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El-Assaad AM, Hamieh T. SARS-CoV-2: Prediction of critical ionic amino acid mutations. Comput Biol Med 2024; 178:108688. [PMID: 38870723 DOI: 10.1016/j.compbiomed.2024.108688] [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: 10/31/2023] [Revised: 05/26/2024] [Accepted: 06/01/2024] [Indexed: 06/15/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), that caused coronavirus disease 2019 (COVID-19), has been studied thoroughly, and several variants are revealed across the world with their corresponding mutations. Studies and vaccines development focus on the genetic mutations of the S protein due to its vital role in allowing the virus attach and fuse with the membrane of a host cell. In this perspective, we study the effects of all ionic amino acid mutations of the SARS-CoV-2 viral spike protein S1 when bound to Antibody CC12.1 within the SARS-CoV-2:CC12.1 complex model. Binding free energy calculations between SARS-CoV-2 and antibody CC12.1 are based on the Analysis of Electrostatic Similarities of Proteins (AESOP) framework, where the electrostatic potentials are calculated using Adaptive Poisson-Boltzmann Solver (APBS). The atomic radii and charges that feed into the APBS calculations are calculated using the PDB2PQR software. Our results are the first to propose in silico potential life-threatening mutations of SARS-CoV-2 beyond the present mutations found in the five common variants worldwide. We find each of the following mutations: K378A, R408A, K424A, R454A, R457A, K458A, and K462A, to play significant roles in the binding to Antibody CC12.1, since they are turned into strong inhibitors on both chains of the S1 protein, whereas the mutations D405A, D420A, and D427A, show to play important roles in this binding, as they are turned into mild inhibitors on both chains of the S1 protein.
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Affiliation(s)
- Atlal M El-Assaad
- Department of Electrical Engineering & Computer Science, University of Toledo (UT), Toledo OH 43606, USA; Department of Computer Science, Lebanese International University (LIU), Bekaa, Lebanon.
| | - Tayssir Hamieh
- Faculty of Science and Engineering, Maastricht University, P.O. Box 616, 6200 MD Maastricht, the Netherlands; Laboratory of Materials, Catalysis, Environment and Analytical Methods (MCEMA), Faculty of Sciences, Lebanese University, Hadath, Lebanon.
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2
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Shen S, Radhakrishnan SK, Harrell JC, Puchalapalli M, Koblinski J, Clevenger C. The Human Intermediate Prolactin Receptor I-tail Contributes Breast Oncogenesis by Targeting Ras/MAPK Pathway. Endocrinology 2024; 165:bqae039. [PMID: 38713636 DOI: 10.1210/endocr/bqae039] [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: 10/19/2023] [Indexed: 05/09/2024]
Abstract
Prolactin and its receptor (PRLr) in humans are significantly involved in breast cancer pathogenesis. The intermediate form of human PRLr (hPRLrI) is produced by alternative splicing and has a novel 13 amino acid tail ("I-tail") gain. hPRLrI induces significant proliferation and anchorage-independent growth of normal mammary epithelia in vitro when coexpressed with the long form hPRLr (hPRLrL). hPRLrL and hPRLrI coexpression is necessary to induce the transformation of mammary epithelia in vivo. The I-tail is associated with the ubiquitin-like protein neural precursor cell expressed developmentally downregulated protein 8. Treatment with the neural precursor cell expressed developmentally downregulated protein 8-activating enzyme inhibitor pevonedistat resulted in increased hPRLrL and the death of breast cancer cells. The goal of this study was to determine the function of the hPRLrI I-tail in hPRLrL/hPRLrI-mediated mammary transformation. hPRLrL/hPRLrI and hPRLrL/hPRLrIΔ13 (I-tail removal mutant) were delivered to MCF10AT cells. Cell proliferation was decreased when hPRLrI I-tail was removed. I-tail deletion decreased anchorage-independent growth and attenuated cell migration. The I-tail was involved in Ras/MAPK signaling but not PI3K/Akt signaling pathway as shown by western blot. I-tail removal resulted in decreased hPRLrI stability. RNA-sequencing data revealed that I-tail removal resulted in differential gene expression induced by prolactin. Ingenuity Pathway Analysis revealed that the activity of ERK was attenuated. Treatment of breast cancer cells with ERK1/2 inhibitor ulixertinib resulted in decreased colony-forming ability and less proliferation. These studies suggest that the hPRLrI I-tail contributed to breast oncogenesis and may be a promising target for the development of new breast cancer therapies.
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Affiliation(s)
- Shanwei Shen
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA
- Wright Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Senthil K Radhakrishnan
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA
- Massey Comprehensive Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - J Chuck Harrell
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA
- Wright Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, VA 23298, USA
- Massey Comprehensive Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Madhavi Puchalapalli
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Jennifer Koblinski
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA
- Massey Comprehensive Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Charles Clevenger
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23298, USA
- Wright Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, VA 23298, USA
- Massey Comprehensive Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
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3
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Gill JK, Shaw GS. Using Förster Resonance Energy Transfer (FRET) to Understand the Ubiquitination Landscape. Chembiochem 2024:e202400193. [PMID: 38632088 DOI: 10.1002/cbic.202400193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 04/19/2024]
Abstract
Förster resonance energy transfer (FRET) is a fluorescence technique that allows quantitative measurement of protein interactions, kinetics and dynamics. This review covers the use of FRET to study the structures and mechanisms of ubiquitination and related proteins. We survey FRET assays that have been developed where donor and acceptor fluorophores are placed on E1, E2 or E3 enzymes and ubiquitin (Ub) to monitor steady-state and real-time transfer of Ub through the ubiquitination cascade. Specialized FRET probes placed on Ub and Ub-like proteins have been developed to monitor Ub removal by deubiquitinating enzymes (DUBs) that result in a loss of a FRET signal upon cleavage of the FRET probes. FRET has also been used to understand conformational changes in large complexes such as multimeric E3 ligases and the proteasome, frequently using sophisticated single molecule methods. Overall, FRET is a powerful tool to help unravel the intricacies of the complex ubiquitination system.
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Affiliation(s)
- Jashanjot Kaur Gill
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada, N6A5C1
| | - Gary S Shaw
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada, N6A5C1
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4
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Hu N, Xiao X, Yao L, Chen X, Li X. The Protein Response of Salt-Tolerant Zygosaccharomyces rouxii to High-Temperature Stress during the Lag Phase. J Fungi (Basel) 2024; 10:48. [PMID: 38248957 PMCID: PMC10817685 DOI: 10.3390/jof10010048] [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: 11/07/2023] [Revised: 12/04/2023] [Accepted: 12/15/2023] [Indexed: 01/23/2024] Open
Abstract
Zygosaccharomyces rouxii used in soy sauce brewing is an osmotolerant and halotolerant yeast, but it is not tolerant to high temperatures and the underlying mechanisms remain poorly understood. Using a synthetic medium containing only Pro as a nitrogen source, the response of Z. rouxii in protein level to high-temperature stress (40 °C, HTS) during the lag phase was investigated. Within the first two h, the total intracellular protein concentration was significantly decreased from 220.99 ± 6.58 μg/mg DCW to 152.63 ± 10.49 μg/mg DCW. The analysis of the amino acid composition of the total protein through vacuum proteolysis technology and HPLC showed that new amino acids (Thr, Tyr, Ser, and His) were added to newborn protein over time during the lag phase under HTS. The nutritional conditions used in this study determined that the main source of amino acid supply for protein synthesis was through amino acid biosynthesis and ubiquitination-mediated protein degradation. Differential expression analysis of the amino acid biosynthesis-related genes in the transcriptome showed that most genes were upregulated under HTS, excluding ARO8, which was consistently repressed during the lag phase. RT-qPCR results showed that high-temperature stress significantly increased the upregulation of proteolysis genes, especially PSH1 (E3 ubiquitin ligase) by 13.23 ± 1.44 fold (p < 0.0001) within 4 h. Overall, these results indicated that Z. rouxii adapt to prolonged high temperatures stress by altering its basal protein composition. This protein renewal was related to the regulation of proteolysis and the biosynthesis of amino acids.
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Affiliation(s)
| | | | | | - Xiong Chen
- Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Biological Engineering and Food, Hubei University of Technology, Wuhan 430068, China; (N.H.); (X.X.); (L.Y.)
| | - Xin Li
- Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Biological Engineering and Food, Hubei University of Technology, Wuhan 430068, China; (N.H.); (X.X.); (L.Y.)
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5
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Tang L, Wei D, Xu X, Mo D, Cheng D, Yan F. FOXO1-regulated lncRNA CYP1B1-AS1 suppresses breast cancer cell proliferation by inhibiting neddylation. Breast Cancer Res Treat 2023; 202:397-408. [PMID: 37640964 PMCID: PMC10505597 DOI: 10.1007/s10549-023-07090-z] [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: 06/08/2023] [Accepted: 08/11/2023] [Indexed: 08/31/2023]
Abstract
PURPOSE Overactivated neddylation is considered to be a common event in cancer. Long non-coding RNAs (lncRNAs) can regulate cancer development by mediating post-translational modifications. However, the role of lncRNA in neddylation modification remains unclear. METHODS LncRNA cytochrome P450 family 1 subfamily B member 1 antisense RNA 1 (CYP1B1-AS1) expression in breast cancer tissues was evaluated by RT-PCR and TCGA BRCA data. Gain and loss of function experiments were performed to explore the role of CYP1B1-AS1 in breast cancer cell proliferation and apoptosis in vitro and in vivo. Luciferase assay, CHIP-qPCR assay, transcriptome sequencing, RNA-pulldown assay, mass spectrometry, RIP-PCR and Western blot were used to investigate the regulatory factors of CYP1B1-AS1 expression and the molecular mechanism of CYP1B1-AS1 involved in neddylation modification. RESULTS We found that CYP1B1-AS1 was down-regulated in breast cancer tissues and correlated with prognosis. In vivo and in vitro functional experiments confirmed that CYP1B1-AS1 inhibited cell proliferation and induced apoptosis. Mechanistically, CYP1B1-AS1 was regulated by the transcription factor, forkhead box O1 (FOXO1), and could be upregulated by inhibiting the PI3K/FOXO1 pathway. Moreover, CYP1B1-AS1 bound directly to NEDD8 activating enzyme E1 subunit 1 (NAE1) to regulate protein neddylation. CONCLUSION This study reports for the first time that CYP1B1-AS1 inhibits protein neddylation to affect breast cancer cell proliferation, which provides a new strategy for the treatment of breast cancer by lncRNA targeting neddylation modification.
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Affiliation(s)
- Li Tang
- Department of Clinical Laboratory, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and the Affiliated Cancer Hospital of Nanjing Medical University, No. 42 Baiziting Road, Nanjing, 210009, People's Republic of China.
| | - Da Wei
- Department of Surgery, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and the Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, 210009, People's Republic of China
| | - Xinyu Xu
- Department of Pathology, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and the Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, 210009, People's Republic of China
| | - Dongping Mo
- Department of Clinical Laboratory, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and the Affiliated Cancer Hospital of Nanjing Medical University, No. 42 Baiziting Road, Nanjing, 210009, People's Republic of China
| | - Daofu Cheng
- Department of Clinical Laboratory, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and the Affiliated Cancer Hospital of Nanjing Medical University, No. 42 Baiziting Road, Nanjing, 210009, People's Republic of China
| | - Feng Yan
- Department of Clinical Laboratory, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research and the Affiliated Cancer Hospital of Nanjing Medical University, No. 42 Baiziting Road, Nanjing, 210009, People's Republic of China.
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Liu H, Shih YH, Wang WL, Chang WL, Wang YC. UBE1C is upregulated and promotes neddylation of p53 in lung cancer. FASEB J 2023; 37:e23181. [PMID: 37668436 DOI: 10.1096/fj.202300629r] [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: 04/02/2023] [Revised: 07/24/2023] [Accepted: 08/23/2023] [Indexed: 09/06/2023]
Abstract
NEDDylation is a type of protein post-translational modification that has high similarity to ubiquitination. UBE1C encodes NEDDylation E1 enzyme, locates at chromatin region 3p14.1 and shows high gene dosage amplification frequency in both Asian and Caucasian lung cancer patients. However, its NEDDylation substrates and roles in tumorigenesis remain elucidated. In this study, we aim to investigate the oncogenic role of UBE1C and its involvement in how NEDDylation regulates p53 in lung cancer. We found that UBE1C mRNA overexpression and DNA amplification in most of the lung cell lines and cancer patients. Patients with UBE1C overexpression showed poor prognosis. Moreover, we demonstrated that overexpression of UBE1C and NEDD8, a NEDDylation moiety, resulted in the p53 NEDDylation with inhibition of p53 acetylation at K373 residue. Importantly, UBE1C-mediated NEDDylation downregulated the transcriptional activity of p53 by inhibiting p53 ability to target promoter regions of its downstream transcription targets, consequently inhibiting the promoter activities and the expression of mRNA and protein of the p53 downstream genes including p21 and PTEN. In addition, UBE1C and NEDD8 overexpression promoted migration, invasion, and proliferation of lung cancer cells. Our findings suggest that UBE1C acts as an oncogene with prognostic potential and highlight a potential role of UBE1C-mediated NEDDylation in downregulation of p53 transcriptional activity in lung cancer.
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Affiliation(s)
- Hsun Liu
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yung-Hsin Shih
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wen-Lun Wang
- Department of Internal Medicine, E-Da Hospital, I-Shou University, Kaohsiung, Taiwan
- School of Medicine, College of Medicine, I-Shou University, Kaohsiung, Taiwan
| | - Wei-Lun Chang
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yi-Ching Wang
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Institute of Basic Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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7
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Lin X, Yang S, Zhou C, Ao C, Sun D. The NEDD8-activating enzyme E1 UBA3 orchestrates the immunosuppressive microenvironment in lung adenocarcinoma via the NF-кB pathway. Med Oncol 2023; 40:286. [PMID: 37656220 PMCID: PMC10474176 DOI: 10.1007/s12032-023-02162-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 08/14/2023] [Indexed: 09/02/2023]
Abstract
Immunosuppressive cells play important roles in generating an immunosuppressive tumor microenvironment and facilitating tumor immune escape. However, the molecular mechanisms underlying their immunosuppressive effects remain unclear. UBA3, the sole catalytic subunit of the neural precursor cell expressed developmentally down-regulated protein 8 (NEDD8)-activating enzyme E1, is highly expressed in various human malignancies, along with an activated neddylation pathway. In this study, we investigated the relationships between the UBA3-dependent neddylation pathway and the infiltration of several immunosuppressive cell populations in lung adenocarcinoma (LUAD). We explored the regulatory mechanisms of UBA3 in LUAD cells by using mRNA sequencing and functional enrichment analyses. Correlations between neddylation and immune infiltrates were assessed by Western blotting, real-time PCR, and analyses of public databases. We found elevated levels of UBA3 expression in LUAD tissues compared to adjacent normal tissues. Blocking UBA3 and the neddylation pathway promoted the accumulation of the phosphorylated nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor (p-IκBα), inhibiting the gene expression of tumor cell-derived cytokines such as C-C motif chemokine ligand (CCL) 2, C-X-C motif ligand (CXCL)1, CXCL2, colony-stimulating factor (CSF) 1, CSF2 interleukin (IL)-6, and IL-1B. Moreover, the overexpression of UBA3 in LUAD cells was associated with the secretion of these cytokines, and the recruitment and infiltration of immunosuppressive cells including tumor-associated macrophages (TAMs), plasmacytoid dendritic cells (pDCs), Th2 cells and T-regulatory cells (Tregs). This could facilitate the tumor immune escape and malignant progression of LUAD. Our findings provide new insights into the role of UBA3 in establishing an immunosuppressive tumor microenvironment by modulating nuclear factor kappa B (NF-кB) signaling and the neddylation pathway.
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Affiliation(s)
- Xiongzhi Lin
- Taizhou Central Hospital (Taizhou University Hospital), Taizhou University, Taizhou, Zhejiang, China
- Graduate School of Medicine, Hebei North University, Zhangjiakou, Hebei, China
| | - Shuhan Yang
- Taizhou Central Hospital (Taizhou University Hospital), Taizhou University, Taizhou, Zhejiang, China
- Medical School, Taizhou University, Taizhou, Zhejiang, China
| | - Caichuan Zhou
- Taizhou Central Hospital (Taizhou University Hospital), Taizhou University, Taizhou, Zhejiang, China
- Medical School, Taizhou University, Taizhou, Zhejiang, China
| | - Chengcheng Ao
- Taizhou Central Hospital (Taizhou University Hospital), Taizhou University, Taizhou, Zhejiang, China
- Medical School, Taizhou University, Taizhou, Zhejiang, China
| | - Dongsheng Sun
- Medical School, Taizhou University, Taizhou, Zhejiang, China.
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8
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Muffels IJ, Schene IF, Rehmann H, Massink MP, van der Wal MM, Bauder C, Labeur M, Armando NG, Lequin MH, Houben ML, Giltay JC, Haitjema S, Huisman A, Vansenne F, Bluvstein J, Pappas J, Shailee LV, Zarate YA, Mokry M, van Haaften GW, Nieuwenhuis EE, Refojo D, van Wijk F, Fuchs SA, van Hasselt PM. Bi-allelic variants in NAE1 cause intellectual disability, ischiopubic hypoplasia, stress-mediated lymphopenia and neurodegeneration. Am J Hum Genet 2023; 110:146-160. [PMID: 36608681 PMCID: PMC9892777 DOI: 10.1016/j.ajhg.2022.12.003] [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: 02/09/2022] [Accepted: 12/07/2022] [Indexed: 01/07/2023] Open
Abstract
Neddylation has been implicated in various cellular pathways and in the pathophysiology of numerous diseases. We identified four individuals with bi-allelic variants in NAE1, which encodes the neddylation E1 enzyme. Pathogenicity was supported by decreased NAE1 abundance and overlapping clinical and cellular phenotypes. To delineate how cellular consequences of NAE1 deficiency would lead to the clinical phenotype, we focused primarily on the rarest phenotypic features, based on the assumption that these would best reflect the pathophysiology at stake. Two of the rarest features, neuronal loss and lymphopenia worsening during infections, suggest that NAE1 is required during cellular stress caused by infections to protect against cell death. In support, we found that stressing the proteasome system with MG132-requiring upregulation of neddylation to restore proteasomal function and proteasomal stress-led to increased cell death in fibroblasts of individuals with NAE1 genetic variants. Additionally, we found decreased lymphocyte counts after CD3/CD28 stimulation and decreased NF-κB translocation in individuals with NAE1 variants. The rarest phenotypic feature-delayed closure of the ischiopubic rami-correlated with significant downregulation of RUN2X and SOX9 expression in transcriptomic data of fibroblasts. Both genes are involved in the pathophysiology of ischiopubic hypoplasia. Thus, we show that NAE1 plays a major role in (skeletal) development and cellular homeostasis during stress. Our approach suggests that a focus on rare phenotypic features is able to provide significant pathophysiological insights in diseases caused by mutations in genes with pleiotropic effects.
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Affiliation(s)
- Irena J.J. Muffels
- Department of Metabolic Diseases, Division Pediatrics, Wilhelmina Children’s Hospital University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, the Netherlands,Center for Translational Immunology (CTI), Division Pediatrics, Wilhelmina Children’s Hospital University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Imre F. Schene
- Department of Metabolic Diseases, Division Pediatrics, Wilhelmina Children’s Hospital University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, the Netherlands
| | - Holger Rehmann
- Department of Energy and Biotechnology, Flensburg University of Applied Sciences, Flensburg, Germany
| | - Maarten P.G. Massink
- Department of Genetics, Division Pediatrics, Wilhelmina Children’s Hospital University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Maria M. van der Wal
- Center for Translational Immunology (CTI), Division Pediatrics, Wilhelmina Children’s Hospital University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Corinna Bauder
- Department of Neuroendocrinology, Max Planck Institute of Psychiatry, Munich, Germany,Institute of Developmental Genetics, Helmholtz Zentrum München, Munich, Germany
| | - Martha Labeur
- Department of Neuroendocrinology, Max Planck Institute of Psychiatry, Munich, Germany
| | - Natalia G. Armando
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Buenos Aires, Argentina
| | - Maarten H. Lequin
- Division Imaging and Oncology University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Michiel L. Houben
- Department of General Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Jaques C. Giltay
- Department of Genetics, Division Pediatrics, Wilhelmina Children’s Hospital University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Saskia Haitjema
- Central Diagnostics Laboratory, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Albert Huisman
- Central Diagnostics Laboratory, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Fleur Vansenne
- Department of Medical Genetics, University Medical Center Groningen, Groningen, the Netherlands
| | - Judith Bluvstein
- Dravet Center and Comprehensive Epilepsy Center, NYU School of Medicine, New York, NY, USA
| | - John Pappas
- NYU Clinical Genetic Services, NYU Grossman School of Medicine, New York, NY, USA
| | - Lala V. Shailee
- Department of Radiology, NYU Grossman School of Medicine, New York, NY, USA
| | - Yuri A. Zarate
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Michal Mokry
- Laboratory of Experimental Cardiology, Department of Cardiology, University Medical Center Utrecht, University of Utrecht, Utrecht, the Netherlands
| | - Gijs W. van Haaften
- Department of Genetics, Division Laboratories, Pharmacy and Biomedical Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Edward E.S. Nieuwenhuis
- Department of Biomedical and Life Sciences, University College Roosevelt, Middelburg, the Netherlands
| | - Damian Refojo
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Buenos Aires, Argentina,Molecular Neurobiology, Max Planck Institute of Psychiatry, Munich, Germany
| | - Femke van Wijk
- Department of Genetics, Division Pediatrics, Wilhelmina Children’s Hospital University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Sabine A. Fuchs
- Department of Metabolic Diseases, Division Pediatrics, Wilhelmina Children’s Hospital University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, the Netherlands
| | - Peter M. van Hasselt
- Department of Metabolic Diseases, Division Pediatrics, Wilhelmina Children’s Hospital University Medical Center Utrecht, Utrecht University, 3584 EA Utrecht, the Netherlands,Corresponding author
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9
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Recasens-Zorzo C, Gâtel P, Brockly F, Bossis G. A Microbead-Based Flow Cytometry Assay to Assess the Activity of Ubiquitin and Ubiquitin-Like Conjugating Enzymes. Methods Mol Biol 2023; 2602:65-79. [PMID: 36446967 DOI: 10.1007/978-1-0716-2859-1_5] [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: 06/16/2023]
Abstract
The peptidic posttranslational modifiers of the ubiquitin (Ub) family (ubiquitin-like, UbLs) are conjugated to thousands of proteins to modify their function and fate. Dysregulation of their conjugation/deconjugation pathways is associated with a variety of pathological disorders. However, the techniques currently available to monitor the levels of target modification by UbLs as well as the activity of UbL-conjugating enzymes are limited and generally not quantitative. Here, we describe a microbead-based flow cytometry assay to accurately quantify UbL conjugation activity. It measures the capacity of UbL-conjugating enzymes, either purified or present in cell extracts, to transfer their respective UbL onto target substrates immobilized on color-coded microbeads. Although this protocol describes its use to study protein modification by Ub, SUMO-1 to SUMO-3, and NEDD8, this assay may be applicable to investigating conjugation of any other UbLs. It should therefore prove a precious tool for both screening UbL-conjugating enzymes inhibitors and following UbL pathway dysregulations in both physiological and pathological settings.
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Affiliation(s)
- Clara Recasens-Zorzo
- IGMM, University of Montpellier, CNRS, Montpellier, France
- Equipe labellisée Ligue contre le Cancer, Paris, France
| | - Pierre Gâtel
- IGMM, University of Montpellier, CNRS, Montpellier, France
- Equipe labellisée Ligue contre le Cancer, Paris, France
| | - Frédérique Brockly
- IGMM, University of Montpellier, CNRS, Montpellier, France
- Equipe labellisée Ligue contre le Cancer, Paris, France
| | - Guillaume Bossis
- IGMM, University of Montpellier, CNRS, Montpellier, France.
- Equipe labellisée Ligue contre le Cancer, Paris, France.
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10
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Liang Q, Liu M, Li J, Tong R, Hu Y, Bai L, Shi J. NAE modulators: A potential therapy for gastric carcinoma. Eur J Med Chem 2022; 231:114156. [DOI: 10.1016/j.ejmech.2022.114156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 01/15/2022] [Accepted: 01/24/2022] [Indexed: 12/24/2022]
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Discovery of a cinnamyl piperidine derivative as new neddylation inhibitor for gastric cancer treatment. Eur J Med Chem 2021; 226:113896. [PMID: 34624825 DOI: 10.1016/j.ejmech.2021.113896] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/20/2021] [Accepted: 09/30/2021] [Indexed: 11/19/2022]
Abstract
Targeting neddylation pathway has been recognized as an attractive anticancer therapeutic strategy, thus discovering potent and selective neddylation inhibitors is highly desirable. Our work reported the discovery of novel cinnamyl piperidine compounds and their antitumor activity in vitro and in vivo. Among these compounds, compound 4g was identified as a novel neddylation inhibitor and decreased the neddylation levels of cullin 1, cullin 3 and cullin 5. Mechanistic studies demonstrated that compound 4g could inhibit the migration ability of gastric cancer cells and induce apoptosis partly mediated by the Nrf2-Keap1 pathway. Furthermore, in vivo anti-tumor studies showed that 4g effectively inhibited tumor growth without obvious toxicity. Collectively, the cinnamyl piperidine derivatives could serve as new lead compounds for developing highly effective neddylation inhibitors for gastric cancer therapy.
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Mutational signatures in GATA3 transcription factor and its DNA binding domain that stimulate breast cancer and HDR syndrome. Sci Rep 2021; 11:22762. [PMID: 34815386 PMCID: PMC8611019 DOI: 10.1038/s41598-021-01832-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/14/2021] [Indexed: 11/08/2022] Open
Abstract
Transcription factors (TFs) play important roles in many biochemical processes. Many human genetic disorders have been associated with mutations in the genes encoding these transcription factors, and so those mutations became targets for medications and drug design. In parallel, since many transcription factors act either as tumor suppressors or oncogenes, their mutations are mostly associated with cancer. In this perspective, we studied the GATA3 transcription factor when bound to DNA in a crystal structure and assessed the effect of different mutations encountered in patients with different diseases and phenotypes. We generated all missense mutants of GATA3 protein and DNA within the adjacent and the opposite GATA3:DNA complex models. We mutated every amino acid and studied the new binding of the complex after each mutation. Similarly, we did for every DNA base. We applied Poisson-Boltzmann electrostatic calculations feeding into free energy calculations. After analyzing our data, we identified amino acids and DNA bases keys for binding. Furthermore, we validated those findings against experimental genetic data. Our results are the first to propose in silico modeling for GATA:DNA bound complexes that could be used to score effects of missense mutations in other classes of transcription factors involved in common and genetic diseases.
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Zhao M, Zhang Y, Yang X, Jin J, Shen Z, Feng X, Zou T, Deng L, Cheng D, Zhang X, Qin C, Niu C, Ye Z, Zhang X, He J, Hou C, Li G, Han G, Cheng Q, Wang Q, Wei L, Dong J, Zhang J. Myeloid neddylation targets IRF7 and promotes host innate immunity against RNA viruses. PLoS Pathog 2021; 17:e1009901. [PMID: 34506605 PMCID: PMC8432861 DOI: 10.1371/journal.ppat.1009901] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 08/16/2021] [Indexed: 12/03/2022] Open
Abstract
Neddylation, an important type of post-translational modification, has been implicated in innate and adapted immunity. But the role of neddylation in innate immune response against RNA viruses remains elusive. Here we report that neddylation promotes RNA virus-induced type I IFN production, especially IFN-α. More importantly, myeloid deficiency of UBA3 or NEDD8 renders mice less resistant to RNA virus infection. Neddylation is essential for RNA virus-triggered activation of Ifna gene promoters. Further exploration has revealed that mammalian IRF7undergoes neddylation, which is enhanced after RNA virus infection. Even though neddylation blockade does not hinder RNA virus-triggered IRF7 expression, IRF7 mutant defective in neddylation exhibits reduced ability to activate Ifna gene promoters. Neddylation blockade impedes RNA virus-induced IRF7 nuclear translocation without hindering its phosphorylation and dimerization with IRF3. By contrast, IRF7 mutant defective in neddylation shows enhanced dimerization with IRF5, an Ifna repressor when interacting with IRF7. In conclusion, our data demonstrate that myeloid neddylation contributes to host anti-viral innate immunity through targeting IRF7 and promoting its transcriptional activity. With the features of high mutation rates and fast propagation, RNA viruses remain a great challenge for the control and prevention of epidemic. Better understanding of the molecular mechanisms involved in host innate immunity against RNA viruses will facilitate the development of anti-viral drugs and vaccines. Neddylation has been implicated in innate and adapted immunity. But the role of neddylation in RNA virus-triggered type I IFN production remains elusive. Here, using mouse models with myeloid deficiency of UBA3 or NEDD8, we report for the first time that neddylation contributes to innate immunity against RNA viruses in mammals. Neddylation is indispensable for RNA virus-induced IFN-α production although its role in IFN-β production is much blunted in macrophages. In mechanism, neddylation directly targets IRF7 and enhances its transcriptional activity through, at least partially, promoting its nuclear translocation and preventing its dimerization with IRF5, an Ifna repressor when interacting with IRF7. Our study provides insight into the regulation of IRF7 and innate immune signaling.
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Affiliation(s)
- Min Zhao
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Yaolin Zhang
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Xiqin Yang
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Jiayang Jin
- Beijing Institute of Basic Medical Sciences, Beijing, China
- Department of Pathogen Biology, Hebei Medical University, Shijiazhuang, Hebei, China
| | - Zhuo Shen
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Xiaoyao Feng
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Tao Zou
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Lijiao Deng
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Daohai Cheng
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Xueting Zhang
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Cheng Qin
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Chunxiao Niu
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Zhenjie Ye
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Xueying Zhang
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Jia He
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Chunmei Hou
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Ge Li
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Gencheng Han
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Qianqian Cheng
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Qingyang Wang
- Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Lin Wei
- Department of Pathogen Biology, Hebei Medical University, Shijiazhuang, Hebei, China
- * E-mail: (LW); (JD); (JZ)
| | - Jie Dong
- Beijing Institute of Basic Medical Sciences, Beijing, China
- * E-mail: (LW); (JD); (JZ)
| | - Jiyan Zhang
- Beijing Institute of Basic Medical Sciences, Beijing, China
- Chinese Institute for Brain Research, Beijing, China
- * E-mail: (LW); (JD); (JZ)
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Zheng YC, Guo YJ, Wang B, Wang C, Mamun MAA, Gao Y, Liu HM. Targeting neddylation E2s: a novel therapeutic strategy in cancer. J Hematol Oncol 2021; 14:57. [PMID: 33827629 PMCID: PMC8028724 DOI: 10.1186/s13045-021-01070-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/29/2021] [Indexed: 12/22/2022] Open
Abstract
Ubiquitin-conjugating enzyme E2 M (UBE2M) and ubiquitin-conjugating enzyme E2 F (UBE2F) are the two NEDD8-conjugating enzymes of the neddylation pathway that take part in posttranslational modification and change the activity of target proteins. The activity of E2 enzymes requires both a 26-residue N-terminal docking peptide and a conserved E2 catalytic core domain, which is the basis for the transfer of neural precursor cell-expressed developmentally downregulated 8 (NEDD8). By recruiting E3 ligases and targeting cullin and non-cullin substrates, UBE2M and UBE2F play diverse biological roles. Currently, there are several inhibitors that target the UBE2M-defective in cullin neddylation protein 1 (DCN1) interaction to treat cancer. As described above, this review provides insights into the mechanism of UBE2M and UBE2F and emphasizes these two E2 enzymes as appealing therapeutic targets for the treatment of cancers.
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Affiliation(s)
- Yi-Chao Zheng
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, Henan, China
| | - Yan-Jia Guo
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, Henan, China
| | - Bo Wang
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, Henan, China
| | - Chong Wang
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - M A A Mamun
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, Henan, China
| | - Ya Gao
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, Henan, China.
| | - Hong-Min Liu
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, Institute of Drug Discovery and Development, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, Henan, China.
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