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Wang M, Yan X, Dong Y, Li X, Gao B. From driver genes to gene families: A computational analysis of oncogenic mutations and ubiquitination anomalies in hepatocellular carcinoma. Comput Biol Chem 2024; 112:108119. [PMID: 38852361 DOI: 10.1016/j.compbiolchem.2024.108119] [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: 03/19/2024] [Revised: 05/22/2024] [Accepted: 06/06/2024] [Indexed: 06/11/2024]
Abstract
Hepatocellular carcinoma (HCC) is a widespread primary liver cancer with a high fatality rate. Despite several genes with oncogenic effects in HCC have been identified, many remain undiscovered. In this study, we conducted a comprehensive computational analysis to explore the involvement of genes within the same families as known driver genes in HCC. Specifically, we expanded the concept beyond single-gene mutations to encompass gene families sharing homologous structures, integrating various omics data to comprehensively understand gene abnormalities in cancer. Our analysis identified 74 domains with an enriched mutation burden, 404 domain mutation hotspots, and 233 dysregulated driver genes. We observed that specific low-frequency somatic mutations may contribute to HCC occurrence, potentially overlooked by single-gene algorithms. Furthermore, we systematically analyzed how abnormalities in the ubiquitinated proteasome system (UPS) impact HCC, finding that abnormal genes in E3, E2, DUB families, and Degron genes often result in HCC by affecting the stability of oncogenic or tumor suppressor proteins. In conclusion, expanding the exploration of driver genes to include gene families with homologous structures emerges as a promising strategy for uncovering additional oncogenic alterations in HCC.
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Affiliation(s)
- Meng Wang
- Faculty of Environment and Life of Beijing University of Technology, Beijing 100124, China
| | - Xinyue Yan
- Faculty of Environment and Life of Beijing University of Technology, Beijing 100124, China
| | - Yanan Dong
- Faculty of Environment and Life of Beijing University of Technology, Beijing 100124, China
| | - Xiaoqin Li
- Faculty of Environment and Life of Beijing University of Technology, Beijing 100124, China.
| | - Bin Gao
- Faculty of Environment and Life of Beijing University of Technology, Beijing 100124, China
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Wang J, Wang Z, Zhang K, Cui Y, Zhou J, Liu J, Li H, Zhao M, Jiang J. The role of the ubiquitin system in the onset and reversal of neuropathic pain. Biomed Pharmacother 2024; 179:117127. [PMID: 39191026 DOI: 10.1016/j.biopha.2024.117127] [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: 05/21/2024] [Revised: 07/07/2024] [Accepted: 07/10/2024] [Indexed: 08/29/2024] Open
Abstract
Neuropathic pain (NP) remains one of the world's most difficult problems, and people suffering from NP have their quality of life affected to a great extent and constantly suffer from pain. Sensitization of injurious receptors, ectopic firing of afferent nerves after nerve injury, and coupling between sympathetic and sensory neurons are involved in the onset or development of NP, but the pathogenesis of NP is still not well understood. We found that the ubiquitin system is involved in the pathogenesis of NP and has a crucial role in it. The ubiquitin system can be involved in the onset or reversal of NP by affecting ion channels, cellular signal transduction, glial cells, and the regulation of non-coding RNAs. This provides new ideas for the treatment of NP. The ubiquitin system may be a new effective target for the treatment of NP. A continued, in-depth understanding of the mechanisms of the ubiquitin system involved in NP could further refine the study of analgesic targets and improve pharmacological studies.
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Affiliation(s)
- Jialin Wang
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Zhijing Wang
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Kexin Zhang
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yanping Cui
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Jingruo Zhou
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Jiazhou Liu
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Huanyi Li
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Mingxia Zhao
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Jingjing Jiang
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang, China.
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Soni U, Singh A, Soni R, Samanta SK, Varadwaj PK, Misra K. Identification of candidate target genes of oral squamous cell carcinoma using high-throughput RNA-Seq data and in silico studies of their interaction with naturally occurring bioactive compounds. J Biomol Struct Dyn 2024; 42:8024-8044. [PMID: 37526306 DOI: 10.1080/07391102.2023.2242515] [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: 02/13/2023] [Accepted: 07/25/2023] [Indexed: 08/02/2023]
Abstract
Oral Squamous Cell Carcinoma (OSCC) accounts for more than 90% of all kinds of oral neoplasms that develop in the oral cavity. It is a type of malignancy that shows high morbidity and recurrence rate, but data on the disease's target genes and biomarkers is still insufficient. In this study, in silico studies have been performed to find out the novel target genes and their potential therapeutic inhibitors for the effective and efficient treatment of OSCC. The DESeq2 package of RStudio was used in the current investigation to screen and identify differentially expressed genes for OSCC. As a result of gene expression analysis, the top 10 novel genes were identified using the Cytohubba plugin of Cytoscape, and among them, the ubiquitin-conjugating enzyme (UBE2D1) was found to be upregulated and playing a significant role in the progression of human oral cancers. Following this, naturally occurring compounds were virtually evaluated and simulated against the discovered novel target as prospective drugs utilizing the Maestro, Schrodinger, and Gromacs software. In a simulated screening of naturally occurring potential inhibitors against the novel target UBE2D1, Epigallocatechin 3-gallate, Quercetin, Luteoline, Curcumin, and Baicalein were identified as potent inhibitors. Novel identified gene UBE2D1 has a significant role in the proliferation of human cancers through suppression of 'guardian of genome' p53 via ubiquitination dependent pathway. Therefore, the treatment of OSCC may benefit significantly from targeting this gene and its discovered naturally occurring inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Unnati Soni
- Department of Applied Sciences, Indian Institute of Information Technology, Prayagraj, India
| | - Anirudh Singh
- Department of Applied Sciences, Indian Institute of Information Technology, Prayagraj, India
| | - Ramendra Soni
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, India
| | - Sintu Kumar Samanta
- Department of Applied Sciences, Indian Institute of Information Technology, Prayagraj, India
| | - Pritish Kumar Varadwaj
- Department of Applied Sciences, Indian Institute of Information Technology, Prayagraj, India
| | - Krishna Misra
- Department of Applied Sciences, Indian Institute of Information Technology, Prayagraj, India
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Lv P, Liu J, Liu X. The role of ubiquitin-conjugating enzyme in the process of spermatogenesis. Reprod Biol Endocrinol 2024; 22:110. [PMID: 39198846 PMCID: PMC11351103 DOI: 10.1186/s12958-024-01282-y] [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: 06/26/2024] [Accepted: 08/15/2024] [Indexed: 09/01/2024] Open
Abstract
The ubiquitination is crucial for controlling cellular homeostasis and protein modification, in which ubiquitin-conjugating enzyme (E2) acts as the central player in the ubiquitination system. Ubiquitin-conjugating enzymes, which have special domains that catalyse substrates, have sequence discrepancies and modulate various pathophysiological processes in different cells of multiple organisms. E2s take part in the mitosis of primordial germ cells, meiosis of spermatocytes and the formation of mature haploid spermatids to maintain normal male fertility. In this review, we summarize the various types of E2s and their functions during distinct stages of spermatogenesis.
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Affiliation(s)
- Peng Lv
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Institute of Andrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jihong Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- Institute of Andrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Xiaming Liu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- Institute of Andrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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Wen J, Wan L, Chen W, Dong X. The prognostic value of ubiquitin/ubiquitin-like-related genes along with immune cell infiltration and clinicopathological features in osteosarcoma. J Orthop Surg Res 2024; 19:356. [PMID: 38879525 PMCID: PMC11179372 DOI: 10.1186/s13018-024-04781-1] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/03/2024] [Indexed: 06/19/2024] Open
Abstract
BACKGROUND Ubiquitin/ubiquitin-like (Ub/UBL)-related genes have been reported to be associated with the survival of osteosarcoma patients but have not yet been systematically explored. METHODS The prognostic value of Ub/UBL-related genes, immune cell infiltration and clinicopathological features of patients were explored by Cox and LASSO regression analyses. A prognostic model was established and then validated in the GSE21257 dataset. The differential expression of hub genes in osteosarcoma was confirmed by qRT-PCR, western blotting and immunohistochemistry. RESULTS Tripartite Motif Containing 8 (TRIM8) and Ubiquitin Like With PHD And Ring Finger Domains 2 (UHRF2) were screened as genes with prognostic value in osteosarcoma. Kaplan-Meier analysis and scatter plots indicated that patients in the high gene significance score group tended to have a worse prognosis. The concordance index, calibration analysis and receiver operating characteristic analysis suggested that the model had good prediction accuracy and high sensitivity and specificity. Decision curve analysis revealed that patients could obtain greater net benefit from this model. Functional analyses of the differentially expressed genes indicated that they were involved in important functions and pathways. TRIM8 and UHRF2 were confirmed to be highly expressed in osteosarcoma cell lines and tissues. CONCLUSIONS TRIM8 and UHRF2 are potential prognostic genes in osteosarcoma, and these results provide insights into the roles of these genes and their implications for patient outcomes.
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Affiliation(s)
- Jian Wen
- Department of Pain Management, The 2nd Affiliated Hospital, Jiangxi Medical College, Nanchang University, No.1 Minde Road, Nanchang, 330006, Jiangxi, China
- JXHC Key Laboratory of Digital Orthopaedics, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, 152 Aiguo Road, Nanchang, 330006, Jiangxi, China
- Department of Orthopedics, Pingxiang People's Hospital, The Sixth Clinical College of Gannan Medical University, Pingxiang, 337000, China
| | - Lijia Wan
- Department of Child Healthcare, Hunan Provincial Maternal and Child Health Hospital, Changsha, 410008, Hunan, China
| | - Wenming Chen
- Department of Orthopedics, Pingxiang People's Hospital, The Sixth Clinical College of Gannan Medical University, Pingxiang, 337000, China.
| | - Xieping Dong
- JXHC Key Laboratory of Digital Orthopaedics, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, 152 Aiguo Road, Nanchang, 330006, Jiangxi, China.
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Roy S, Singh J, Ray SS. Weighted Combination of Łukasiewicz implication and Fuzzy Jaccard similarity in Hybrid Ensemble Framework (WCLFJHEF) for Gene Selection. Comput Biol Med 2024; 170:107981. [PMID: 38262204 DOI: 10.1016/j.compbiomed.2024.107981] [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: 07/25/2023] [Revised: 01/02/2024] [Accepted: 01/12/2024] [Indexed: 01/25/2024]
Abstract
A framework is developed for gene expression analysis by introducing fuzzy Jaccard similarity (FJS) and combining Łukasiewicz implication with it through weights in hybrid ensemble framework (WCLFJHEF) for gene selection in cancer. The method is called weighted combination of Łukasiewicz implication and fuzzy Jaccard similarity in hybrid ensemble framework (WCLFJHEF). While the fuzziness in Jaccard similarity is incorporated by using the existing Gödel fuzzy logic, the weights are obtained by maximizing the average F-score of selected genes in classifying the cancer patients. The patients are first divided into different clusters, based on the number of patient groups, using average linkage agglomerative clustering and a new score, called WCLFJ (weighted combination of Łukasiewicz implication and fuzzy Jaccard similarity). The genes are then selected from each cluster separately using filter based Relief-F and wrapper based SVMRFE (Support Vector Machine with Recursive Feature Elimination). A gene (feature) pool is created by considering the union of selected features for all the clusters. A set of informative genes is selected from the pool using sequential backward floating search (SBFS) algorithm. Patients are then classified using Naïve Bayes'(NB) and Support Vector Machine (SVM) separately, using the selected genes and the related F-scores are calculated. The weights in WCLFJ are then updated iteratively to maximize the average F-score obtained from the results of the classifier. The effectiveness of WCLFJHEF is demonstrated on six gene expression datasets. The average values of accuracy, F-score, recall, precision and MCC over all the datasets, are 95%, 94%, 94%, 94%, and 90%, respectively. The explainability of the selected genes is shown using SHapley Additive exPlanations (SHAP) values and this information is further used to rank them. The relevance of the selected gene set are biologically validated using the KEGG Pathway, Gene Ontology (GO), and existing literatures. It is seen that the genes that are selected by WCLFJHEF are candidates for genomic alterations in the various cancer types. The source code of WCLFJHEF is available at http://www.isical.ac.in/~shubhra/WCLFJHEF.html.
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Affiliation(s)
- Sukriti Roy
- Machine Intelligence Unit, Indian Statistical Institute, Kolkata 700108, India.
| | - Joginder Singh
- Center for Soft Computing Research, Indian Statistical Institute, Kolkata 700108, India.
| | - Shubhra Sankar Ray
- Machine Intelligence Unit, Indian Statistical Institute, Kolkata 700108, India; Center for Soft Computing Research, Indian Statistical Institute, Kolkata 700108, India.
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Pakjoo M, Ahmadi SE, Zahedi M, Jaafari N, Khademi R, Amini A, Safa M. Interplay between proteasome inhibitors and NF-κB pathway in leukemia and lymphoma: a comprehensive review on challenges ahead of proteasome inhibitors. Cell Commun Signal 2024; 22:105. [PMID: 38331801 PMCID: PMC10851565 DOI: 10.1186/s12964-023-01433-5] [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] [Received: 08/13/2023] [Accepted: 12/11/2023] [Indexed: 02/10/2024] Open
Abstract
The current scientific literature has extensively explored the potential role of proteasome inhibitors (PIs) in the NF-κB pathway of leukemia and lymphoma. The ubiquitin-proteasome system (UPS) is a critical component in regulating protein degradation in eukaryotic cells. PIs, such as BTZ, are used to target the 26S proteasome in hematologic malignancies, resulting in the prevention of the degradation of tumor suppressor proteins, the activation of intrinsic mitochondrial-dependent cell death, and the inhibition of the NF-κB signaling pathway. NF-κB is a transcription factor that plays a critical role in the regulation of apoptosis, cell proliferation, differentiation, inflammation, angiogenesis, and tumor migration. Despite the successful use of PIs in various hematologic malignancies, there are limitations such as resistant to these inhibitors. Some reports suggest that PIs can induce NF-κB activation, which increases the survival of malignant cells. This article discusses the various aspects of PIs' effects on the NF-κB pathway and their limitations. Video Abstract.
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Affiliation(s)
- Mahdi Pakjoo
- Department of Hematology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
- ATMP department, Breast cancer research center, Motamed cancer institute, ACECR, P.O. BOX:15179/64311, Tehran, Iran
| | - Seyed Esmaeil Ahmadi
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Zahedi
- Department of Medical Biotechnology, School of Allied Medicine, Student Research Committee, Iran University of Medical Sciences, Tehran, Iran
| | - Niloofar Jaafari
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Reyhane Khademi
- Thalassemia & Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ali Amini
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran.
| | - Majid Safa
- Department of Hematology and Blood Banking, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran.
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Rodriguez Tirado C, Wang C, Li X, Deng S, Gonzalez J, Johnson NA, Xu Y, Metang LA, Sundar Rajan M, Yang Y, Yin Y, Hofstad M, Raj GV, Zhang S, Lemoff A, He W, Fan J, Wang Y, Wang T, Mu P. UBE2J1 is the E2 ubiquitin-conjugating enzyme regulating androgen receptor degradation and antiandrogen resistance. Oncogene 2024; 43:265-280. [PMID: 38030789 PMCID: PMC10798893 DOI: 10.1038/s41388-023-02890-5] [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: 08/16/2023] [Revised: 10/27/2023] [Accepted: 11/07/2023] [Indexed: 12/01/2023]
Abstract
Prostate cancer (PCa) is primarily driven by aberrant Androgen Receptor (AR) signaling. Although there has been substantial advancement in antiandrogen therapies, resistance to these treatments remains a significant obstacle, often marked by continuous or enhanced AR signaling in resistant tumors. While the dysregulation of the ubiquitination-based protein degradation process is instrumental in the accumulation of oncogenic proteins, including AR, the molecular mechanism of ubiquitination-driven AR degradation remains largely undefined. We identified UBE2J1 as the critical E2 ubiquitin-conjugating enzyme responsible for guiding AR ubiquitination and eventual degradation. The absence of UBE2J1, found in 5-15% of PCa patients, results in disrupted AR ubiquitination and degradation. This disruption leads to an accumulation of AR proteins, promoting resistance to antiandrogen treatments. By employing a ubiquitination-based AR degrader to adeptly restore AR ubiquitination, we reestablished AR degradation and inhibited the proliferation of antiandrogen-resistant PCa tumors. These findings underscore the fundamental role of UBE2J1 in AR degradation and illuminate an uncharted mechanism through which PCa maintains heightened AR protein levels, fostering resistance to antiandrogen therapies.
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Affiliation(s)
| | - Choushi Wang
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Xiaoling Li
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Su Deng
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Julisa Gonzalez
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Nickolas A Johnson
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yaru Xu
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Lauren A Metang
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Medha Sundar Rajan
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yuqiu Yang
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yi Yin
- Department of Urology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Mia Hofstad
- Department of Urology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Ganesh V Raj
- Department of Urology, UT Southwestern Medical Center, Dallas, TX, USA
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
| | - Song Zhang
- Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, USA
| | - Andrew Lemoff
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX, USA
| | - Wei He
- Accutar Biotechnology, Inc., Wilmington, DE, USA
| | - Jie Fan
- Accutar Biotechnology, Inc., Wilmington, DE, USA
| | - Yunguan Wang
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | - Tao Wang
- Quantitative Biomedical Research Center, Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center, Dallas, TX, USA
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
| | - Ping Mu
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA.
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA.
- Hamon Center for Regenerative Science and Medicine, UT Southwestern Medical Center, Dallas, TX, USA.
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Mamun MAA, Liu S, Zhao L, Zhao L, Li ZR, Shen D, Zheng Y, Zheng YC, Liu HM. Micafungin: A promising inhibitor of UBE2M in cancer cell growth suppression. Eur J Med Chem 2023; 260:115732. [PMID: 37651876 DOI: 10.1016/j.ejmech.2023.115732] [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: 06/24/2023] [Revised: 08/08/2023] [Accepted: 08/15/2023] [Indexed: 09/02/2023]
Abstract
Neddylation is a protein modification process similar to ubiquitination, carried out through a series of activating (E1), conjugating (E2), and ligating (E3) enzymes. This process has been found to be overactive in various cancers, leading to increased oncogenic activities. Ubiquitin-conjugating enzyme 2 M (UBE2M) is one of two neddylation enzymes that play a vital role in this pathway. Studies have shown that targeting UBE2M in cancer treatment is crucial, as it regulates many molecular mechanisms like DNA damage, apoptosis, and cell proliferation. However, developing small molecule inhibitors against UBE2M remains challenging due to the lack of suitable druggable pockets. We have discovered that Micafungin, an antifungal agent that inhibits the production of 1,3-β-D-glucan in fungal cell walls, acts as a neddylation inhibitor that targets UBE2M. Biochemical studies reveal that Micafungin obstructs neddylation and stabilizes UBE2M. In cellular experiments, the drug was found to interact with UBE2M, prevent neddylation, accumulate cullin ring ligases (CRLs) substrates, reduce cell survival and migration, and induce DNA damage in gastric cancer cells. This research uncovers a new anti-cancer mechanism for Micafungin, paving the way for the development of a novel class of neddylation inhibitors that target UBE2M.
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Affiliation(s)
- M A A Mamun
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, China; XNA platform, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, China
| | - Shuan Liu
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, China; XNA platform, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, China
| | - Lijie Zhao
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, China; XNA platform, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, China
| | - Lijuan Zhao
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, China; XNA platform, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, China; State Key Laboratory of Esophageal Cancer Prevention and Treatment, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, China
| | - Zhong-Rui Li
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, China; XNA platform, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, China
| | - Dandan Shen
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China; Key Laboratory of Endometrial Disease Prevention and Treatment Zhengzhou China, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Yu Zheng
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, China; XNA platform, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, China
| | - Yi-Chao Zheng
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, China; XNA platform, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, China; State Key Laboratory of Esophageal Cancer Prevention and Treatment, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, China.
| | - Hong-Min Liu
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, China; XNA platform, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, China; State Key Laboratory of Esophageal Cancer Prevention and Treatment, School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, 450001, China.
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10
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Ye Z, Yang J, Jiang H, Zhan X. The roles of protein ubiquitination in tumorigenesis and targeted drug discovery in lung cancer. Front Endocrinol (Lausanne) 2023; 14:1220108. [PMID: 37795365 PMCID: PMC10546409 DOI: 10.3389/fendo.2023.1220108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/31/2023] [Indexed: 10/06/2023] Open
Abstract
The malignant lung cancer has a high morbidity rate and very poor 5-year survival rate. About 80% - 90% of protein degradation in human cells is occurred through the ubiquitination enzyme pathway. Ubiquitin ligase (E3) with high specificity plays a crucial role in the ubiquitination process of the target protein, which usually occurs at a lysine residue in a substrate protein. Different ubiquitination forms have different effects on the target proteins. Multiple short chains of ubiquitination residues modify substrate proteins, which are favorable signals for protein degradation. The dynamic balance adapted to physiological needs between ubiquitination and deubiquitination of intracellular proteins is beneficial to the health of the organism. Ubiquitination of proteins has an impact on many biological pathways, and imbalances in these pathways lead to diseases including lung cancer. Ubiquitination of tumor suppressor protein factors or deubiquitination of tumor carcinogen protein factors often lead to the progression of lung cancer. Ubiquitin proteasome system (UPS) is a treasure house for research and development of new cancer drugs for lung cancer, especially targeting proteasome and E3s. The ubiquitination and degradation of oncogene proteins with precise targeting may provide a bright prospect for drug development in lung cancer; Especially proteolytic targeted chimerism (PROTAC)-induced protein degradation technology will offer a new strategy in the discovery and development of new drugs for lung cancer.
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Affiliation(s)
- Zhen Ye
- Medical Science and Technology Innovation Center, Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
- School of Clinical and Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Jingru Yang
- Medical Science and Technology Innovation Center, Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Hanming Jiang
- School of Clinical and Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
| | - Xianquan Zhan
- Medical Science and Technology Innovation Center, Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
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11
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Badawi S, Mohamed FE, Varghese DS, Ali BR. Genetic disruption of mammalian endoplasmic reticulum-associated protein degradation: Human phenotypes and animal and cellular disease models. Traffic 2023. [PMID: 37188482 DOI: 10.1111/tra.12902] [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: 03/02/2023] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 05/17/2023]
Abstract
Endoplasmic reticulum-associated protein degradation (ERAD) is a stringent quality control mechanism through which misfolded, unassembled and some native proteins are targeted for degradation to maintain appropriate cellular and organelle homeostasis. Several in vitro and in vivo ERAD-related studies have provided mechanistic insights into ERAD pathway activation and its consequent events; however, a majority of these have investigated the effect of ERAD substrates and their consequent diseases affecting the degradation process. In this review, we present all reported human single-gene disorders caused by genetic variation in genes that encode ERAD components rather than their substrates. Additionally, after extensive literature survey, we present various genetically manipulated higher cellular and mammalian animal models that lack specific components involved in various stages of the ERAD pathway.
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Affiliation(s)
- Sally Badawi
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Feda E Mohamed
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Divya Saro Varghese
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Bassam R Ali
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
- ASPIRE Precision Medicine Research Institute Abu Dhabi, United Arab Emirates University, Al Ain, United Arab Emirates
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12
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Wenger A, Karlsson I, Kling T, Carén H. CRISPR-Cas9 knockout screen identifies novel treatment targets in childhood high-grade glioma. Clin Epigenetics 2023; 15:80. [PMID: 37161535 PMCID: PMC10170782 DOI: 10.1186/s13148-023-01498-6] [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: 02/09/2023] [Accepted: 05/03/2023] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND Brain tumours are the leading cause of cancer-related death in children, and there is no effective treatment. A growing body of evidence points to deregulated epigenetics as a tumour driver, particularly in paediatric cancers as they have relatively few genomic alterations, and key driver mutations have been identified in histone 3 (H3). Cancer stem cells (CSC) are implicated in tumour development, relapse and therapy resistance and thus particularly important to target. We therefore aimed to identify novel epigenetic treatment targets in CSC derived from H3-mutated high-grade glioma (HGG) through a CRISPR-Cas9 knockout screen. RESULTS The knockout screen identified more than 100 novel genes essential for the growth of CSC derived from paediatric HGG with H3K27M mutation. We successfully validated 12 of the 13 selected hits by individual knockout in the same two CSC lines, and for the top six hits we included two additional CSC lines derived from H3 wild-type paediatric HGG. Knockout of these genes led to a significant decrease in CSC growth, and altered stem cell and differentiation markers. CONCLUSIONS The screen robustly identified essential genes known in the literature, but also many novel genes essential for CSC growth in paediatric HGG. Six of the novel genes (UBE2N, CHD4, LSM11, KANSL1, KANSL3 and EED) were validated individually thus demonstrating their importance for CSC growth in H3-mutated and wild-type HGG. These genes should be further studied and evaluated as novel treatment targets in paediatric HGG.
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Affiliation(s)
- Anna Wenger
- Sahlgrenska Center for Cancer Research, Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 1F, 405 30, Gothenburg, Sweden
| | - Ida Karlsson
- Sahlgrenska Center for Cancer Research, Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 1F, 405 30, Gothenburg, Sweden
| | - Teresia Kling
- Sahlgrenska Center for Cancer Research, Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 1F, 405 30, Gothenburg, Sweden
| | - Helena Carén
- Sahlgrenska Center for Cancer Research, Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 1F, 405 30, Gothenburg, Sweden.
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13
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Gu J, Pang L, Yan D, Wang C, Song Y, Jin Z, Xu Z, Mao Y, Liu S, Chen S. Ubiquitin-proteasome system-mediated ubiquitination modification patterns and characterization of tumor microenvironment infiltration, stemness and cellular senescence in low-grade glioma. Aging (Albany NY) 2023; 15:2970-2998. [PMID: 37053008 DOI: 10.18632/aging.204650] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 03/28/2023] [Indexed: 04/14/2023]
Abstract
The Ubiquitin-proteasome system (UPS) performs a crucial role in immune activation and tumorigenesis. Nevertheless, the comprehensive role of the ubiquitin-proteasome system in the low-grade glioma (LGG) tumor microenvironment (TME) remains unknown. Ubiquitination modification patterns in LGG patients and corresponding characteristics of tumor immune traits, CSC stemness, and cellular senescence were evaluated via a comprehensive analysis of 20 ubiquitination modification regulators. For quantification of the ubiquitination modification status of individual patients, the UM-score was constructed and associated with TME characteristics, clinical features, cancer stem cell stemness, cellular senescence, prognosis, and immunotherapy efficacy. We identified that alterations in multiple ubiquitination regulators are linked to patient survival and the shaping of the tumor microenvironment. We found two different styles of ubiquitination modification in patients with low-grade glioma (immune-inflamed differentiation and immune-exclude dedifferentiation), characterized by high and low UM-score, and the two regulatory patterns of ubiquitination modification on immunity, stemness feature, and cellular senescence. We demonstrate that the UM-score could forecast the subtype of LGG, the immunologic infiltration traits, the biological process, the stemness feature, and the cellular senescence trait. Notably, the UM-score was related to immunotherapeutic efficacy, implying that modifying ubiquitination modification patterns by targeting ubiquitination modification regulators or ubiquitination modification pattern signature genes to reverse unfavorable TME properties will provide new insights into cancer immunotherapy. This research indicated that the ubiquitin-proteasome system is crucial in the formation of TME complexity and multiformity. The UM-score can determine ubiquitination modification status in individual patients, bringing about more personalized and effective immunotherapeutic tactics.
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Affiliation(s)
- Jun Gu
- The Affiliated Jiangsu Shengze Hospital of Nanjing Medical University, Suzhou, Jiangsu, China
| | - Lijun Pang
- The Affiliated Jiangsu Shengze Hospital of Nanjing Medical University, Suzhou, Jiangsu, China
| | - Donghua Yan
- The Affiliated Jiangsu Shengze Hospital of Nanjing Medical University, Suzhou, Jiangsu, China
| | - Chunming Wang
- The Affiliated Jiangsu Shengze Hospital of Nanjing Medical University, Suzhou, Jiangsu, China
| | - Yuekun Song
- The Affiliated Jiangsu Shengze Hospital of Nanjing Medical University, Suzhou, Jiangsu, China
| | - Zhengshuai Jin
- The Affiliated Jiangsu Shengze Hospital of Nanjing Medical University, Suzhou, Jiangsu, China
| | - Zhenwei Xu
- The Affiliated Jiangsu Shengze Hospital of Nanjing Medical University, Suzhou, Jiangsu, China
| | - Yuanqing Mao
- The Affiliated Jiangsu Shengze Hospital of Nanjing Medical University, Suzhou, Jiangsu, China
| | - Shengzhe Liu
- The Affiliated Jiangsu Shengze Hospital of Nanjing Medical University, Suzhou, Jiangsu, China
| | - Sheng Chen
- The Affiliated Jiangsu Shengze Hospital of Nanjing Medical University, Suzhou, Jiangsu, China
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14
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Li J, Qi C, Shao S, Chen Y, Peng Z, Shen Q, Zhang Z. SP1 transcriptionally regulates UBE2N expression to promote lung adenocarcinoma progression. MOLECULAR BIOMEDICINE 2023; 4:7. [PMID: 36964266 PMCID: PMC10039148 DOI: 10.1186/s43556-023-00118-2] [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: 12/12/2022] [Accepted: 02/05/2023] [Indexed: 03/26/2023] Open
Abstract
Lung adenocarcinoma (LUAD) is the main cause of cancer-related death worldwide. Understanding the mechanisms of LUAD progression may provide insights into targeted therapy approaches for this malignancy. Ubiquitin-conjugating enzyme 2 N (UBE2N) has been demonstrated to play key roles in the progression of various cancers. However, the functions and mechanisms underlying UBE2N expression in LUAD are still unclear. In this study, we found that UBE2N is highly expressed in LUAD and patients with high UBE2N expression in their tumors have poor clinical outcomes. Moreover, we showed that UBE2N interference significantly inhibited LUAD progression in vitro and in vivo. At the molecular level, we demonstrated that the UBE2N is a bona fide target of transcription factor SP1. SP1 directly bound to the promoter of UBE2N and upregulated its expression in LUAD cells, which in turn contributed to the progression of LUAD. Furthermore, we found that there is a strong positive correlation between the expression of SP1 and UBE2N in LUAD samples. Importantly, LUAD patients with concomitantly high expression of SP1 and UBE2N were significantly associated with poor clinical outcomes. In conclusion, our study demonstrated that the SP1-UBE2N signaling axis might play a key role in the malignant progression of LUAD, which provides new targets and strategies for the treatment of LUAD.
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Affiliation(s)
- Jianjun Li
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China
- Suzhou Key Laboratory for Respiratory Diseases, Suzhou, 215006, China
- Institute of Respiratory Diseases, Soochow University, Suzhou, 215006, China
| | - Chunchun Qi
- Medical College of Nankai University, Tianjin, 300071, China
| | - Shanshan Shao
- Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yanru Chen
- Institute of Clinical Medicine, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, 152 Aiguo Road, Nanchang, Jiangxi, 330006, China
| | - Zimei Peng
- Institute of Clinical Medicine, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, 152 Aiguo Road, Nanchang, Jiangxi, 330006, China
| | - Qinglin Shen
- Institute of Clinical Medicine, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, 152 Aiguo Road, Nanchang, Jiangxi, 330006, China.
- Department of Oncology, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Jiangxi, Nanchang, 330006, China.
| | - Zhen Zhang
- Institute of Clinical Medicine, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, 152 Aiguo Road, Nanchang, Jiangxi, 330006, China.
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15
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Fan J, Ding Y, Huang H, Xiong S, He L, Guo J. High expression of ABCF1 is an independent predictor of poor prognosis in bladder cancer. BMC Urol 2023; 23:37. [PMID: 36932399 PMCID: PMC10022215 DOI: 10.1186/s12894-023-01211-y] [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: 12/03/2022] [Accepted: 03/13/2023] [Indexed: 03/19/2023] Open
Abstract
ABCF1, a member of the ATP-binding cassette (ABC) transporter family, is involved in the malignant progression of tumors. However, the role of ABCF1 in bladder cancer is poorly understood. In our study, we explored the differential expression of ABCF1 in bladder cancer and normal bladder tissues based on bioinformatic analysis and immunohistochemical results. GSEA was performed to ascertain the potential related signaling pathways of ABCF1. The relationship between ABCF1 expression and bladder cancer progression was analyzed using the GSE13507 dataset. In addition, the differential expression of ABCF1 in the cell lines was verified by quantitative real-time polymerase chain reaction (qRT‒PCR) and Western blotting. ABCF1 was upregulated in bladder cancer, and the high expression of ABCF1 was closely related to sex (P = 0.00056), grade (P = 0.00049), T stage (P = 0.00007), and N stage (P = 0.0076). High expression of ABCF1 was correlated with poor overall survival in bladder cancer patients (P < 0.001). In addition, univariate and multivariate Cox regression analyses showed that high ABCF1 expression was an independent factor for poor prognosis in bladder cancer patients. Therefore, ABCF1 expression is closely related to the progression of bladder cancer and can be used as a potential indicator of poor prognosis and a therapeutic target for bladder cancer.
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Affiliation(s)
- JiaWen Fan
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Yi Ding
- The Second Affiliated Hospital of Jiujiang University, Jiujiang, Jiangxi, China
| | - HaoXuan Huang
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - ShiDa Xiong
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Liang He
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Ju Guo
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China.
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16
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Lei X, Hu X, Lu Q, Fu W, Sun W, Ma Q, Huang D, Xu Q. Ubiquitin‑conjugating enzymes as potential biomarkers and therapeutic targets for digestive system cancers (Review). Oncol Rep 2023; 49:63. [PMID: 36799184 PMCID: PMC9944987 DOI: 10.3892/or.2023.8500] [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: 11/04/2022] [Accepted: 01/16/2023] [Indexed: 02/15/2023] Open
Abstract
Digestive system cancers are the leading cause of cancer‑related death worldwide due to their high morbidity and mortality rates. The current treatment methods include surgical treatment, chemotherapy, radiotherapy and endoscopic treatment, and the precisely targeted therapy of digestive system cancers requires to be further studied. The ubiquitin‑proteasome system is the main pathway for protein degradation in cells and the ubiquitin‑conjugating enzymes (E2s) have a decisive role in the specific selection of target proteins for degradation. The E2s have an important physiological role in digestive system cancers, which is related to the clinical tumor stage, differentiation degree and poor prognosis. Furthermore, they are involved in the physiological processes of digestive system tumor cell proliferation, migration, invasion, stemness, drug resistance and autophagy. In the present article, the progress and achievements of the E2s in gastric cancer, hepatocellular carcinoma, pancreatic cancer, colorectal cancer, intrahepatic cholangiocarcinoma, gallbladder cancer and esophageal squamous cell carcinoma were reviewed, which may provide early screening indicators and reliable therapeutic targets for digestive system cancers.
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Affiliation(s)
- Xiangxiang Lei
- Institute of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang 310053, P.R. China
| | - Xiaoge Hu
- The Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, P.R. China
| | - Qiliang Lu
- Qingdao Medical College, Qingdao University, Qingdao, Shandong 266000, P.R. China
| | - Wen Fu
- Qingdao Medical College, Qingdao University, Qingdao, Shandong 266000, P.R. China
| | - Wen Sun
- Second Clinical Medical Institute, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, P.R. China
| | - Qiancheng Ma
- Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, P.R. China
| | - Dongsheng Huang
- The Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, P.R. China,Correspondence to: Dr Dongsheng Huang or Dr Qiuran Xu, The Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, 158 Shangtang Road, Gongshu, Hangzhou, Zhejiang 310014, P.R. China, E-mail:
| | - Qiuran Xu
- The Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang 310014, P.R. China,Correspondence to: Dr Dongsheng Huang or Dr Qiuran Xu, The Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, 158 Shangtang Road, Gongshu, Hangzhou, Zhejiang 310014, P.R. China, E-mail:
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17
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Wang T, Jin C, Yang P, Chen Z, Ji J, Sun Q, Yang S, Feng Y, Tang J, Sun Y. UBE2J1 inhibits colorectal cancer progression by promoting ubiquitination and degradation of RPS3. Oncogene 2023; 42:651-664. [PMID: 36567344 PMCID: PMC9957728 DOI: 10.1038/s41388-022-02581-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 12/10/2022] [Accepted: 12/13/2022] [Indexed: 12/27/2022]
Abstract
Ubiquitin-conjugating enzyme E2 J1 (UBE2J1) has been proven to participate in the ubiquitination of multiple substrate proteins. However, the underlying mechanisms of UBE2J1 as a ubiquitin-conjugating enzyme participating in cancer development and progression remain largely unknown. Here, we identified that UBE2J1 is downregulated in colorectal cancer (CRC) tissues and cell lines which are mediated by DNA hypermethylation of its promoter, and decreased UBE2J1 is associated with poor prognosis. Functionally, UBE2J1 serving as a suppressor gene inhibits the proliferation and metastasis of CRC cells. Mechanistically, UBE2J1-TRIM25, forming an E2-E3 complex, physically interacts with and targets RPS3 for ubiquitination and degradation at the K214 residue. The downregulated RPS3 caused by UBE2J1 overexpression restrains NF-κB translocation into the nucleus and therefore inactivates the NF-κB signaling pathway. Our study revealed a novel role of UBE2J1-mediated RPS3 poly-ubiquitination and degradation in disrupting the NF-κB signaling pathway, which may serve as a novel and promising biomarker and therapeutic target for CRC.
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Affiliation(s)
- Tuo Wang
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984Nanjing Medical University, Nanjing, China
| | - Chi Jin
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984Nanjing Medical University, Nanjing, China
| | - Peng Yang
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984Nanjing Medical University, Nanjing, China
| | - Zhihao Chen
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984Nanjing Medical University, Nanjing, China
| | - Jiangzhou Ji
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984Nanjing Medical University, Nanjing, China
| | - Qingyang Sun
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984Nanjing Medical University, Nanjing, China
| | - Sheng Yang
- grid.412676.00000 0004 1799 0784Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu People’s Republic of China ,grid.89957.3a0000 0000 9255 8984The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984The Colorectal Institute of Nanjing Medical University, Nanjing, China ,grid.89957.3a0000 0000 9255 8984Nanjing Medical University, Nanjing, China
| | - Yifei Feng
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China. .,The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China. .,The Colorectal Institute of Nanjing Medical University, Nanjing, China. .,Nanjing Medical University, Nanjing, China.
| | - Junwei Tang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China. .,The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China. .,The Colorectal Institute of Nanjing Medical University, Nanjing, China. .,Nanjing Medical University, Nanjing, China.
| | - Yueming Sun
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China. .,The First School of Clinical Medicine, Nanjing Medical University, Nanjing, China. .,The Colorectal Institute of Nanjing Medical University, Nanjing, China. .,Nanjing Medical University, Nanjing, China.
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18
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Dutta R, Guruvaiah P, Reddi KK, Bugide S, Reddy Bandi D, Edwards YJK, Singh K, Gupta R. UBE2T promotes breast cancer tumor growth by suppressing DNA replication stress. NAR Cancer 2022; 4:zcac035. [PMID: 36338541 PMCID: PMC9629447 DOI: 10.1093/narcan/zcac035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 10/10/2022] [Accepted: 10/17/2022] [Indexed: 11/05/2022] Open
Abstract
Breast cancer is a leading cause of cancer-related deaths among women, and current therapies benefit only a subset of these patients. Here, we show that ubiquitin-conjugating enzyme E2T (UBE2T) is overexpressed in patient-derived breast cancer samples, and UBE2T overexpression predicts poor prognosis. We demonstrate that the transcription factor AP-2 alpha (TFAP2A) is necessary for the overexpression of UBE2T in breast cancer cells, and UBE2T inhibition suppresses breast cancer tumor growth in cell culture and in mice. RNA sequencing analysis identified interferon alpha-inducible protein 6 (IFI6) as a key downstream mediator of UBE2T function in breast cancer cells. Consistently, UBE2T inhibition downregulated IFI6 expression, promoting DNA replication stress, cell cycle arrest, and apoptosis and suppressing breast cancer cell growth. Breast cancer cells with IFI6 inhibition displayed similar phenotypes as those with UBE2T inhibition, and ectopic IFI6 expression in UBE2T-knockdown breast cancer cells prevented DNA replication stress and apoptosis and partly restored breast cancer cell growth. Furthermore, UBE2T inhibition enhanced the growth-suppressive effects of DNA replication stress inducers. Taken together, our study identifies UBE2T as a facilitator of breast cancer tumor growth and provide a rationale for targeting UBE2T for breast cancer therapies.
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Affiliation(s)
- Roshan Dutta
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Praveen Guruvaiah
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Kiran Kumar Reddi
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Suresh Bugide
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Dhana Sekhar Reddy Bandi
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Yvonne J K Edwards
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Kamaljeet Singh
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI 02912, USA
| | - Romi Gupta
- Department of Biochemistry and Molecular Genetics, The University of Alabama at Birmingham, Birmingham, AL 35233, USA
- O’Neal Comprehensive Cancer Center, The University of Alabama at Birmingham, Birmingham, AL 35233, USA
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19
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Tan L, Shan H, Han C, Zhang Z, Shen J, Zhang X, Xiang H, Lu K, Qi C, Li Y, Zhuang G, Chen G, Tan L. Discovery of Potent OTUB1/USP8 Dual Inhibitors Targeting Proteostasis in Non-Small-Cell Lung Cancer. J Med Chem 2022; 65:13645-13659. [PMID: 36221183 DOI: 10.1021/acs.jmedchem.2c00408] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Deubiquitinating enzymes (DUBs) are key regulatory components of the ubiquitination system. Many DUBs have been revealed to play key roles in normal physiology and diseases. However, only very limited DUB members have well-characterized inhibitors. OTUB1 and USP8 are two DUBs reported to promote both immune evasion and tumorigenesis in tumor models, yet their targeted inhibitors are in the early stages of development. Here, we describe the lead identification and optimization of an OTUB1/USP8 dual inhibitor, 61, which exhibits highly potent and selective inhibition of both targets with subnanomolar IC50s in vitro. By inhibiting both DUBs, 61 phenocopies the double knockdown of OTUB1/USP8 and exerts pronounced antiproliferative effects in H1975 and other non-small-cell lung cancer (NSCLC) cell lines. Moreover, 61 efficaciously mitigates tumor growth in vivo. Collectively, our results provide a useful tool for pharmacological perturbation of OTUB1/USP8 and introduce a promising therapeutic strategy of dual DUB inhibition for treating NSCLC.
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Affiliation(s)
- Lingli Tan
- School of Pharmacy, Fudan University, Shanghai 201203, China.,Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Hengyue Shan
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Han
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhenfeng Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiali Shen
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Huaijiang Xiang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kuankuan Lu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunting Qi
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Ying Li
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Guanglei Zhuang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Gang Chen
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Li Tan
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
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20
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A.V.S SK, Sinha S, Donakonda S. Virus-host interaction network analysis in Colorectal cancer identifies core virus network signature and small molecules. Comput Struct Biotechnol J 2022; 20:4025-4039. [PMID: 35983230 PMCID: PMC9356043 DOI: 10.1016/j.csbj.2022.07.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 07/23/2022] [Accepted: 07/23/2022] [Indexed: 11/15/2022] Open
Abstract
Systematic analysis of virus-host networks identified key pathways in CRC. Core virus-CRC network revealed the growth pathway regulated by viruses. Short linear motif analysis identified druggable regions in virus proteins. Virtual screening revealed key anti-viral molecules against viral proteins. Molecular dynamics simulations showed the effect of anti-viral molecules.
Colorectal cancer (CRC) is a significant contributor to cancer-related deaths caused by an unhealthy lifestyle. Multiple studies reveal that viruses are involved in colorectal tumorigenesis. The viruses such as Human Cytomegalovirus (HCMV), Human papillomaviruses (HPV16 & HPV18), and John Cunningham virus (JCV) are known to cause colorectal cancer. The molecular mechanisms of cancer genesis and maintenance shared by these viruses remain unclear. We analysed the virus-host networks and connected them with colorectal cancer proteome datasets and extracted the core shared interactions in the virus-host CRC network. Our network topology analysis identified prominent virus proteins RL6 (HCMV), VE6 (HPV16 and HPV18), and Large T antigen (JCV). Sequence analysis uncovered short linear motifs (SLiMs) in each viral target. We used these targets to identify the antiviral drugs through a structure-based virtual screening approach. This analysis highlighted that temsavir, pimodivir, famotine, and bictegravir bind to each virus protein target, respectively. We also assessed the effect of drug binding using molecular dynamic simulations, which shed light on the modulatory effect of drug molecules on SLiM regions in viral targets. Hence, our systematic screening of virus-host networks revealed viral targets, which could be crucial for cancer therapy.
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Affiliation(s)
- Sai Krishna A.V.S
- Department of Biotechnology, Faculty of Life and Allied Health Sciences, MS Ramaiah University of Applied Sciences, Bengaluru, India
| | - Swati Sinha
- Department of Biotechnology, Faculty of Life and Allied Health Sciences, MS Ramaiah University of Applied Sciences, Bengaluru, India
| | - Sainitin Donakonda
- Institute of Molecular Immunology and Experimental Oncology, Klinikum Rechts Der Isar, Technical University of Munich, Munich, Germany
- Corresponding author.
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21
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Pereira J, Dias R, Ramos I. Knockdown of E1- and E2-ubiquitin enzymes triggers defective chorion biogenesis and modulation of autophagy-related genes in the follicle cells of the vector Rhodnius prolixus. J Cell Physiol 2022; 237:3356-3368. [PMID: 35670557 DOI: 10.1002/jcp.30806] [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: 01/19/2022] [Revised: 05/04/2022] [Accepted: 05/19/2022] [Indexed: 12/27/2022]
Abstract
In insects, the last stage of oogenesis is the process where the chorion layers (eggshell) are synthesized and deposited on the surface of the oocytes by the follicle cells. Protein homeostasis is determined by the fine-tuning of translation and degradation pathways, and the ubiquitin-proteasome system is one of the major degradative routes in eukaryotic cells. The conjugation of ubiquitin to targeted substrates is mediated by the ordered action of E1-activating, E2-conjugating, and E3-ligase enzymes, which covalently link ubiquitin to degradation-targeted proteins delivering them to the proteolytic complex proteasome. Here, we found that the mRNAs encoding polyubiquitin (pUbq), E1, and E2 enzymes are highly expressed in the ovaries of the insect vector of Chagas Disease Rhodnius prolixus. RNAi silencing of pUbq was lethal whereas the silencing of E1 and E2 enzymes resulted in drastic decreases in oviposition and embryo viability. Eggs produced by the E1- and E2-silenced insects presented particular phenotypes of altered chorion ultrastructure observed by high-resolution scanning electron microscopy as well as readings for dityrosine cross-linking and X-ray elemental microanalysis, suggesting a disruption in the secretory routes responsible for the chorion biogenesis. In addition, the ovaries from silenced insects presented altered levels of autophagy-related genes as well as a tendency of upregulation in ER chaperones, indicating a disturbance in the general biosynthetic-secretory pathway. Altogether, we found that E1 and E2 enzymes are essential for chorion biogenesis and that their silencing triggers the modulation of autophagy genes suggesting a coordinated function of both pathways for the progression of choriogenesis.
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Affiliation(s)
- Jéssica Pereira
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Raphael Dias
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Isabela Ramos
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Avenida Carlos Chagas Filho, 373, Rio de Janeiro, Rio de Janeiro, Brazil
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22
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Jayathirtha M, Neagu AN, Whitham D, Alwine S, Darie CC. Investigation of the effects of overexpression of jumping translocation breakpoint (JTB) protein in MCF7 cells for potential use as a biomarker in breast cancer. Am J Cancer Res 2022; 12:1784-1823. [PMID: 35530281 PMCID: PMC9077082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/27/2022] [Indexed: 06/14/2023] Open
Abstract
Jumping translocation breakpoint (JTB) gene acts as a tumor suppressor or an oncogene in different malignancies, including breast cancer (BC), where it was reported as overexpressed. However, the molecular functions, biological processes and underlying mechanisms through which JTB protein causes increased cell growth, proliferation and invasion is still not fully deciphered. Our goal is to identify the functions of JTB protein by cellular proteomics approaches. MCF7 breast cancer cells were transfected with sense orientation of hJTB cDNA in HA, His and FLAG tagged CMV expression vector to overexpress hJTB and the expression levels were confirmed by Western blotting (WB). Proteins extracted from transfected cells were separated by SDS-PAGE and the in-gel digested peptides were analyzed by nano-liquid chromatography tandem mass spectrometry (nanoLC-MS/MS). By comparing the proteome of cells with upregulated conditions of JTB vs control and identifying the protein dysregulation patterns, we aim to understand the function of this protein and its contribution to tumorigenesis. Gene Set Enrichment Analysis (GSEA) algorithm was performed to investigate the biological processes and pathways that are associated with the JTB protein upregulation. The results demonstrated four significantly enriched gene sets from the following significantly upregulated pathways: mitotic spindle assembly, estrogen response late, epithelial-to-mesenchymal transition (EMT) and estrogen response early. JTB protein itself is involved in mitotic spindle pathway by its role in cell division/cytokinesis, and within estrogen response early and late pathways, contributing to discrimination between luminal and mesenchymal breast cancer. Thus, the overexpressed JTB condition was significantly associated with an increased expression of ACTNs, FLNA, FLNB, EZR, MYOF, COL3A1, COL11A1, HSPA1A, HSP90A, WDR, EPPK1, FASN and FOXA1 proteins related to deregulation of cytoskeletal organization and biogenesis, mitotic spindle organization, ECM remodeling, cellular response to estrogen, proliferation, migration, metastasis, increased lipid biogenesis, endocrine therapy resistance, antiapoptosis and discrimination between different breast cancer subtypes. Other upregulated proteins for overexpressed JTB condition are involved in multiple cellular functions and pathways that become dysregulated, such as tumor microenvironment (TME) acidification, the transmembrane transport pathways, glycolytic flux, iron metabolism and oxidative stress, metabolic reprogramming, nucleocytosolic mRNA transport, transcriptional activation, chromatin remodeling, modulation of cell death pathways, stress responsive pathways, and cancer drug resistance. The downregulated proteins for overexpressed JTB condition are involved in adaptive communication between external and internal environment of cells and maintenance between pro-apoptotic and anti-apoptotic signaling pathways, vesicle trafficking and secretion, DNA lesions repair and suppression of genes involved in tumor progression, proteostasis, redox state regulation, biosynthesis of macromolecules, lipolytic pathway, carbohydrate metabolism, dysregulation of ubiquitin-mediated degradation system, cancer cell immune escape, cell-to-cell and cell-to-ECM interactions, and cytoskeletal behaviour. There were no significantly enriched downregulated pathways.
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Affiliation(s)
- Madhuri Jayathirtha
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson UniversityPotsdam, NY 13699-5810, USA
| | - Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, “Alexandru Ioan Cuza” University of IasiCarol I Bvd. No. 22, Iasi 700505, Romania
| | - Danielle Whitham
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson UniversityPotsdam, NY 13699-5810, USA
| | - Shelby Alwine
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson UniversityPotsdam, NY 13699-5810, USA
| | - Costel C Darie
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson UniversityPotsdam, NY 13699-5810, USA
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23
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Ni LP, Sun HT, Wang P, Wang J, Zhou JH, Cao RQ, Yue L, Chen YG, Shen FR. Hyperthermia enhances the efficacy of chemotherapeutic drugs in heat-sensitive cells through interfering with DNA damage repair. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:463. [PMID: 35571421 PMCID: PMC9096405 DOI: 10.21037/atm-22-955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/08/2022] [Indexed: 11/19/2022]
Abstract
Background Hyperthermic intraperitoneal chemotherapy (HIPEC) has been shown to be clinically effective, but the mechanisms by which hyperthermia enhances the sensitivity of cells to chemotherapeutic drugs has not yet been elucidated. Methods To identify the key molecules involved in thermochemotherapy, this study used mass spectrometry (MS)-based quantitative proteomics technology to analyze the effects of thermochemotherapy on the heat-sensitive ovarian cancer cell line A2780. We divided the A2780 cell line into four groups, one group served as blank control, and the other three groups were stimulated by oxaliplatin, stimulated by hyperthermia at 42 ℃, and stimulated by hyperthermia combined with oxaliplatin. Samples were then collected for tandem mass tag (TMT) labeling, high-performance liquid chromatography fractionation, and MS-based quantitative proteomics for analysis The differentially expressed proteins were quantitatively compared and identified, and Gene Ontology (GO) assessment and cluster analyses were performed. Finally, the above MS results were verified again by Western blotting experiments. Results A total of 349 differentially expressed proteins were identified between cells treated with chemotherapy alone (group B) and cells treated with a combination of chemotherapy and hyperthermia (group D). There were 145 upregulated proteins and 204 downregulated proteins. Among the top 20 proteins with significantly different expression levels, nearly two-thirds were involved in DNA damage repair. These proteins were subsequently verified by Western blot analysis. Indeed, consistent with MS data, the expression of the RBL1 protein was significantly upregulated in cells treated with thermochemotherapy (group D) compared to cells treated with chemotherapy alone (group B). Conclusions In heat-sensitive ovarian cancer cells, the damage repair of tumor cell DNA is disturbed by hyperthermia, making it unable to fully repair when damaged by chemotherapeutic drugs. As a result, hyperthermia enhances the efficacy of chemotherapeutic drugs. RBL1, as a tumor suppressor gene, may be associated with the repair of DNA damage, and thus it may be a key target for hyperthermia to enhance the sensitivity of thermosensitive cells to chemotherapeutic drugs.
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Affiliation(s)
- Li-Ping Ni
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Hua-Ting Sun
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Ping Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Juan Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jin-Hua Zhou
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Ruo-Qi Cao
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, China
| | - Ling Yue
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, China
| | - You-Guo Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Fang-Rong Shen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou, China
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24
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Modulating the Ubiquitin–Proteasome System: A Therapeutic Strategy for Autoimmune Diseases. Cells 2022; 11:cells11071093. [PMID: 35406655 PMCID: PMC8997991 DOI: 10.3390/cells11071093] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/20/2022] [Accepted: 03/22/2022] [Indexed: 12/12/2022] Open
Abstract
Multiple sclerosis (MS) is an autoimmune, neurodegenerative disease associated with the central nervous system (CNS). Autoimmunity is caused by an abnormal immune response to self-antigens, which results in chronic inflammation and tissue death. Ubiquitination is a post-translational modification in which ubiquitin molecules are attached to proteins by ubiquitinating enzymes, and then the modified proteins are degraded by the proteasome system. In addition to regulating proteasomal degradation of proteins, ubiquitination also regulates other cellular functions that are independent of proteasomal degradation. It plays a vital role in intracellular protein turnover and immune signaling and responses. The ubiquitin–proteasome system (UPS) is primarily responsible for the nonlysosomal proteolysis of intracellular proteins. The 26S proteasome is a multicatalytic adenosine-triphosphate-dependent protease that recognizes ubiquitin covalently attached to particular proteins and targets them for degradation. Damaged, oxidized, or misfolded proteins, as well as regulatory proteins that govern many essential cellular functions, are removed by this degradation pathway. When this system is affected, cellular homeostasis is altered, resulting in the induction of a range of diseases. This review discusses the biochemistry and molecular biology of the UPS, including its role in the development of MS and proteinopathies. Potential therapies and targets involving the UPS are also addressed.
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25
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Jin JO, Puranik N, Bui QT, Yadav D, Lee PCW. The Ubiquitin System: An Emerging Therapeutic Target for Lung Cancer. Int J Mol Sci 2021; 22:9629. [PMID: 34502538 PMCID: PMC8431782 DOI: 10.3390/ijms22179629] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/03/2021] [Accepted: 09/03/2021] [Indexed: 12/25/2022] Open
Abstract
The ubiquitin system, present in all eukaryotes, contributes to regulating multiple types of cellular protein processes such as cell signaling, cell cycle, and receptor trafficking, and it affects the immune response. In most types of cancer, unusual events in ubiquitin-mediated signaling pathway modulation can lead to a variety of clinical outcomes, including tumor formation and metastasis. Similarly, ubiquitination acts as a core component, which contributes to the alteration of cell signaling activity, dictating biosignal turnover and protein fates. As lung cancer acquires the most commonly mutated proteins, changes in the ubiquitination of the proteins contribute to the development of lung cancer. Various inhibitors targeting the ubiquitin system have been developed for clinical applications in lung cancer treatment. In this review, we summarize the current research advances in therapeutics for lung cancer by targeting the ubiquitin system.
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Affiliation(s)
- Jun-O Jin
- Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 201508, China
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea
| | - Nidhi Puranik
- Biological Sciences Department, Bharathiar University, Coimbatore 641046, Tamil Nadu, India;
| | - Quyen Thu Bui
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Korea;
| | - Dhananjay Yadav
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan 38541, Korea
| | - Peter Chang-Whan Lee
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Korea;
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