxia-inducible factor-vascular endothelial growth factor pathways. In addition, because SOCS and VHL promote nerve regeneration, they are expected to be applied in neuronal regenerative medicine for traumatic brain injury and stroke.
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Affiliation(s)
- Hiroshi Kanno
- Department of Neurosurgery, School of Medicine, Yokohama City University, Yokohama 232-0024, Japan
- Department of Neurosurgery, Asahi Hospital, Tokyo 121-0078, Japan
- Correspondence: ; Tel.: +81-3-5242-5800
| | - Shutaro Matsumoto
- Department of Neurosurgery, School of Medicine, Yokohama City University, Yokohama 232-0024, Japan
- Department of Neurosurgery, Asahi Hospital, Tokyo 121-0078, Japan
| | - Tetsuya Yoshizumi
- Department of Neurosurgery, St. Mariannna Medical University, Kawasaki 216-8511, Japan
| | - Kimihiro Nakahara
- Department of Neurosurgery, International University of Health and Welfare, Atami 413-0012, Japan
| | | | - Hidetoshi Murata
- Department of Neurosurgery, St. Mariannna Medical University, Kawasaki 216-8511, Japan
| | - Taro Shuin
- Kochi Medical School Hospital, Nangoku 783-0043, Japan
| | - Hoi-Sang U
- Department of Electrical Engineering, University of California San Diego, San Diego, CA 92093, USA
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Rosenberg SC, Shanahan F, Yamazoe S, Kschonsak M, Zeng YJ, Lee J, Plise E, Yen I, Rose CM, Quinn JG, Gazzard LJ, Walters BT, Kirkpatrick DS, Staben ST, Foster SA, Malek S. Ternary complex dissociation kinetics contribute to mutant-selective EGFR degradation. Cell Chem Biol 2023; 30:S2451-9456(23)00030-2. [PMID: 36773603 DOI: 10.1016/j.chembiol.2023.01.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 09/02/2022] [Accepted: 01/23/2023] [Indexed: 02/12/2023]
Abstract
Targeted degradation of proteins by chimeric heterobifunctional degraders has emerged as a major drug discovery paradigm. Despite the increased interest in this approach, the criteria dictating target protein degradation by a degrader remain poorly understood, and potent target engagement by a degrader does not strongly correlate with target degradation. In this study, we present the biochemical characterization of an epidermal growth factor receptor (EGFR) degrader that potently binds both wild-type and mutant EGFR, but only degrades EGFR mutant variants. Mechanistic studies reveal that ternary complex half-life strongly correlates with processive ubiquitination with purified components and mutant-selective degradation in cells. We present cryoelectron microscopy and hydrogen-deuterium exchange mass spectroscopy data on wild-type and mutant EGFR ternary complexes, which demonstrate that potent target degradation can be achieved in the absence of stable compound-induced protein-protein interactions. These results highlight the importance of considering target conformation during degrader development as well as leveraging heterobifunctional ligand binding kinetics to achieve robust target degradation.
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Affiliation(s)
- Scott C Rosenberg
- Department of Discovery Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Frances Shanahan
- Department of Discovery Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Sayumi Yamazoe
- Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Marc Kschonsak
- Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Yi J Zeng
- Department of Structural Biology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - James Lee
- Department of Discovery Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Emile Plise
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Ivana Yen
- Department of Discovery Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Christopher M Rose
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - John G Quinn
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Lewis J Gazzard
- Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Benjamin T Walters
- Department of Biochemical and Cellular Pharmacology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Donald S Kirkpatrick
- Department of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Steven T Staben
- Department of Discovery Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Scott A Foster
- Department of Discovery Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Shiva Malek
- Department of Discovery Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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Naseripour M, Azimi F, Talebi S, Mirshahi R, Kiaee R, Sedaghat A, Zohre AK, Khakpour G. Investigation of germline VHL variants in Iranian patients with retinal capillary hemangioblastoma and genotype-phenotype analysis. Ophthalmic Genet 2023; 44:211-217. [PMID: 36715412 DOI: 10.1080/13816810.2022.2138455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
BACKGROUND Retinal capillary hemangioblastoma (RCH), while sporadic in some cases, is the most common and earliest manifestation of von Hippel-Lindau disease (VHL). This is the first report on different types of VHL variants and genotype-phenotype correlations in Iranian families with RCH. MATERIALS AND METHODS In this prospective observational case series study, 17 families with RCH were included. PCR was performed to amplify 3 exons of VHL gene. Afterward, Sanger sequencing was performed on all PCR products. For the detection of VHL copy number variations, MLPA was used. RESULTS Our study identified 10 different types of VHL variants. Missense mutations were the most common variants found and affected the structure of α domain of the VHL protein (pVHL). The majority of mutations (72.7%) in the patients with RCH and central nervous system hemangioblastoma (CNS-HB) were located on α domain. CONCLUSION α domain of VHL may play a potential role in the pathogenesis of RCH. Our findings suggest that genotype-phenotype characteristics in those variants in α- domain may predispose patients to RCH with CNS-HB.
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Affiliation(s)
- Masood Naseripour
- Eye Research Center, the Five Senses Institute, Rassoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran.,Stem cell and regenerative medicine research center, Iran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Azimi
- Eye Research Center, the Five Senses Institute, Rassoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Said Talebi
- Departments of Medical Genetics, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Reza Mirshahi
- Eye Research Center, the Five Senses Institute, Rassoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Reza Kiaee
- Eye Research Center, the Five Senses Institute, Rassoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Ahad Sedaghat
- Eye Research Center, the Five Senses Institute, Rassoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Ataei Kachoei Zohre
- Departments of Medical Genetics, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Golnaz Khakpour
- Eye Research Center, the Five Senses Institute, Rassoul Akram Hospital, Iran University of Medical Sciences, Tehran, Iran.,Departments of Medical Genetics, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
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Vetrano IG, Gioppo A, Faragò G, Pinzi V, Pollo B, Broggi M, Schiariti M, Ferroli P, Acerbi F. Hemangioblastomas and Other Vascular Origating Tumors of Brain or Spinal Cord. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1405:377-403. [PMID: 37452946 DOI: 10.1007/978-3-031-23705-8_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Hemangioblastomas (HBs) are highly vascularized, slow-growing, rare benign tumors (WHO grade I). They account for about 2% of intracranial neoplasms; however, they are the most common primary cerebellar tumors in adults. Another frequent seat is the spinal cord (2-10% of primary spinal cord tumors). HBs are constituted by stromal and capillary vascular cells; macroscopically, HBs appear as nodular tumors, with or without cystic components. Although most of the HBs are sporadic (57-75%), they represent a particular component of von Hippel-Lindau disease (VHL), an autosomal dominant syndrome with high penetrance, due to a germline pathogenic mutation in the VHL gene, which is a tumor suppressor with chromosomal location on the short arm of chromosome three. VHL disease determines a variety of malignant and benign tumors, most frequently HBs, renal cell carcinomas, pheochromocytomas/paragangliomas, pancreatic neuroendocrine tumors, and endolymphatic sac tumors. Up to 20% of cases are due to de novo pathogenic variants without a family history. Many epidemiologic details of these tumors, especially the sporadic forms, are not well known. The median age of patients with sporadic HBS is about 40 years. More than two-third of VHL patients develop one or more central nervous system HBs during their lifetime; in case of VHL, patients at first diagnosis are usually younger than the patients with sporadic tumors. The most common presenting signs and symptoms are related to increased intracranial pressure, cerebellar signs, or spinal cord alterations in case of spinal involvement. Magnetic resonance imaging is the gold standard for the diagnosis, assessment, and follow-up of HBs, both sporadic and syndrome-related; angiography is rarely performed because the diagnosis is easily obtained with magnetic resonance. However, the diagnosis of an asymptomatic lesion does not automatically result in therapeutic actions, as the risks of treatment and the onset of possible neurological deficit need to be balanced, considering that HBs may remain asymptomatic and have a static or slow-growing behavior. In such cases, regular follow-up can represent a valid therapeutic option until the patients remain asymptomatic. There are no actual pharmacological therapies that are demonstrated to be effective for HBs. Surgery represents the primary therapeutic approach for these tumors. Observation or radiotherapy also plays a role in the long-term management of patients harboring HBs, especially in VHL; in few selected cases, endovascular treatment has been suggested before surgical removal. This chapter presents a systematic overview of epidemiology, clinical appearance, histopathological and neuroradiological characteristics of central nervous system HBs. Moreover, the genetic and molecular biology of sporadic and VHL HBS deserves special attention. Furthermore, we will describe all the available therapeutic options, along with the follow-up management. Finally, we will briefly report other vascular originating tumors as hemangioendotheliomas, hemangiomas, or angiosarcomas.
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Affiliation(s)
- Ignazio G Vetrano
- Neurovascular Surgery Unit, Department of Neurosurgery, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Andrea Gioppo
- Interventional Neuroradiology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Giuseppe Faragò
- Interventional Neuroradiology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Valentina Pinzi
- Radiotherapy Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Bianca Pollo
- Neuropathology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Morgan Broggi
- Neurovascular Surgery Unit, Department of Neurosurgery, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Marco Schiariti
- Neurovascular Surgery Unit, Department of Neurosurgery, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Paolo Ferroli
- Neurovascular Surgery Unit, Department of Neurosurgery, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Francesco Acerbi
- Neurovascular Surgery Unit and Experimental Microsurgical Laboratory, Department of Neurosurgery, Fondazione IRCCS Istituto Neurologico Carlo Besta, Via G. Celoria 11, 20133, Milan, Italy.
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Lee SH, Park KH, Woo SJ, Park SJ, Joo K. Clinical and Genetic Characteristics of Retinal Capillary Hemangioblastoma in Korean Patients. KOREAN JOURNAL OF OPHTHALMOLOGY 2022; 36:543-549. [PMID: 36281577 DOI: 10.3341/kjo.2022.0079] [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: 06/15/2022] [Accepted: 10/17/2022] [Indexed: 12/14/2022] Open
Abstract
PURPOSE We investigated the clinical features of Korean patients with retinal capillary hemangioblastoma (RCH) and genetic variants of the von Hippel-Lindau (VHL) gene. METHODS A retrospective analysis was performed on patients with RCH from 2003 to 2021 at Seoul National University Bundang Hospital. Sporadic and hereditary RCH associated with VHL disease were classified based on the specific tumors and family history. Clinical features, including the location and number of RCH and bilateral involvement, were investigated. Multiplex ligation-dependent probe amplification and direct sequencing targeting the VHL gene were performed for six RCH cases associated with VHL disease. RESULTS A total of 18 patients (23 eyes) were enrolled in this study. The mean age at diagnosis was 37 ± 15 years. Twelve patients had hereditary RCH associated with VHL disease, and six patients had sporadic RCH. All five patients with bilateral RCH were clinically diagnosed with VHL disease, and 13 patients had unilateral RCH. Juxtapapillary RCH was only observed in patients with VHL. The most common complication of RCH was the epiretinal membrane, followed by the subretinal fluid. Pathogenic variants were identified in four patients. All three patients with type 1 VHL had the well-known missense mutation p.Glu70Lys, and one patient with type 2 VHL had the nonsense mutation p.Trp88Ter. CONCLUSIONS In Korean patients with RCH, bilateral involvement and juxtapapillary RCH are highly likely to be associated with VHL disease. Because RCH may be the first clinical manifestation in patients with VHL, active genetic testing of the VHL gene and systemic evaluation are required.
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Affiliation(s)
- Sang Ha Lee
- Department of Ophthalmology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Kyu Hyung Park
- Department of Ophthalmology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Se Joon Woo
- Department of Ophthalmology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Sang Jun Park
- Department of Ophthalmology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Kwangsic Joo
- Department of Ophthalmology, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
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Choi C, Im JH, Lee J, Kwon SI, Kim WY, Park SR, Hwang DJ. OsDWD1 E3 ligase-mediated OsNPR1 degradation suppresses basal defense in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:966-981. [PMID: 36168109 DOI: 10.1111/tpj.15985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 09/05/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
Many ubiquitin E3 ligases function in plant immunity. Here, we show that Oryza sativa (rice) DDB1 binding WD (OsDWD1) suppresses immune responses by targeting O. sativa non-expresser of pathogenesis-related gene 1 (OsNPR1) for degradation. Knock-down and overexpression experiments in rice plants showed that OsDWD1 is a negative regulator of the immune response and that OsNPR1 is a substrate of OsDWD1 and a substrate receptor of OsCRL4. After constructing the loss-of-function mutant OsDWD1R239A , we showed that the downregulation of OsNPR1 seen in rice lines overexpressing wild-type (WT) OsDWD1 (OsDWD1WT -ox) was compromised in OsDWD1R239A -ox lines, and that OsNPR1 upregulation enhanced resistance to pathogen infection, confirming that OsCRL4OsDWD1 regulates OsNPR1 protein levels. The enhanced disease resistance seen in OsDWD1 knock-down (OsDWD1-kd) lines contrasted with the reduced disease resistance in double knock-down (OsDWD1/OsNPR1-kd) lines, indicating that the enhanced disease resistance of OsDWD1-kd resulted from the accumulation of OsNPR1. Moreover, an in vivo heterologous protein degradation assay in Arabidopsis thaliana ddb1 mutants confirmed that the CUL4-based E3 ligase system can also influence OsNPR1 protein levels in Arabidopsis. Although OsNPR1 was degraded by the OsCRL4OsDWD1 -mediated ubiquitination system, the phosphodegron-motif-mutated NPR1 was partially degraded in the DWD1-ox protoplasts. This suggests that there might be another degradation process for OsNPR1. Taken together, these results indicate that OsDWD1 regulates OsNPR1 protein levels in rice to suppress the untimely activation of immune responses.
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Affiliation(s)
- Changhyun Choi
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874, Republic of Korea
| | - Jong Hee Im
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874, Republic of Korea
| | - Jinjeong Lee
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874, Republic of Korea
| | - Soon Il Kwon
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874, Republic of Korea
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21 Four), Institute of Agricultural and Life Sciences, Research Institute of Life Sciences, Gyeongsang National University, Jinju, 52825, Republic of Korea
| | - Sang Ryeol Park
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874, Republic of Korea
| | - Duk-Ju Hwang
- National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874, Republic of Korea
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50
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Chesnel F, Jullion E, Delalande O, Couturier A, Alusse A, Le Goff X, Lenglet M, Gardie B, Abadie C, Arlot-Bonnemains Y. Mutation of the proline P81 into a serine modifies the tumour suppressor function of the von Hippel-Lindau gene in the ccRCC. Br J Cancer 2022; 127:1954-1962. [PMID: 36175619 PMCID: PMC9681884 DOI: 10.1038/s41416-022-01985-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 08/29/2022] [Accepted: 09/07/2022] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND The von Hippel-Lindau disease is an autosomal dominant syndrome associated with tumour formation in various tissues, such as retina, central nervous system, kidney, and adrenal glands. VHL gene deletion or mutations support the development of various cancers. Unclassified VHL variants also referred as "of unknown significance" result from gene mutations that have an unknown or unclear effect on protein functions. The P81S mutation has been linked to low penetrance Type 1 disease but its pathogenic function was not clearly determined. METHODS We established a stable cell line expressing the pVHL213 (c.241C>T, P81S) mutant. Using biochemical and physiological approaches, we herein analysed pVHL folding, stability and function in the context of this VHL single missense mutation. RESULTS The P81S mutation mostly affects the non-canonical function of the pVHL protein. The cells expressing the pVHL213P81S acquire invasive properties in relation with modified architecture network. CONCLUSION We demonstrated the pathogenic role of this mutation in tumour development in vhl patients and confirm a medical follow up of family carrying the c.241C>T, P81S.
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Affiliation(s)
- Franck Chesnel
- CNRS UMR6290, Université Rennes 1, SFR-UMSCNRS 3480-INSERM 018, 2 ave du Pr L Bernard, 35042, Rennes, France
| | - Emmanuelle Jullion
- CNRS UMR6290, Université Rennes 1, SFR-UMSCNRS 3480-INSERM 018, 2 ave du Pr L Bernard, 35042, Rennes, France
| | - Olivier Delalande
- CNRS UMR6290, Université Rennes 1, SFR-UMSCNRS 3480-INSERM 018, 2 ave du Pr L Bernard, 35042, Rennes, France
| | - Anne Couturier
- CNRS UMR6290, Université Rennes 1, SFR-UMSCNRS 3480-INSERM 018, 2 ave du Pr L Bernard, 35042, Rennes, France
| | - Adrien Alusse
- CNRS UMR6290, Université Rennes 1, SFR-UMSCNRS 3480-INSERM 018, 2 ave du Pr L Bernard, 35042, Rennes, France
| | - Xavier Le Goff
- CNRS UMR6290, Université Rennes 1, SFR-UMSCNRS 3480-INSERM 018, 2 ave du Pr L Bernard, 35042, Rennes, France
| | - Marion Lenglet
- Ecole Pratique des Hautes Etudes, EPHE, Université Paris Sciences et Lettres, Paris, France
- Nantes Université, CNRS, INSERM, l'Institut du Thorax, F-44000, Nantes, France
| | - Betty Gardie
- Ecole Pratique des Hautes Etudes, EPHE, Université Paris Sciences et Lettres, Paris, France
- Nantes Université, CNRS, INSERM, l'Institut du Thorax, F-44000, Nantes, France
| | - Caroline Abadie
- Institut de Cancérologie, Boulevard Jacques Monod, 44805, Saint-Herblain, France
| | - Yannick Arlot-Bonnemains
- CNRS UMR6290, Université Rennes 1, SFR-UMSCNRS 3480-INSERM 018, 2 ave du Pr L Bernard, 35042, Rennes, France.
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