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Zhao X, Ni W, Zheng W, Ni W, Sun C, Gu Y, Gu Z. Multi-regulatory potency of USP1 on inflammasome components promotes pyroptosis in thyroid follicular cells and contributes to the progression of Hashimoto's thyroiditis. Mol Med 2024; 30:121. [PMID: 39134949 PMCID: PMC11318162 DOI: 10.1186/s10020-024-00885-w] [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: 02/12/2024] [Accepted: 07/22/2024] [Indexed: 08/16/2024] Open
Abstract
BACKGROUND Inflammatory diseases are often initiated by the activation of inflammasomes triggered by pathogen-associated molecular patterns (PAMPs) and endogenous damage-associated molecular patterns (DAMPs), which mediate pyroptosis. Although pyroptosis resulting from aberrant inflammasome triggering in thyroid follicular cells (TFCs) has been observed in Hashimoto's thyroiditis (HT) patients, the underlying mechanisms remain largely unknown. Given the extensive involvement of protein ubiquitination and deubiquitination in inflammatory diseases, we aimed to investigate how deubiquitinating enzymes regulate thyroid follicular cell pyroptosis and HT pathogenesis. METHODS Our study specifically investigated the role of Ubiquitin-specific peptidase 1 (USP1), a deubiquitinase (DUB), in regulating the inflammasome components NLRP3 and AIM2, which are crucial in pyroptosis. We conducted a series of experiments to elucidate the function of USP1 in promoting pyroptosis associated with inflammasomes and the progression of HT. These experiments involved techniques such as USP1 knockdown or inhibition, measurement of key pyroptosis indicators including caspase-1, caspase-1 p20, and GSDMD-N, and examination of the effects of USP1 abrogation on HT using a mouse model. Furthermore, we explored the impact of USP1 on NLRP3 transcription and its potential interaction with p65 nuclear transportation. RESULTS Our findings provide compelling evidence indicating that USP1 plays a pivotal role in promoting inflammasome-mediated pyroptosis and HT progression by stabilizing NLRP3 and AIM2 through deubiquitination. Furthermore, we discovered that USP1 modulates the transcription of NLRP3 by facilitating p65 nuclear transportation. Knockdown or inhibition of USP1 resulted in weakened cell pyroptosis, as evidenced by reduced levels of caspase-1 p20 and GSDMD-N, which could be restored upon AIM2 overexpression. Remarkably, USP1 abrogation significantly ameliorated HT in the mice model, likely to that treating mice with pyroptosis inhibitors VX-765 and disulfiram. CONCLUSIONS Our study highlights a regulatory mechanism of USP1 on inflammasome activation and pyroptosis in TFCs during HT pathogenesis. These findings expand our understanding of HT and suggest that inhibiting USP1 may be a potential treatment strategy for managing HT.
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Affiliation(s)
- Xuying Zhao
- Dalian Medical University, Dalian, Liaoning, China
- Department of Endocrinology and Metabolism, Affiliated Hospital of Nantong University, No. 20 Xisi Road, Nantong, 226001, Jiangsu, China
| | - Wenyu Ni
- Department of Endocrinology and Metabolism, Qidong People's Hospital, Nantong, Jiangsu, China
| | - Wenjie Zheng
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Wenkai Ni
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Chunfeng Sun
- Department of Nuclear Medicine, Affiliated Hospital of Nantong University, No. 20 Xisi Road, Nantong, 226001, Jiangsu, China.
| | - Yunjuan Gu
- Department of Endocrinology and Metabolism, Affiliated Hospital of Nantong University, No. 20 Xisi Road, Nantong, 226001, Jiangsu, China.
| | - Zhifeng Gu
- Dalian Medical University, Dalian, Liaoning, China.
- Department of Rheumatology, Affiliated Hospital of Nantong University, No. 20 Xisi Road, Nantong, 226001, Jiangsu, China.
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2
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van der Laan L, ten Voorde N, Mannens MMAM, Henneman P. Molecular signatures in Mendelian neurodevelopment: a focus on ubiquitination driven DNA methylation aberrations. Front Mol Neurosci 2024; 17:1446686. [PMID: 39135741 PMCID: PMC11317395 DOI: 10.3389/fnmol.2024.1446686] [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: 06/17/2024] [Accepted: 07/17/2024] [Indexed: 08/15/2024] Open
Abstract
Mendelian disorders, arising from pathogenic variations within single genetic loci, often manifest as neurodevelopmental disorders (NDDs), affecting a significant portion of the pediatric population worldwide. These disorders are marked by atypical brain development, intellectual disabilities, and various associated phenotypic traits. Genetic testing aids in clinical diagnoses, but inconclusive results can prolong confirmation processes. Recent focus on epigenetic dysregulation has led to the discovery of DNA methylation signatures, or episignatures, associated with NDDs, accelerating diagnostic precision. Notably, TRIP12 and USP7, genes involved in the ubiquitination pathway, exhibit specific episignatures. Understanding the roles of these genes within the ubiquitination pathway sheds light on their potential influence on episignature formation. While TRIP12 acts as an E3 ligase, USP7 functions as a deubiquitinase, presenting contrasting roles within ubiquitination. Comparison of phenotypic traits in patients with pathogenic variations in these genes reveals both distinctions and commonalities, offering insights into underlying pathophysiological mechanisms. This review contextualizes the roles of TRIP12 and USP7 within the ubiquitination pathway, their influence on episignature formation, and the potential implications for NDD pathogenesis. Understanding these intricate relationships may unveil novel therapeutic targets and diagnostic strategies for NDDs.
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Affiliation(s)
- Liselot van der Laan
- Department of Human Genetics, Amsterdam UMC, Amsterdam, Netherlands
- Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Nicky ten Voorde
- Department of Human Genetics, Amsterdam UMC, Amsterdam, Netherlands
| | - Marcel M. A. M. Mannens
- Department of Human Genetics, Amsterdam UMC, Amsterdam, Netherlands
- Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Peter Henneman
- Department of Human Genetics, Amsterdam UMC, Amsterdam, Netherlands
- Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
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3
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Zheng LL, Wang LT, Pang YW, Sun LP, Shi L. Recent advances in the development of deubiquitinases inhibitors as antitumor agents. Eur J Med Chem 2024; 266:116161. [PMID: 38262120 DOI: 10.1016/j.ejmech.2024.116161] [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: 11/01/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/25/2024]
Abstract
Ubiquitination is a type of post-translational modification that covalently links ubiquitin to a target protein, which plays a critical role in modulating protein activity, stability, and localization. In contrast, this process is reversed by deubiquitinases (DUBs), which remove ubiquitin from ubiquitinated substrates. Dysregulation of DUBs is associated with several human diseases, such as cancer, inflammation, neurodegenerative disorders, and autoimmune diseases. Thus, DUBs have become promising targets for drug development. Although the physiological and pathological effects of DUBs are increasingly well understood, the clinical drug discovery of selective DUB inhibitors has been challenging. Herein, we summarize the structures and functions of main classes of DUBs and discuss the recent progress in developing selective small-molecule DUB inhibitors as antitumor agents.
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Affiliation(s)
- Li-Li Zheng
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Li-Ting Wang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Ye-Wei Pang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Li-Ping Sun
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
| | - Lei Shi
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
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4
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Yuan D, Shen H, Bai L, Li M, Ye Q. Identification of Key Ubiquitination-Related Genes and Their Association with Immune Infiltration in Osteoarthritis Based on the mRNA-miRNA Network. Crit Rev Immunol 2024; 44:91-102. [PMID: 38505924 DOI: 10.1615/critrevimmunol.2024051440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Osteoarthritis (OA) is a prevalent degenerative joint disease that is closely associated with functions of ubiquitination and immune cells, yet the mechanism remains ambiguous. This study aimed to find core ubiquitination-related genes and their correlative immune infiltration in OA using weighted gene co-expression network analysis (WGCNA). The ubiquitination-related genes, datasets GSE55235 and GSE143514 were obtained from open databases. WGCNA got used to investigate key co-expressed genes. Then, we screened differentially expressed miRNAs by "limma" package in R, and constructed mRNA-miRNA network. We conducted function enrichment analysis on the identified genes. CIBERSORT was then utilized to analyze the relevance between immune infiltration and genes. Lastly, RT-qPCR was further used to verify the prediction of bioinformatics. A sum of 144 ubiquitination-related genes in OA were acquired. Enrichment analysis indicated that obtained genes obviously involved in mTOR pathway to regulate the OA development. GRB2 and SEH1L and L-arginine synergistically regulate the mTOR signaling pathway in OA. Moreover, GRB2 and SEH1L were remarkably bound up with immune cell infiltration. Additionally, GRB2 expression was upregulated and SEH1L level was downregulated in the OA development by RT-qPCR experiment. The present study identified GRB2 and SEH1L as key ubiquitination-related genes which were involved in immune infiltration in OA patients, thereby providing new drug targets for OA.
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Affiliation(s)
- Dalu Yuan
- Department of Rehabilitation Treatment Center, Affiliated Hospital of Shaoxing University (The Shaoxing Municipal Hospital), Shaoxing, Zhejiang, China
| | - Hailiang Shen
- Department of Orthopedics, Affiliated Hospital of Shaoxing University (The Shaoxing Municipal Hospital), Shaoxing, Zhejiang, China
| | - Lina Bai
- Department of Rehabilitation Treatment Center, Affiliated Hospital of Shaoxing University (The Shaoxing Municipal Hospital), Shaoxing, Zhejiang, China
| | - Menglin Li
- Department of Rehabilitation Treatment Center, Affiliated Hospital of Shaoxing University (The Shaoxing Municipal Hospital), Shaoxing, Zhejiang, China
| | - Qiujie Ye
- Affiliated Hospital of Shaoxing University (The Shaoxing Municipal Hospital)
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5
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Zheng C, Chen J, Wu Y, Wang X, Lin Y, Shu L, Liu W, Wang P. Elucidating the role of ubiquitination and deubiquitination in osteoarthritis progression. Front Immunol 2023; 14:1217466. [PMID: 37359559 PMCID: PMC10288844 DOI: 10.3389/fimmu.2023.1217466] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 06/01/2023] [Indexed: 06/28/2023] Open
Abstract
Osteoarthritis is non-inflammatory degenerative joint arthritis, which exacerbates disability in elder persons. The molecular mechanisms of osteoarthritis are elusive. Ubiquitination, one type of post-translational modifications, has been demonstrated to accelerate or ameliorate the development and progression of osteoarthritis via targeting specific proteins for ubiquitination and determining protein stability and localization. Ubiquitination process can be reversed by a class of deubiquitinases via deubiquitination. In this review, we summarize the current knowledge regarding the multifaceted role of E3 ubiquitin ligases in the pathogenesis of osteoarthritis. We also describe the molecular insight of deubiquitinases into osteoarthritis processes. Moreover, we highlight the multiple compounds that target E3 ubiquitin ligases or deubiquitinases to influence osteoarthritis progression. We discuss the challenge and future perspectives via modulation of E3 ubiquitin ligases and deubiquitinases expression for enhancement of the therapeutic efficacy in osteoarthritis patients. We conclude that modulating ubiquitination and deubiquitination could alleviate the osteoarthritis pathogenesis to achieve the better treatment outcomes in osteoarthritis patients.
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Affiliation(s)
- Chenxiao Zheng
- Department of Orthopaedics and Traumatology, Zhongshan Hospital of Traditional Chinese Medicine Affiliated to Guangzhou University of Traditional Chinese Medicine, Zhongshan, Guangdong, China
| | - Jiayi Chen
- Department of Orthopaedics and Traumatology, Zhongshan Hospital of Traditional Chinese Medicine Affiliated to Guangzhou University of Traditional Chinese Medicine, Zhongshan, Guangdong, China
| | - Yurui Wu
- Department of Orthopaedics and Traumatology, Zhongshan Hospital of Traditional Chinese Medicine Affiliated to Guangzhou University of Traditional Chinese Medicine, Zhongshan, Guangdong, China
| | - Xiaochao Wang
- Department of Orthopaedics, The Second Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Yongan Lin
- South China University of Technology, Guangzhou, Guangdong, China
| | - Lilu Shu
- Department of Medicine, Zhejiang Zhongwei Medical Research Center, Hangzhou, Zhejiang, China
| | - Wenjun Liu
- Department of Medicine, Zhejiang Zhongwei Medical Research Center, Hangzhou, Zhejiang, China
| | - Peter Wang
- Department of Medicine, Zhejiang Zhongwei Medical Research Center, Hangzhou, Zhejiang, China
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McClary WD, Catala A, Zhang W, Gamboni F, Dzieciatkowska M, Sidhu SS, D'Alessandro A, Catalano CE. A Designer Nanoparticle Platform for Controlled Intracellular Delivery of Bioactive Macromolecules: Inhibition of Ubiquitin-Specific Protease 7 in Breast Cancer Cells. ACS Chem Biol 2022; 17:1853-1865. [PMID: 35796308 DOI: 10.1021/acschembio.2c00256] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Biological therapeutics represent an increasing and critical component of newly approved drugs; however, the inability to deliver biologics intracellularly in a controlled manner remains a major limitation. We have developed a semi-synthetic, tunable phage-like particle (PLP) platform derived from bacteriophage λ. The shell surface can be decorated with small-molecule, biological and synthetic moieties, alone or in combination and in defined ratios. Here, we demonstrate that the platform can be used to deliver biological macromolecules intracellularly and in a controlled manner. Ubiquitin-specific protease 7 (USP7) is a deubiquitinating enzyme that has been widely recognized as an ideal target for the treatment of a variety of cancers. Recently, UbV.7.2, a novel biologic derived from the ubiquitin scaffold, was developed for inhibition of USP7, but issues remain in achieving efficient and controlled intracellular delivery of the biologic. We have shown that decoration of PLPs with trastuzumab (Trz), a HER2-targeted therapeutic used in the treatment of various cancers, results in specific targeting and uptake of Trz-PLPs into HER2-overexpressing breast cancer cells. By simultaneously decorating PLPs with Trz and UbV.7.2, we now show that these particles are also internalized by HER2-positive cells, thus providing a means for intracellular delivery of the biologic in a controlled fashion. Internalized particles retain USP7 inhibition activity of UbV.7.2 and alter the metabolic and proteomic landscapes of these cells. This study demonstrates that the λ "designer nanoparticles" represent a powerful system for the intracellular delivery of biologics in a defined dose.
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Affiliation(s)
- Wynton D McClary
- The Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, Colorado 80045, United States
| | - Alexis Catala
- The Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, Colorado 80045, United States
| | - Wei Zhang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, ON N1G2W1, Canada.,Donnelly Centre for Cellular and Biomolecular Research and Department of Molecular Genetics, University of Toronto, Toronto, ON M5S3E1, Canada
| | - Fabia Gamboni
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, United States
| | - Monika Dzieciatkowska
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, United States
| | - Sachdev S Sidhu
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, ON N1G2W1, Canada.,Donnelly Centre for Cellular and Biomolecular Research and Department of Molecular Genetics, University of Toronto, Toronto, ON M5S3E1, Canada
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, United States.,Department of Medicine - Division of Hematology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, United States
| | - Carlos E Catalano
- The Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, Colorado 80045, United States
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7
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On the Study of Deubiquitinases: Using the Right Tools for the Job. Biomolecules 2022; 12:biom12050703. [PMID: 35625630 PMCID: PMC9139131 DOI: 10.3390/biom12050703] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 05/05/2022] [Accepted: 05/12/2022] [Indexed: 02/01/2023] Open
Abstract
Deubiquitinases (DUBs) have been the subject of intense scrutiny in recent years. Many of their diverse enzymatic mechanisms are well characterized in vitro; however, our understanding of these enzymes at the cellular level lags due to the lack of quality tool reagents. DUBs play a role in seemingly every biological process and are central to many human pathologies, thus rendering them very desirable and challenging therapeutic targets. This review aims to provide researchers entering the field of ubiquitination with knowledge of the pharmacological modulators and tool molecules available to study DUBs. A focus is placed on small molecule inhibitors, ubiquitin variants (UbVs), and activity-based probes (ABPs). Leveraging these tools to uncover DUB biology at the cellular level is of particular importance and may lead to significant breakthroughs. Despite significant drug discovery efforts, only approximately 15 chemical probe-quality small molecule inhibitors have been reported, hitting just 6 of about 100 DUB targets. UbV technology is a promising approach to rapidly expand the library of known DUB inhibitors and may be used as a combinatorial platform for structure-guided drug design.
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Liu P, Wu A, Li H, Zhang J, Ni J, Quan Z, Qing H. Rab21 Protein Is Degraded by Both the Ubiquitin-Proteasome Pathway and the Autophagy-Lysosome Pathway. Int J Mol Sci 2022; 23:ijms23031131. [PMID: 35163051 PMCID: PMC8835697 DOI: 10.3390/ijms23031131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/17/2022] [Accepted: 01/17/2022] [Indexed: 02/05/2023] Open
Abstract
Rab21 is a GTPase protein that is functional in intracellular trafficking and involved in the pathologies of many diseases, such as Alzheimer’s disease (AD), glioma, cancer, etc. Our previous work has reported its interaction with the catalytic subunit of gamma-secretase, PS1, and it regulates the activity of PS1 via transferring it from the early endosome to the late endosome/lysosome. However, it is still unknown how Rab21 protein itself is regulated. This work revealed that Rab21 protein, either endogenously or exogenously, can be degraded by the ubiquitin-proteasome pathway and the autophagy-lysosome pathway. It is further observed that the ubiquitinated Rab21 is increased, but the total protein is unchanged in AD model mice. We further observed that overexpression of Rab21 leads to increased expression of a series of genes involved in the autophagy-lysosome pathway. We speculated that even though the ubiquitinated Rab21 is increased due to the impaired proteasome function in the AD model, the autophagy-lysosome pathway functions in parallel to degrade Rab21 to keep its protein level in homeostasis. In conclusion, understanding the characters of Rab21 protein itself help explore its potential as a target for therapeutic strategy in diseases.
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