1
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Budayeva HG, Ma TP, Wang S, Choi M, Rose CM. Increasing the Throughput and Reproducibility of Activity-Based Proteome Profiling Studies with Hyperplexing and Intelligent Data Acquisition. J Proteome Res 2024; 23:2934-2947. [PMID: 38251652 PMCID: PMC11301772 DOI: 10.1021/acs.jproteome.3c00598] [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: 09/14/2023] [Revised: 11/16/2023] [Accepted: 12/27/2023] [Indexed: 01/23/2024]
Abstract
Intelligent data acquisition (IDA) strategies, such as a real-time database search (RTS), have improved the depth of proteome coverage for experiments that utilize isobaric labels and gas phase purification techniques (i.e., SPS-MS3). In this work, we introduce inSeqAPI, an instrument application programing interface (iAPI) program that enables construction of novel data acquisition algorithms. First, we analyze biotinylated cysteine peptides from ABPP experiments to demonstrate that a real-time search method within inSeqAPI performs similarly to an equivalent vendor method. Then, we describe PairQuant, a method within inSeqAPI designed for the hyperplexing approach that utilizes protein-level isotopic labeling and peptide-level TMT labeling. PairQuant allows for TMT analysis of 36 conditions in a single sample and achieves ∼98% coverage of both peptide pair partners in a hyperplexed experiment as well as a 40% improvement in the number of quantified cysteine sites compared with non-RTS acquisition. We applied this method in the ABPP study of ligandable cysteine sites in the nucleus leading to an identification of additional druggable sites on protein- and DNA-interaction domains of transcription regulators and on nuclear ubiquitin ligases.
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Affiliation(s)
- Hanna G. Budayeva
- Department
of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., South
San Francisco, California 94080, United States
| | - Taylur P. Ma
- Department
of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., South
San Francisco, California 94080, United States
| | - Shuai Wang
- Department
of Metabolism and Pharmacokinetics, Genentech,
Inc., South San Francisco, California 94080, United States
| | - Meena Choi
- Department
of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., South
San Francisco, California 94080, United States
| | - Christopher M. Rose
- Department
of Microchemistry, Proteomics and Lipidomics, Genentech, Inc., South
San Francisco, California 94080, United States
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2
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Apoorva CC, Ananthaneni A, Kumar AJ, Guduru VS, Puneeth HK. Evaluation of USP22 and Ki-67 expression in oral squamous cell carcinoma: An immunohistochemical study. J Oral Maxillofac Pathol 2023; 27:679-684. [PMID: 38304522 PMCID: PMC10829464 DOI: 10.4103/jomfp.jomfp_262_23] [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: 06/07/2023] [Revised: 06/13/2023] [Accepted: 09/01/2023] [Indexed: 02/03/2024] Open
Abstract
Background and Aim USP22 is a positive regulator in tumor growth, its depletion leads to cell cycle arrest at G1 phase. USP22 over expression was positively correlated with proteins involved in proliferation and negatively correlated with tumor suppressor protein tumor supprn. Ki-67 expression is associated with USP22 over expression in oral squamous cell carcinoma (OSCC) and also in cervical and prostate cancers. The aim of this study is to evaluate the expression of USP22 and Ki-67 in OSCC by using an immunohistochemical staining procedure. Materials and Methods Immunohistochemistry was used to determine the expression of USP22 protein in 50 archival tissue blocks of histopathologically diagnosed OSCC and 15 normal oral mucosa tissue blocks. The histopathological correlation of USP22 with Ki-67 was done. Results Expression of USP22 and Ki-67 was seen in the nuclei of epithelial cells. Statistical analysis of the mean expression of USP22 in OSCC and normal tissue showed a significant difference (P = 0.000000119). A significant difference was also observed in Ki-67 between OSCC and normal tissue (P = 0.00000086). Correlation test showed a weak correlation (R = 0.19) between USP22 and Ki-67 expression of group 1. Similarly, a weak correlation (R = 0.51) was observed in group 2. Conclusion A statistically significant difference in the expression of USP22 and Ki-67 was observed between normal mucosa and OSCC. It can be used in early diagnosis of OSCC but its use as a prognostic indicator is questionable and should be exemplified with a larger study sample.
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Affiliation(s)
- Chelikani Chaitra Apoorva
- Department of Oral Pathology, St Joseph Dental College and Hospital, Duggirala, Eluru, Andhra Pradesh, India
| | - Anuradha Ananthaneni
- Department of Oral Pathology, St Joseph Dental College and Hospital, Duggirala, Eluru, Andhra Pradesh, India
| | - A. Jagadeesh Kumar
- Department of Oral Pathology, St Joseph Dental College and Hospital, Duggirala, Eluru, Andhra Pradesh, India
| | - Vijay Srinivas Guduru
- Department of Oral Pathology, St Joseph Dental College and Hospital, Duggirala, Eluru, Andhra Pradesh, India
| | - H K Puneeth
- Department of Oral Pathology, St Joseph Dental College and Hospital, Duggirala, Eluru, Andhra Pradesh, India
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3
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Chang HR. RNF126, 168 and CUL1: The Potential Utilization of Multi-Functional E3 Ubiquitin Ligases in Genome Maintenance for Cancer Therapy. Biomedicines 2023; 11:2527. [PMID: 37760968 PMCID: PMC10526535 DOI: 10.3390/biomedicines11092527] [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: 08/03/2023] [Revised: 08/27/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Ubiquitination is a post-translational modification (PTM) that is involved in proteolysis, protein-protein interaction, and signal transduction. Accumulation of mutations and genomic instability are characteristic of cancer cells, and dysfunction of the ubiquitin pathway can contribute to abnormal cell physiology. Because mutations can be critical for cells, DNA damage repair, cell cycle regulation, and apoptosis are pathways that are in close communication to maintain genomic integrity. Uncontrolled cell proliferation due to abnormal processes is a hallmark of cancer, and mutations, changes in expression levels, and other alterations of ubiquitination factors are often involved. Here, three E3 ubiquitin ligases will be reviewed in detail. RNF126, RNF168 and CUL1 are involved in DNA damage response (DDR), DNA double-strand break (DSB) repair, cell cycle regulation, and ultimately, cancer cell proliferation control. Their involvement in multiple cellular pathways makes them an attractive candidate for cancer-targeting therapy. Functional studies of these E3 ligases have increased over the years, and their significance in cancer is well reported. There are continuous efforts to develop drugs targeting the ubiquitin pathway for anticancer therapy, which opens up the possibility for these E3 ligases to be evaluated for their potential as a target protein for anticancer therapy.
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Affiliation(s)
- Hae Ryung Chang
- Department of Life Science, Handong Global University, Pohang 37554, Republic of Korea
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4
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Gao H, Yin J, Ji C, Yu X, Xue J, Guan X, Zhang S, Liu X, Xing F. Targeting ubiquitin specific proteases (USPs) in cancer immunotherapy: from basic research to preclinical application. J Exp Clin Cancer Res 2023; 42:225. [PMID: 37658402 PMCID: PMC10472646 DOI: 10.1186/s13046-023-02805-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/21/2023] [Indexed: 09/03/2023] Open
Abstract
Tumors have evolved in various mechanisms to evade the immune system, hindering the antitumor immune response and facilitating tumor progression. Immunotherapy has become a potential treatment strategy specific to different cancer types by utilizing multifarious molecular mechanisms to enhance the immune response against tumors. Among these mechanisms, the ubiquitin-proteasome system (UPS) is a significant non-lysosomal pathway specific to protein degradation, regulated by deubiquitinating enzymes (DUBs) that counterbalance ubiquitin signaling. Ubiquitin-specific proteases (USPs), the largest DUB family with the strongest variety, play critical roles in modulating immune cell function, regulating immune response, and participating in antigen processing and presentation during tumor progression. According to recent studies, the expressions of some USP family members in tumor cells are involved in tumor immune escape and immune microenvironment. This review explores the potential of targeting USPs as a new approach for cancer immunotherapy, highlighting recent basic and preclinical studies investigating the applications of USP inhibitors. By providing insights into the structure and function of USPs in cancer immunity, this review aims at assisting in developing new therapeutic approaches for enhancing the immunotherapy efficacy.
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Affiliation(s)
- Hongli Gao
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Jianqiao Yin
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Ce Ji
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Xiaopeng Yu
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Jinqi Xue
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Xin Guan
- Department of Gastroenterology, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Shuang Zhang
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Xun Liu
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China.
| | - Fei Xing
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, 110004, China.
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5
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Wei Z, Su L, Gao S. The roles of ubiquitination in AML. Ann Hematol 2023:10.1007/s00277-023-05415-y. [PMID: 37603061 DOI: 10.1007/s00277-023-05415-y] [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: 04/25/2023] [Accepted: 08/10/2023] [Indexed: 08/22/2023]
Abstract
Acute myeloid leukemia (AML) is a heterogeneously malignant disorder resulting in poor prognosis. Ubiquitination, a major post-translational modification (PTM), plays an essential role in regulating various cellular processes and determining cell fate. Despite these initial insights, the precise role of ubiquitination in AML pathogenesis and treatment remains largely unknown. In order to address this knowledge gap, we explore the relationship between ubiquitination and AML from the perspectives of signal transduction, cell differentiation, and cell cycle control; and try to find out how this relationship can be utilized to inform new therapeutic strategies for AML patients.
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Affiliation(s)
- Zhifeng Wei
- Department of Hematology, The First Hospital of Jilin University, Changchun, China
| | - Long Su
- Department of Hematology, The First Hospital of Jilin University, Changchun, China
| | - Sujun Gao
- Department of Hematology, The First Hospital of Jilin University, Changchun, China.
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6
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Liu R, Wu J, Guo H, Yao W, Li S, Lu Y, Jia Y, Liang X, Tang J, Zhang H. Post-translational modifications of histones: Mechanisms, biological functions, and therapeutic targets. MedComm (Beijing) 2023; 4:e292. [PMID: 37220590 PMCID: PMC10200003 DOI: 10.1002/mco2.292] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 05/25/2023] Open
Abstract
Histones are DNA-binding basic proteins found in chromosomes. After the histone translation, its amino tail undergoes various modifications, such as methylation, acetylation, phosphorylation, ubiquitination, malonylation, propionylation, butyrylation, crotonylation, and lactylation, which together constitute the "histone code." The relationship between their combination and biological function can be used as an important epigenetic marker. Methylation and demethylation of the same histone residue, acetylation and deacetylation, phosphorylation and dephosphorylation, and even methylation and acetylation between different histone residues cooperate or antagonize with each other, forming a complex network. Histone-modifying enzymes, which cause numerous histone codes, have become a hot topic in the research on cancer therapeutic targets. Therefore, a thorough understanding of the role of histone post-translational modifications (PTMs) in cell life activities is very important for preventing and treating human diseases. In this review, several most thoroughly studied and newly discovered histone PTMs are introduced. Furthermore, we focus on the histone-modifying enzymes with carcinogenic potential, their abnormal modification sites in various tumors, and multiple essential molecular regulation mechanism. Finally, we summarize the missing areas of the current research and point out the direction of future research. We hope to provide a comprehensive understanding and promote further research in this field.
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Affiliation(s)
- Ruiqi Liu
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
- Graduate DepartmentBengbu Medical College, BengbuAnhuiChina
| | - Jiajun Wu
- Graduate DepartmentBengbu Medical College, BengbuAnhuiChina
- Otolaryngology & Head and Neck CenterCancer CenterDepartment of Head and Neck SurgeryZhejiang Provincial People's HospitalAffiliated People's Hospital, Hangzhou Medical CollegeHangzhouZhejiangChina
| | - Haiwei Guo
- Otolaryngology & Head and Neck CenterCancer CenterDepartment of Head and Neck SurgeryZhejiang Provincial People's HospitalAffiliated People's Hospital, Hangzhou Medical CollegeHangzhouZhejiangChina
| | - Weiping Yao
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
- Graduate DepartmentBengbu Medical College, BengbuAnhuiChina
| | - Shuang Li
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
- Graduate DepartmentJinzhou Medical UniversityJinzhouLiaoningChina
| | - Yanwei Lu
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
| | - Yongshi Jia
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
| | - Xiaodong Liang
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
- Graduate DepartmentBengbu Medical College, BengbuAnhuiChina
| | - Jianming Tang
- Department of Radiation OncologyThe First Hospital of Lanzhou UniversityLanzhou UniversityLanzhouGansuChina
| | - Haibo Zhang
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
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7
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Wang H, Langlais D, Nijnik A. Histone H2A deubiquitinases in the transcriptional programs of development and hematopoiesis: a consolidated analysis. Int J Biochem Cell Biol 2023; 157:106384. [PMID: 36738766 DOI: 10.1016/j.biocel.2023.106384] [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: 08/11/2022] [Accepted: 01/31/2023] [Indexed: 02/05/2023]
Abstract
Monoubiquitinated lysine 119 of histone H2A (H2AK119ub) is a highly abundant epigenetic mark, associated with gene repression and deposited on chromatin by the polycomb repressor complex 1 (PRC1), which is an essential regulator of diverse transcriptional programs in mammalian development and tissue homeostasis. While multiple deubiquitinases (DUBs) with catalytic activity for H2AK119ub (H2A-DUBs) have been identified, we lack systematic analyses of their roles and cross-talk in transcriptional regulation. Here, we address H2A-DUB functions in epigenetic regulation of mammalian development and tissue maintenance by conducting a meta-analysis of 248 genomics datasets from 32 independent studies, focusing on the mouse model and covering embryonic stem cells (ESCs), hematopoietic, and immune cell lineages. This covers all the publicly available datasets that map genomic H2A-DUB binding and H2AK119ub distributions (ChIP-Seq), and all datasets assessing dysregulation in gene expression in the relevant H2A-DUB knockout models (RNA-Seq). Many accessory datasets for PRC1-2 and DUB-interacting proteins are also analyzed and interpreted, as well as further data assessing chromatin accessibility (ATAC-Seq) and transcriptional activity (RNA-seq). We report co-localization in the binding of H2A-DUBs BAP1, USP16, and to a lesser extent others that is conserved across different cell-types, and also the enrichment of antagonistic PRC1-2 protein complexes at the same genomic locations. Such conserved sites enriched for the H2A-DUBs and PRC1-2 are proximal to transcriptionally active genes that engage in housekeeping cellular functions. Nevertheless, they exhibit H2AK119ub levels significantly above the genomic average that can undergo further increase with H2A-DUB knockout. This indicates a cooperation between H2A-DUBs and PRC1-2 in the modulation of housekeeping transcriptional programs, conserved across many cell types, likely operating through their antagonistic effects on H2AK119ub and the regulation of local H2AK119ub turnover. Our study further highlights existing knowledge gaps and discusses important directions for future work.
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Affiliation(s)
- HanChen Wang
- Department of Physiology, McGill University, Montreal, QC, Canada; McGill University Research Centre on Complex Traits, McGill University, QC, Canada
| | - David Langlais
- McGill University Research Centre on Complex Traits, McGill University, QC, Canada; Department of Human Genetics, McGill University, Montreal, QC, Canada; McGill Genome Centre, Montreal, QC, Canada.
| | - Anastasia Nijnik
- Department of Physiology, McGill University, Montreal, QC, Canada; McGill University Research Centre on Complex Traits, McGill University, QC, Canada.
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8
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Gregory S, Xu Y, Xie P, Fan J, Gao B, Mani N, Iyer R, Tang A, Wei J, Chaudhuri SM, Wang S, Liu H, Zhang B, Fang D. The ubiquitin-specific peptidase 22 is a deubiquitinase of CD73 in breast cancer cells. Am J Cancer Res 2022; 12:5564-5575. [PMID: 36628293 PMCID: PMC9827093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/12/2022] [Indexed: 01/12/2023] Open
Abstract
Cancer cells evade the immune system by expressing inhibitory immune checkpoint receptors such as ecto-5'-nucleotidase (NT5E), also known as CD73, which consequently suppress tumor neoantigen-specific immune response. Blockade of CD73 in mouse models of breast cancer showed a reduction in tumor growth and metastasis. CD73 expression is elevated in a variety of human tumors including breast cancer. While the regulation of CD73 expression at the transcriptional level has been well understood, the factors involved in regulating CD73 expression at the post-transcriptional level have not been identified. Herein, we discovered that the ubiquitin-specific peptidase 22 (USP22), a deubiquitinase associated with poor prognosis and overexpressed in breast cancers, is a positive regulator for CD73. Targeted USP22 deletion resulted in a statistically significant reduction in CD73 protein expression. In contrast, CD73 mRNA expression levels were not reduced, but even slightly increased by USP22 deletion. Further analysis demonstrated that USP22 is a deubiquitinase that specifically interacts with and inhibits CD73 ubiquitination. Consequently, USP22 protects CD73 from ubiquitin-mediated proteasomal degradation in breast cancer cells. Targeted USP22 deletion, inhibits syngeneic breast cancer growth. Collectively, our study reveals USP22 as a positive regulator to promote CD73 expression in breast cancer and provides a rationale to target USP22 in antitumor immune therapy.
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Affiliation(s)
- Shana Gregory
- Department of Pathology, Northwestern University Feinberg School of Medicine303 E. Chicago Ave, Chicago, IL 60611, USA
| | - Yanan Xu
- Department of Pathology, Northwestern University Feinberg School of Medicine303 E. Chicago Ave, Chicago, IL 60611, USA
| | - Ping Xie
- Department of Medicine (Hematology and Oncology), Northwestern University Feinberg School of Medicine303 E. Chicago Ave, Chicago, IL 60611, USA
| | - Jie Fan
- Department of Medicine (Hematology and Oncology), Northwestern University Feinberg School of Medicine303 E. Chicago Ave, Chicago, IL 60611, USA
| | - Beixue Gao
- Department of Pathology, Northwestern University Feinberg School of Medicine303 E. Chicago Ave, Chicago, IL 60611, USA
| | - Nikita Mani
- Department of Pathology, Northwestern University Feinberg School of Medicine303 E. Chicago Ave, Chicago, IL 60611, USA
| | - Radhika Iyer
- Department of Pathology, Northwestern University Feinberg School of Medicine303 E. Chicago Ave, Chicago, IL 60611, USA
| | - Amy Tang
- Department of Pathology, Northwestern University Feinberg School of Medicine303 E. Chicago Ave, Chicago, IL 60611, USA
| | - Juncheng Wei
- Department of Pathology, Northwestern University Feinberg School of Medicine303 E. Chicago Ave, Chicago, IL 60611, USA
| | - Shuvam Mohan Chaudhuri
- Department of Pathology, Northwestern University Feinberg School of Medicine303 E. Chicago Ave, Chicago, IL 60611, USA
| | - Shengnan Wang
- Department of Pathology, Northwestern University Feinberg School of Medicine303 E. Chicago Ave, Chicago, IL 60611, USA
| | - Huiping Liu
- Department of Pharmacology, Northwestern University Feinberg School of Medicine303 E. Superior St, Chicago, IL 60611, USA
| | - Bin Zhang
- Department of Medicine (Hematology and Oncology), Northwestern University Feinberg School of Medicine303 E. Chicago Ave, Chicago, IL 60611, USA
| | - Deyu Fang
- Department of Pathology, Northwestern University Feinberg School of Medicine303 E. Chicago Ave, Chicago, IL 60611, USA
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9
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Fanourgakis S, Synacheri AC, Lavigne MD, Konstantopoulos D, Fousteri M. Histone H2Bub dynamics in the 5' region of active genes are tightly linked to the UV-induced transcriptional response. Comput Struct Biotechnol J 2022; 21:614-629. [PMID: 36659919 PMCID: PMC9823127 DOI: 10.1016/j.csbj.2022.12.013] [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: 08/15/2022] [Revised: 11/22/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
The timing and location of writing and erasing of histone modifications determine gene expression programs and are tightly controlled processes. One such modification is the monoubiquitination of histone H2B (H2Bub), whose precise level during transcription elongation is dynamically regulated by the synergistic action of RNF20/40 ubiquitin-ligase and the de-ubiquitinase (DUB) of the ATXN7L3-containing DUB modules. Here, we characterize the dynamics of H2Bub in transcription and explore its role in perspective with the recently updated model of UV damage-induced transcription reorganization. Employing integrative analysis of genome-wide high-throughput approaches, transcription inhibitors and ATXN7L3-DUB knockdown cells, we find that H2Bub levels and patterns depend on intron-exon architecture both in steady state and upon UV. Importantly, our analysis reveals a widespread redistribution of this histone mark, rather than a uniform loss as previously suggested, which closely mirrors the post-UV dynamics of elongating RNA Polymerase II (RNAPII) at transcribed loci. The observed effects are due to a direct inter-dependence on RNAPII local concentration and speed, and we show that deficient ATXN7L3-mediated DUB activity leads to increased elongation rates in both non-irradiated and irradiated conditions. Our data and the implementation of a high-resolution computational framework reveal that the H2Bub pattern follows that of RNAPII, both in the ATXNL3 knockdown and in response to UV guaranteeing faithful elongation speed, especially in the context of the transcription-driven DNA damage response.
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10
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Characterizing and exploiting the many roles of aberrant H2B monoubiquitination in cancer pathogenesis. Semin Cancer Biol 2022; 86:782-798. [PMID: 34953650 DOI: 10.1016/j.semcancer.2021.12.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 12/08/2021] [Accepted: 12/19/2021] [Indexed: 01/27/2023]
Abstract
Monoubiquitination of histone H2B on lysine 120 (H2Bub1) is implicated in the control of multiple essential processes, including transcription, DNA damage repair and mitotic chromosome segregation. Accordingly, aberrant regulation of H2Bub1 can induce transcriptional reprogramming and genome instability that may promote oncogenesis. Remarkably, alterations of the ubiquitin ligases and deubiquitinating enzymes regulating H2Bub1 are emerging as ubiquitous features in cancer, further supporting the possibility that the misregulation of H2Bub1 is an underlying mechanism contributing to cancer pathogenesis. To date, aberrant H2Bub1 dynamics have been reported in multiple cancer types and are associated with transcriptional changes that promote oncogenesis in a cancer type-specific manner. Owing to the multi-functional nature of H2Bub1, misregulation of its writers and erasers may drive disease initiation and progression through additional synergistic processes. Accordingly, understanding the molecular determinants and pathogenic impacts associated with aberrant H2Bub1 regulation may reveal novel drug targets and therapeutic vulnerabilities that can be exploited to develop innovative precision medicine strategies that better combat cancer. In this review, we present the normal functions of H2Bub1 in the control of DNA-associated processes and describe the pathogenic implications associated with its misregulation in cancer. We further discuss the challenges coupled with the development of therapeutic strategies targeting H2Bub1 misregulation and expose the potential benefits of designing treatments that synergistically exploit the multiple functionalities of H2Bub1 to improve treatment selectivity and efficacy.
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11
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Sun T, Zhang K, Li W, Liu Y, Pangeni RP, Li A, Arvanitis L, Raz DJ. Transcription factor AP2 enhances malignancy of non-small cell lung cancer through upregulation of USP22 gene expression. Cell Commun Signal 2022; 20:147. [PMID: 36123698 PMCID: PMC9484186 DOI: 10.1186/s12964-022-00946-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 07/23/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ubiquitin-specific protease 22 (USP22), a putative cancer stem cell marker, is frequently upregulated in cancers, and USP22 overexpression is associated with aggressive growth, metastasis, and therapy resistance in various human cancers including lung cancer. However, USP22 gene amplification seldom occurs, and the mechanism underlying USP22 upregulation in human cancers remains largely unknown. METHODS A luciferase reporter driven by a promoter region of USP22 gene was selectively constructed to screen against a customized siRNA library targeting 89 selected transcription factors to identify potential transcription factors (TFs) that regulate USP22 expression in human non-small cell lung cancers (NSCLC). Association of identified TFs with USP22 and potential role of the TFs were validated and explored in NSCLC by biological assays and immunohistochemistry analysis. RESULTS Luciferase reporter assays revealed that SP1 and activating transcription factor 3 (ATF3) inhibit USP22 transcription, while transcription factor AP-2 Alpha/Beta (TFAP2A/2B) and c-Myc promote USP22 transcription. Binding site-directed mutagenesis and chromosome immunoprecipitation (ChIP) assays validated AP2α and AP2β are novel TFs of USP22. Furthermore, overexpression of AP2A and AP2B significantly upregulates USP22 expression, and its target: Cyclin D1, concurrently enhances the proliferation, migration, and invasion of NSCLC A549 and H1299 cells in a partially USP22-dependent manner. Moreover, AP2 protein level correlated with USP22 protein in human NSCLC tissues. CONCLUSION Our findings indicate AP2α and AP2β are important transcription factors driving USP22 gene expression to promote the progression of NSCLC, and further support USP22 as a potential biomarker and therapeutic target for lung cancer. Video Abstract.
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Affiliation(s)
- Ting Sun
- Division of Thoracic Surgery, City of Hope National Medical Center, Duarte, CA, USA.,Laboratory of Surgery, The General Hospital of Ningxia Medical University, Yinchuan, China.,Faculty of Health Science, University of Macau, Macau, China
| | - Keqiang Zhang
- Division of Thoracic Surgery, City of Hope National Medical Center, Duarte, CA, USA.
| | - Wendong Li
- Division of Thoracic Surgery, City of Hope National Medical Center, Duarte, CA, USA
| | - Yunze Liu
- Faculty of Health Science, University of Macau, Macau, China
| | - Rajendra P Pangeni
- Division of Thoracic Surgery, City of Hope National Medical Center, Duarte, CA, USA
| | - Aimin Li
- Department of Pathology, City of Hope National Medical Center, Duarte, CA, USA
| | - Leonidas Arvanitis
- Department of Pathology, City of Hope National Medical Center, Duarte, CA, USA
| | - Dan J Raz
- Division of Thoracic Surgery, City of Hope National Medical Center, Duarte, CA, USA.
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12
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Yin X, Liu Q, Liu F, Tian X, Yan T, Han J, Jiang S. Emerging Roles of Non-proteolytic Ubiquitination in Tumorigenesis. Front Cell Dev Biol 2022; 10:944460. [PMID: 35874839 PMCID: PMC9298949 DOI: 10.3389/fcell.2022.944460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/15/2022] [Indexed: 12/13/2022] Open
Abstract
Ubiquitination is a critical type of protein post-translational modification playing an essential role in many cellular processes. To date, more than eight types of ubiquitination exist, all of which are involved in distinct cellular processes based on their structural differences. Studies have indicated that activation of the ubiquitination pathway is tightly connected with inflammation-related diseases as well as cancer, especially in the non-proteolytic canonical pathway, highlighting the vital roles of ubiquitination in metabolic programming. Studies relating degradable ubiquitination through lys48 or lys11-linked pathways to cellular signaling have been well-characterized. However, emerging evidence shows that non-degradable ubiquitination (linked to lys6, lys27, lys29, lys33, lys63, and Met1) remains to be defined. In this review, we summarize the non-proteolytic ubiquitination involved in tumorigenesis and related signaling pathways, with the aim of providing a reference for future exploration of ubiquitination and the potential targets for cancer therapies.
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Affiliation(s)
- Xiu Yin
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China
| | - Qingbin Liu
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China
| | - Fen Liu
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China
| | - Xinchen Tian
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China.,Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Tinghao Yan
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China.,Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jie Han
- Department of Thyroid and Breast Surgery, Jining First People's Hospital, Jining Medical University, Jining, China
| | - Shulong Jiang
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China
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13
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Ohanna M, Biber P, Deckert M. Emerging Role of Deubiquitinating Enzymes (DUBs) in Melanoma Pathogenesis. Cancers (Basel) 2022; 14:cancers14143371. [PMID: 35884430 PMCID: PMC9322030 DOI: 10.3390/cancers14143371] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 02/04/2023] Open
Abstract
Metastatic melanoma is the leading cause of death from skin cancer. Therapies targeting the BRAF oncogenic pathway and immunotherapies show remarkable clinical efficacy. However, these treatments are limited to subgroups of patients and relapse is common. Overall, the majority of patients require additional treatments, justifying the development of new therapeutic strategies. Non-genetic and genetic alterations are considered to be important drivers of cellular adaptation mechanisms to current therapies and disease relapse. Importantly, modification of the overall proteome in response to non-genetic and genetic events supports major cellular changes that are required for the survival, proliferation, and migration of melanoma cells. However, the mechanisms underlying these adaptive responses remain to be investigated. The major contributor to proteome remodeling involves the ubiquitin pathway, ubiquitinating enzymes, and ubiquitin-specific proteases also known as DeUBiquitinases (DUBs). In this review, we summarize the current knowledge regarding the nature and roles of the DUBs recently identified in melanoma progression and therapeutic resistance and discuss their potential as novel sources of vulnerability for melanoma therapy.
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Affiliation(s)
- Mickael Ohanna
- Université Côte d’Azur, INSERM, C3M, 06204 Nice, France; (P.B.); (M.D.)
- Team MicroCan, Equipe Labellisée Ligue Contre le Cancer, 06204 Nice, France
- Correspondence: ; Tel.: +33-(0)4-8915-3853
| | - Pierric Biber
- Université Côte d’Azur, INSERM, C3M, 06204 Nice, France; (P.B.); (M.D.)
- Team MicroCan, Equipe Labellisée Ligue Contre le Cancer, 06204 Nice, France
| | - Marcel Deckert
- Université Côte d’Azur, INSERM, C3M, 06204 Nice, France; (P.B.); (M.D.)
- Team MicroCan, Equipe Labellisée Ligue Contre le Cancer, 06204 Nice, France
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14
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Highly Expressing SCARA5 Promotes Proliferation and Migration of Esophageal Squamous Cell Carcinoma. J Immunol Res 2022; 2022:2555647. [PMID: 35755171 PMCID: PMC9232322 DOI: 10.1155/2022/2555647] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/06/2022] [Accepted: 05/16/2022] [Indexed: 11/18/2022] Open
Abstract
Background Thrombospondin type 1 domain-containing 7A (THSD7A) was reported to play a procancer role in esophageal squamous cell carcinoma (ESCC). The aim of the study was to screen the downstream functional genes of THSD7A and explore their functions in ESCC, based on the reported research into THSD7A function and on gene microarrays. Methods We adopted quantitative reverse-transcription polymerase chain reaction (qRT-PCR) and Celigo high-content screening (HCS) technology to screen the downstream genes of THSD7A. The expression level of target genes was examined by PCR, western blot, and immunohistochemistry (IHC). The effects of these target genes on ESCC malignant biological behavior were performed in vivo and in vitro. The Kaplan-Meier (K-M) survival analysis and Cox regression were used to analyze the prognostic significance of target genes in ESCC patients. Experiments in the literature on liver cancer (LC) were repeated to verify the functions of these genes in different tumors. We further explored the cancer-promoting mechanism of target genes in ESCC by sequencing of the genes' exons. Results Scavenger receptor class A member 5 (SCARA5) was proved to be the downstream driving gene of THSD7A. SCARA5 promoted cell proliferation and migration but inhibited apoptosis in ESCC. IHC results confirmed that SCARA5 expression in ESCC exceeded that in normal tissues. The K-M survival analysis indicated that SCARA5 expression quantity was not related to prognosis, but tumor volume and T classification were both the independent prognostic factors. Repetition of experiments in LC in the literature confirmed that SCARA5 had exactly opposite functions in EC and LC. Conclusion SCARA5 was related to the development and occurrence of ESCC. Our findings suggested that it was a potentially diagnostic individualized therapeutic target for ESCC in the future and that its application could possibly be combined with that of upstream THSD7A gene.
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15
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Ning Z, Guo X, Liu X, Lu C, Wang A, Wang X, Wang W, Chen H, Qin W, Liu X, Zhou L, Ma C, Du J, Lin Z, Luo H, Otkur W, Qi H, Chen D, Xia T, Liu J, Tan G, Xu G, Piao HL. USP22 regulates lipidome accumulation by stabilizing PPARγ in hepatocellular carcinoma. Nat Commun 2022; 13:2187. [PMID: 35449157 PMCID: PMC9023467 DOI: 10.1038/s41467-022-29846-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 03/30/2022] [Indexed: 12/13/2022] Open
Abstract
Elevated de novo lipogenesis is considered to be a crucial factor in hepatocellular carcinoma (HCC) development. Herein, we identify ubiquitin-specific protease 22 (USP22) as a key regulator for de novo fatty acid synthesis, which directly interacts with deubiquitinates and stabilizes peroxisome proliferator-activated receptor gamma (PPARγ) through K48-linked deubiquitination, and in turn, this stabilization increases acetyl-CoA carboxylase (ACC) and ATP citrate lyase (ACLY) expressions. In addition, we find that USP22 promotes de novo fatty acid synthesis and contributes to HCC tumorigenesis, however, this tumorigenicity is suppressed by inhibiting the expression of PPARγ, ACLY, or ACC in in vivo tumorigenesis experiments. In HCC, high expression of USP22 positively correlates with PPARγ, ACLY or ACC expression, and associates with a poor prognosis. Taken together, we identify a USP22-regulated lipogenesis mechanism that involves the PPARγ-ACLY/ACC axis in HCC tumorigenesis and provide a rationale for therapeutic targeting of lipogenesis via USP22 inhibition. Different deubiquitinases are associated to cancer development. Here, the authors show that PPARgamma is stabilized by USP22-mediated deubiquitination leading to lipid accumulation and promoting hepatocellular carcinoma.
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Affiliation(s)
- Zhen Ning
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.,The First Affiliated Hospital of Dalian Medical University, Dalian Medical University, Dalian, 116000, China.,Liaoning Key Laboratory of Molecular Targeted Drugs in Hepatobiliary and Pancreatic Cancer, Dalian, 116000, China
| | - Xin Guo
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.,The First Affiliated Hospital of Dalian Medical University, Dalian Medical University, Dalian, 116000, China
| | - Xiaolong Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Chang Lu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.,The First Affiliated Hospital of Dalian Medical University, Dalian Medical University, Dalian, 116000, China
| | - Aman Wang
- The First Affiliated Hospital of Dalian Medical University, Dalian Medical University, Dalian, 116000, China.,Liaoning Key Laboratory of Molecular Targeted Drugs in Hepatobiliary and Pancreatic Cancer, Dalian, 116000, China
| | - Xiaolin Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Wen Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Huan Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Wangshu Qin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Xinyu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Lina Zhou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Chi Ma
- The First Affiliated Hospital of Dalian Medical University, Dalian Medical University, Dalian, 116000, China.,Liaoning Key Laboratory of Molecular Targeted Drugs in Hepatobiliary and Pancreatic Cancer, Dalian, 116000, China
| | - Jian Du
- The First Affiliated Hospital of Dalian Medical University, Dalian Medical University, Dalian, 116000, China.,Liaoning Key Laboratory of Molecular Targeted Drugs in Hepatobiliary and Pancreatic Cancer, Dalian, 116000, China
| | - Zhikun Lin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.,The First Affiliated Hospital of Dalian Medical University, Dalian Medical University, Dalian, 116000, China.,Liaoning Key Laboratory of Molecular Targeted Drugs in Hepatobiliary and Pancreatic Cancer, Dalian, 116000, China
| | - Haifeng Luo
- The First Affiliated Hospital of Dalian Medical University, Dalian Medical University, Dalian, 116000, China.,Liaoning Key Laboratory of Molecular Targeted Drugs in Hepatobiliary and Pancreatic Cancer, Dalian, 116000, China
| | - Wuxiyar Otkur
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Huan Qi
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Di Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Tian Xia
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Jiwei Liu
- The First Affiliated Hospital of Dalian Medical University, Dalian Medical University, Dalian, 116000, China.,Liaoning Key Laboratory of Molecular Targeted Drugs in Hepatobiliary and Pancreatic Cancer, Dalian, 116000, China
| | - Guang Tan
- The First Affiliated Hospital of Dalian Medical University, Dalian Medical University, Dalian, 116000, China. .,Liaoning Key Laboratory of Molecular Targeted Drugs in Hepatobiliary and Pancreatic Cancer, Dalian, 116000, China.
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
| | - Hai-Long Piao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Department of Biochemistry & Molecular Biology, School of Life Sciences, China Medical University, Shenyang, 110122, China.
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16
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Thompson LL, Rutherford KA, Lepage CC, McManus KJ. Aberrant SKP1 Expression: Diverse Mechanisms Impacting Genome and Chromosome Stability. Front Cell Dev Biol 2022; 10:859582. [PMID: 35345853 PMCID: PMC8957228 DOI: 10.3389/fcell.2022.859582] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 02/22/2022] [Indexed: 11/26/2022] Open
Abstract
The S-phase Kinase-Associated Protein 1 (SKP1) is a core component of the SKP1, Cullin 1, F-box protein (SCF) complex, an E3 ubiquitin ligase that serves to poly-ubiquitinate a vast array of protein targets as a signal for their proteasomal degradation, thereby playing a critical role in the regulation of downstream biological processes. Many of the proteins regulated by SKP1 and the SCF complex normally function within pathways that are essential for maintaining genome stability, including DNA damage repair, apoptotic signaling, and centrosome dynamics. Accordingly, aberrant SKP1 and SCF complex expression and function is expected to disrupt these essential pathways, which may have pathological implications in diseases like cancer. In this review, we summarize the central role SKP1 plays in regulating essential cellular processes; we describe functional models in which SKP1 expression is altered and the corresponding impacts on genome stability; and we discuss the prevalence of SKP1 somatic copy number alterations, mutations, and altered protein expression across different cancer types, to identify a potential link between SKP1 and SCF complex dysfunction to chromosome/genome instability and cancer pathogenesis. Ultimately, understanding the role of SKP1 in driving chromosome instability will expand upon our rudimentary understanding of the key events required for genome/chromosome stability that may aid in our understanding of cancer pathogenesis, which will be critical for future studies to establish whether SKP1 may be useful as prognostic indicator or as a therapeutic target.
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Affiliation(s)
- Laura L Thompson
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB, Canada.,Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada
| | - Kailee A Rutherford
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB, Canada.,Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada
| | - Chloe C Lepage
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB, Canada.,Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada
| | - Kirk J McManus
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB, Canada.,Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada
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17
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Chang YS, Su CW, Chen SC, Chen YY, Liang YJ, Wu JC. Upregulation of USP22 and ABCC1 during Sorafenib Treatment of Hepatocellular Carcinoma Contribute to Development of Resistance. Cells 2022; 11:cells11040634. [PMID: 35203285 PMCID: PMC8870465 DOI: 10.3390/cells11040634] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/28/2022] [Accepted: 02/10/2022] [Indexed: 12/10/2022] Open
Abstract
Sorafenib is a small molecule that blocks tumor proliferation by targeting the activity of multi-kinases for the treatment of advanced hepatocellular carcinoma (HCC). Increasing sorafenib resistance following long-term treatment is frequently encountered. Mechanisms underlying sorafenib resistance remain not completely clear. To further understand the mechanism of sorafenib resistance in HCC, we established sorafenib-resistant cell lines by slowly increasing sorafenib concentration in cell culture medium. Upregulation of USP22 and ABCC1 were found in Sorafenib-resistant cells. Sorafenib-resistant cells treated with USP22 siRNA showed significant reduction in endogenous mRNA and protein levels of ABCC1. During sorafenib treatment, upregulation of USP22 increases ABCC1 expression and subsequently contributes to sorafenib resistance in HCC cells. Immunohistochemical analysis revealed a positive correlation between USP22 and ABCC1 expression in tissue samples from sorafenib-resistant patients (Pearson’s correlation = 0.59, p = 0.03). Our findings indicate that upregulation of USP22 and ABCC1 expression during treatment contribute to sorafenib resistance in HCC cells and that USP22 has strong potential as a therapeutic target for overcoming sorafenib resistance in HCC patients.
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Affiliation(s)
- Yung-Sheng Chang
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan; (Y.-S.C.); (S.-C.C.)
| | - Chien-Wei Su
- Faculty of Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan;
- Division of Gastroenterology and Hepatology, Department of Medicine, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - San-Chi Chen
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan; (Y.-S.C.); (S.-C.C.)
- Faculty of Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan;
- Department of Oncology, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Yen-Ying Chen
- Department of Pathology, Taipei Veterans General Hospital, Taipei 11217, Taiwan;
| | - Yuh-Jin Liang
- Medical Research Department, Taipei Veterans General Hospital, Taipei 11217, Taiwan;
| | - Jaw-Ching Wu
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan; (Y.-S.C.); (S.-C.C.)
- Medical Research Department, Taipei Veterans General Hospital, Taipei 11217, Taiwan;
- Cancer Progression Research Center, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
- Correspondence: ; Tel.: +886-2-28712121 (ext. 3218)
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18
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Sun J, Song W, Chang Y, Wang Y, Lu T, Zhang Z. OsLMP1, Encoding a Deubiquitinase, Regulates the Immune Response in Rice. FRONTIERS IN PLANT SCIENCE 2022; 12:814465. [PMID: 35116051 PMCID: PMC8805587 DOI: 10.3389/fpls.2021.814465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
Lesion mimic mutants have become an effective material for understanding plant-microbe interactions and the immune mechanism in plants. Although many mechanisms responsible for the lesion mimic phenotype have been clarified in plants, the mechanism by which lesion mimic is regulated by posttranslational modification remained largely elusive, especially in rice. In this study, a mutant with the lesion mimic phenotype was obtained and named lmp1-1. Physiological measurements and quantitative real-time PCR analysis showed that the defense response was activated in the mutants. Transcriptome analysis showed that the phenylalanine ammonia lyase (PAL) pathway was activated in the mutant, causing the accumulation of salicylic acid (SA). The results of mapping based cloning showed that OsLMP1 encodes a deubiquitinase. OsLMP1 can cleave ubiquitination precursors. Furthermore, OsLMP1 epigenetically modifies SA synthetic pathway genes by deubiquitinating H2B and regulates the immune response in rice. In summary, this study deepens our understanding of the function of OsLMP1 in the plant immune response and provides further insight into the relationship between plants and pathogenic microorganisms.
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19
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Liu R, Zhang W, Cai J, Lin W, Zheng Q, Wu Y. USP22 Mediates High Glucose-Induced Injury and Epithelial-Mesenchymal Transition in Podocytes via Regulating the RIPK3/MLKL Signaling Pathway. J HARD TISSUE BIOL 2022. [DOI: 10.2485/jhtb.31.187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Renhua Liu
- Department of Nephrology, Huizhou Municipal Central Hospital
| | | | - Jun Cai
- Department of Nephrology, Huizhou Municipal Central Hospital
| | - Weiping Lin
- Department of Nephrology, Huizhou Municipal Central Hospital
| | - Qingfa Zheng
- Department of Nephrology, Huizhou Municipal Central Hospital
| | - Yong Wu
- Department of Nephrology, Huizhou Municipal Central Hospital
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20
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Li W, Wu H, Sui S, Wang Q, Xu S, Pang D. Targeting Histone Modifications in Breast Cancer: A Precise Weapon on the Way. Front Cell Dev Biol 2021; 9:736935. [PMID: 34595180 PMCID: PMC8476812 DOI: 10.3389/fcell.2021.736935] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/16/2021] [Indexed: 12/27/2022] Open
Abstract
Histone modifications (HMs) contribute to maintaining genomic stability, transcription, DNA repair, and modulating chromatin in cancer cells. Furthermore, HMs are dynamic and reversible processes that involve interactions between numerous enzymes and molecular components. Aberrant HMs are strongly associated with tumorigenesis and progression of breast cancer (BC), although the specific mechanisms are not completely understood. Moreover, there is no comprehensive overview of abnormal HMs in BC, and BC therapies that target HMs are still in their infancy. Therefore, this review summarizes the existing evidence regarding HMs that are involved in BC and the potential mechanisms that are related to aberrant HMs. Moreover, this review examines the currently available agents and approved drugs that have been tested in pre-clinical and clinical studies to evaluate their effects on HMs. Finally, this review covers the barriers to the clinical application of therapies that target HMs, and possible strategies that could help overcome these barriers and accelerate the use of these therapies to cure patients.
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Affiliation(s)
- Wei Li
- Harbin Medical University Third Hospital: Tumor Hospital of Harbin Medical University, Harbin, China
| | - Hao Wu
- Harbin Medical University Third Hospital: Tumor Hospital of Harbin Medical University, Harbin, China
| | - Shiyao Sui
- Harbin Medical University Third Hospital: Tumor Hospital of Harbin Medical University, Harbin, China
| | - Qin Wang
- Harbin Medical University Third Hospital: Tumor Hospital of Harbin Medical University, Harbin, China
| | - Shouping Xu
- Harbin Medical University Third Hospital: Tumor Hospital of Harbin Medical University, Harbin, China
| | - Da Pang
- Harbin Medical University Third Hospital: Tumor Hospital of Harbin Medical University, Harbin, China.,Heilongjiang Academy of Medical Sciences, Harbin, China
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21
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Thompson LL, Rutherford KA, Lepage CC, McManus KJ. The SCF Complex Is Essential to Maintain Genome and Chromosome Stability. Int J Mol Sci 2021; 22:8544. [PMID: 34445249 PMCID: PMC8395177 DOI: 10.3390/ijms22168544] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 07/29/2021] [Accepted: 08/05/2021] [Indexed: 12/20/2022] Open
Abstract
The SKP1, CUL1, F-box protein (SCF) complex encompasses a group of 69 SCF E3 ubiquitin ligase complexes that primarily modify protein substrates with poly-ubiquitin chains to target them for proteasomal degradation. These SCF complexes are distinguishable by variable F-box proteins, which determine substrate specificity. Although the function(s) of each individual SCF complex remain largely unknown, those that have been characterized regulate a wide array of cellular processes, including gene transcription and the cell cycle. In this regard, the SCF complex regulates transcription factors that modulate cell signaling and ensures timely degradation of primary cell cycle regulators for accurate replication and segregation of genetic material. SCF complex members are aberrantly expressed in a myriad of cancer types, with altered expression or function of the invariable core SCF components expected to have a greater impact on cancer pathogenesis than that of the F-box proteins. Accordingly, this review describes the normal roles that various SCF complexes have in maintaining genome stability before discussing the impact that aberrant SCF complex expression and/or function have on cancer pathogenesis. Further characterization of the SCF complex functions is essential to identify and develop therapeutic approaches to exploit aberrant SCF complex expression and function.
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Affiliation(s)
- Laura L. Thompson
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada; (L.L.T.); (K.A.R.); (C.C.L.)
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Kailee A. Rutherford
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada; (L.L.T.); (K.A.R.); (C.C.L.)
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Chloe C. Lepage
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada; (L.L.T.); (K.A.R.); (C.C.L.)
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Kirk J. McManus
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada; (L.L.T.); (K.A.R.); (C.C.L.)
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
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22
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Guo JN, Xia BR, Deng SH, Yang C, Pi YN, Cui BB, Jin WL. Deubiquitinating Enzymes Orchestrate the Cancer Stem Cell-Immunosuppressive Niche Dialogue: New Perspectives and Therapeutic Potential. Front Cell Dev Biol 2021; 9:680100. [PMID: 34179009 PMCID: PMC8220152 DOI: 10.3389/fcell.2021.680100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 05/17/2021] [Indexed: 11/13/2022] Open
Abstract
Cancer stem cells (CSCs) are sparks for igniting tumor recurrence and the instigators of low response to immunotherapy and drug resistance. As one of the important components of tumor microenvironment, the tumor associated immune microenvironment (TAIM) is driving force for the heterogeneity, plasticity and evolution of CSCs. CSCs create the inhibitory TAIM (ITAIM) mainly through four stemness-related signals (SRSs), including Notch-nuclear factor-κB axis, Hedgehog, Wnt and signal transducer and activator of transcription. Ubiquitination and deubiquitination in proteins related to the specific stemness of the CSCs have a profound impact on the regulation of ITAIM. In regulating the balance between ubiquitination and deubiquitination, it is crucial for deubiquitinating enzymes (DUBs) to cleave ubiquitin chains from substrates. Ubiquitin-specific peptidases (USPs) comprise the largest family of DUBs. Growing evidence suggests that they play novel functions in contribution of ITAIM, including regulating tumor immunogenicity, activating stem cell factors, upregulating the SRSs, stabilizing anti-inflammatory receptors, and regulating anti-inflammatory cytokines. These overactive or abnormal signaling may dampen antitumor immune responses. The inhibition of USPs could play a regulatory role in SRSs and reversing ITAIM, and also have great potential in improving immune killing ability against tumor cells, including CSCs. In this review, we focus on the USPs involved in CSCs signaling pathways and regulating ITAIM, which are promising therapeutic targets in antitumor therapy.
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Affiliation(s)
- Jun-Nan Guo
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Bai-Rong Xia
- Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, Anhui Provincial Cancer Hospital, University of Science and Technology of China, Hefei, China
| | - Shen-Hui Deng
- Department of Anesthesiology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Chang Yang
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Ya-Nan Pi
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Bin-Bin Cui
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Wei-Lin Jin
- Medical Frontier Innovation Research Center, The First Hospital of Lanzhou University, Institute of Cancer Neuroscience, The First Clinical Medical College of Lanzhou University, Lanzhou, China
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23
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Prokakis E, Dyas A, Grün R, Fritzsche S, Bedi U, Kazerouni ZB, Kosinsky RL, Johnsen SA, Wegwitz F. USP22 promotes HER2-driven mammary carcinoma aggressiveness by suppressing the unfolded protein response. Oncogene 2021; 40:4004-4018. [PMID: 34007022 PMCID: PMC8195738 DOI: 10.1038/s41388-021-01814-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 04/08/2021] [Accepted: 04/23/2021] [Indexed: 02/06/2023]
Abstract
The Ubiquitin-Specific Protease 22 (USP22) is a deubiquitinating subunit of the mammalian SAGA transcriptional co-activating complex. USP22 was identified as a member of the so-called "death-from-cancer" signature predicting therapy failure in cancer patients. However, the importance and functional role of USP22 in different types and subtypes of cancer remain largely unknown. In the present study, we leveraged human cell lines and genetic mouse models to investigate the role of USP22 in HER2-driven breast cancer (HER2+-BC) and demonstrate for the first time that USP22 is required for the tumorigenic properties in murine and human HER2+-BC models. To get insight into the underlying mechanisms, we performed transcriptome-wide gene expression analyses and identified the Unfolded Protein Response (UPR) as a pathway deregulated upon USP22 loss. The UPR is normally induced upon extrinsic or intrinsic stresses that can promote cell survival and recovery if shortly activated or programmed cell death if activated for an extended period. Strikingly, we found that USP22 actively suppresses UPR induction in HER2+-BC cells by stabilizing the major endoplasmic reticulum (ER) chaperone HSPA5. Consistently, loss of USP22 renders tumor cells more sensitive to apoptosis and significantly increases the efficiency of therapies targeting the ER folding capacity. Together, our data suggest that therapeutic strategies targeting USP22 activity may sensitize tumor cells to UPR induction and could provide a novel, effective approach to treat HER2+-BC.
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Affiliation(s)
- Evangelos Prokakis
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Anna Dyas
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Regina Grün
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Sonja Fritzsche
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
- Department of Gynecology and Obstetrics, University Medical Center Göttingen, Göttingen, Germany
| | - Upasana Bedi
- Chromatin Remodeling Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India, 110067
| | - Zahra B Kazerouni
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Robyn L Kosinsky
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
- Gene Regulatory Mechanisms and Molecular Epigenetics Lab, Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First St SW, Rochester, MN, 55905, USA
| | - Steven A Johnsen
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany.
- Gene Regulatory Mechanisms and Molecular Epigenetics Lab, Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First St SW, Rochester, MN, 55905, USA.
| | - Florian Wegwitz
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany.
- Department of Gynecology and Obstetrics, University Medical Center Göttingen, Göttingen, Germany.
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24
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Vriend J, Nachtigal MW. Ubiquitin Proteasome Pathway Transcriptome in Epithelial Ovarian Cancer. Cancers (Basel) 2021; 13:cancers13112659. [PMID: 34071321 PMCID: PMC8198060 DOI: 10.3390/cancers13112659] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 05/22/2021] [Accepted: 05/24/2021] [Indexed: 12/26/2022] Open
Abstract
In this article, we reviewed the transcription of genes coding for components of the ubiquitin proteasome pathway in publicly available datasets of epithelial ovarian cancer (EOC). KEGG analysis was used to identify the major pathways distinguishing EOC of low malignant potential (LMP) from invasive high-grade serous ovarian carcinomas (HGSOC), and to identify the components of the ubiquitin proteasome system that contributed to these pathways. We identified elevated transcription of several genes encoding ubiquitin conjugases associated with HGSOC. Fifty-eight genes coding for ubiquitin ligases and more than 100 genes encoding ubiquitin ligase adaptors that were differentially expressed between LMP and HGSOC were also identified. Many differentially expressed genes encoding E3 ligase adaptors were Cullin Ring Ligase (CRL) adaptors, and 64 of them belonged to the Cullin 4 DCX/DWD family of CRLs. The data suggest that CRLs play a role in HGSOC and that some of these proteins may be novel therapeutic targets. Differential expression of genes encoding deubiquitinases and proteasome subunits was also noted.
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Affiliation(s)
- Jerry Vriend
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- Correspondence: ; Tel.: +1-204-789-3732
| | - Mark W. Nachtigal
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada;
- Department of Obstetrics, Gynecology & Reproductive Sciences, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- CancerCare Manitoba Research Institute, Winnipeg, MB R3E 0V9, Canada
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25
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Feng T, Ling S, Xu C, Ying L, Su D, Xu X. Ubiquitin-specific peptidase 22 in cancer. Cancer Lett 2021; 514:30-37. [PMID: 33989708 DOI: 10.1016/j.canlet.2021.05.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/21/2021] [Accepted: 05/05/2021] [Indexed: 02/07/2023]
Abstract
Recently, many studies have shown that deubiquitination modification of proteins is of great significance in major physiological processes such as cell proliferation, apoptosis, and differentiation. The ubiquitin-specific peptidase (USP) family is one of the most numerous and structurally diverse of the deubiquitinates known to date. USP22, an important member of the USP family, has been found to be closely associated with tumor cell cycle regulation, stemness maintenance, invasion and metastasis, chemoresistance, and immune regulation. We focus on recent advances regarding USP22's function in cancer and discuss the prospect of USP22 in this review.
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Affiliation(s)
- Tingting Feng
- Department of Pathology, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer(IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China; Cancer Research Institute, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer(IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China; Department of Colorectal Medicine, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer(IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China; Department of Hepatobiliary and Pancreatic Surgery, The Center for Integrated Oncology and Precision Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
| | - Sunbin Ling
- Department of Hepatobiliary and Pancreatic Surgery, The Center for Integrated Oncology and Precision Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China
| | - Chenyang Xu
- Department of Pathology, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer(IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Lisha Ying
- Cancer Research Institute, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer(IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Dan Su
- Department of Pathology, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer(IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China.
| | - Xiao Xu
- Department of Hepatobiliary and Pancreatic Surgery, The Center for Integrated Oncology and Precision Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China.
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26
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Gui D, Dong Z, Peng W, Jiang W, Huang G, Liu G, Ye Z, Wang Y, Xu Z, Fu J, Luo S, Zhao Y. Ubiquitin-specific peptidase 53 inhibits the occurrence and development of clear cell renal cell carcinoma through NF-κB pathway inactivation. Cancer Med 2021; 10:3674-3688. [PMID: 33973730 PMCID: PMC8178486 DOI: 10.1002/cam4.3911] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 12/12/2022] Open
Abstract
Background Clear cell renal cell carcinoma (ccRCC) is one of the most prevalent malignant diseases in the urinary system with more than 140,000 related deaths annually. Ubiquitination–deubiquitination homeostasis is an important factor in ccRCC progression; ubiquitin‐specific peptidase 53 (USP53) belongs to the family of deubiquitinating enzymes, but its functions are rarely reported. Methods Databases obtained from GEO and TCGA were analyzed to reveal the role of USP53 in ccRCC. CCK‐8/BrdU and EDU assays were used to detect the proliferation of ccRCC after USP53 overexpression or knockdown. A tumor xenograft experiment was used to verify the effect of the proliferation of ccRCC after USP53 knockdown. Transwell assays were used to detect the metastasis of ccRCC after USP53 overexpression or knockdown. RNA sequencing and western blot analysis were employed to detect the change in genes after USP53 overexpression and knockdown. Then we tested the effect of USP53 on IκBα protein stability through western blot analysis. Detect the effect of USP53 on IκBα ubiquitination in vitro by immunoprecipitation method. Results USP53 expression was downregulated in ccRCC tissues and USP53 expression was significantly negatively correlated with the tumor progression and clinical prognosis. The ability of growth and metastasis of ccRCC was inhibited after USP53 overexpression. In addition, USP53 knockdown promoted ccRCC growth and metastasis. Moreover, USP53 knockdown promoted the ability of clone formation of ccRCC in vivo. NF‐κB signaling pathway significantly enriched and downregulated in USP53 overexpressed cells, and genes in the NF‐κB pathway (such as IL1B, CXCL1‐3, RELA, RELB, etc.) were obviously downregulated in USP53 overexpressed cells. USP53 overexpression decreased the phosphorylation of IKKβ and P65 in both Caki‐1 and 786‐O cells, and the expression of IκBα was increased. Phosphorylation of IKKβ and P65 was increased in both Caki‐1 and 786‐O cells after USP53 knockdown. As the expression of USP53 increases, the protein expression of IκBα was also gradually increased and USP53 reduced the ubiquitination of IκBα. Conclusion In summary, our data indicate that USP53 inhibits the inactivation of the NF‐κB pathway by reducing the ubiquitination of IκBα to further inhibit ccRCC proliferation and metastasis. These findings may help understand the pathogenesis of ccRCC and introduce new potential therapeutic targets for kidney cancer patients.
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Affiliation(s)
- Dingwen Gui
- Department of Urology, Huangshi Central Hospital (Affiliated Hospital of Hubei Polytechnic University), Edong Healthcare Group, Huangshi, P.R. China.,Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, Wuhan, P.R. China
| | - Zhufeng Dong
- Wuhan University School of Basic Medical Sciences, Wuhan, P.R. China
| | - Wei Peng
- Department of Urology, Huangshi Central Hospital (Affiliated Hospital of Hubei Polytechnic University), Edong Healthcare Group, Huangshi, P.R. China.,Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, Wuhan, P.R. China
| | - Weidong Jiang
- Department of Urology, Huangshi Central Hospital (Affiliated Hospital of Hubei Polytechnic University), Edong Healthcare Group, Huangshi, P.R. China.,Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, Wuhan, P.R. China
| | - Geng Huang
- Department of Urology, Huangshi Central Hospital (Affiliated Hospital of Hubei Polytechnic University), Edong Healthcare Group, Huangshi, P.R. China.,Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, Wuhan, P.R. China
| | - Gang Liu
- Department of Urology, Huangshi Central Hospital (Affiliated Hospital of Hubei Polytechnic University), Edong Healthcare Group, Huangshi, P.R. China.,Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, Wuhan, P.R. China
| | - Zhihua Ye
- Department of Urology, Huangshi Central Hospital (Affiliated Hospital of Hubei Polytechnic University), Edong Healthcare Group, Huangshi, P.R. China.,Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, Wuhan, P.R. China
| | - Yang Wang
- Department of Urology, Huangshi Central Hospital (Affiliated Hospital of Hubei Polytechnic University), Edong Healthcare Group, Huangshi, P.R. China.,Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, Wuhan, P.R. China
| | - Zuwei Xu
- Department of Urology, Huangshi Central Hospital (Affiliated Hospital of Hubei Polytechnic University), Edong Healthcare Group, Huangshi, P.R. China.,Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, Wuhan, P.R. China
| | - Jinlun Fu
- Department of Urology, Huangshi Central Hospital (Affiliated Hospital of Hubei Polytechnic University), Edong Healthcare Group, Huangshi, P.R. China.,Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, Wuhan, P.R. China
| | - Shuai Luo
- Department of Urology, Huangshi Central Hospital (Affiliated Hospital of Hubei Polytechnic University), Edong Healthcare Group, Huangshi, P.R. China.,Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, Wuhan, P.R. China
| | - Yunfei Zhao
- Department of Urology, Huangshi Central Hospital (Affiliated Hospital of Hubei Polytechnic University), Edong Healthcare Group, Huangshi, P.R. China.,Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, Wuhan, P.R. China
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27
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Soares F, Chen B, Lee JB, Ahmed M, Ly D, Tin E, Kang H, Zeng Y, Akhtar N, Minden MD, He HH, Zhang L. CRISPR screen identifies genes that sensitize AML cells to double-negative T-cell therapy. Blood 2021; 137:2171-2181. [PMID: 33270841 DOI: 10.1182/blood.2019004108] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 11/24/2020] [Indexed: 02/06/2023] Open
Abstract
Acute myeloid leukemia (AML) remains a devastating disease in need of new therapies to improve patient survival. Targeted adoptive T-cell therapies have achieved impressive clinical outcomes in some B-cell leukemias and lymphomas but not in AML. Double-negative T cells (DNTs) effectively kill blast cells from the majority of AML patients and are now being tested in clinical trials. However, AML blasts obtained from ∼30% of patients show resistance to DNT-mediated cytotoxicity; the markers or mechanisms underlying this resistance have not been elucidated. Here, we used a targeted clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) screen to identify genes that cause susceptibility of AML cells to DNT therapy. Inactivation of the Spt-Ada-Gcn5-acetyltransferase (SAGA) deubiquitinating complex components sensitized AML cells to DNT-mediated cytotoxicity. In contrast, CD64 inactivation resulted in resistance to DNT-mediated cytotoxicity. Importantly, the level of CD64 expression correlated strongly with the sensitivity of AML cells to DNT treatment. Furthermore, the ectopic expression of CD64 overcame AML resistance to DNTs in vitro and in vivo. Altogether, our data demonstrate the utility of CRISPR/Cas9 screens to uncover mechanisms underlying the sensitivity to DNT therapy and suggest CD64 as a predictive marker for response in AML patients.
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Affiliation(s)
| | - Branson Chen
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada; and
- Department of Laboratory Medicine and Pathobiology
| | - Jong Bok Lee
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada; and
- Department of Immunology, and
| | | | - Dalam Ly
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada; and
- Department of Immunology, and
| | - Enoch Tin
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada; and
- Department of Immunology, and
| | - Hyeonjeong Kang
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada; and
- Department of Laboratory Medicine and Pathobiology
| | | | | | | | - Housheng Hansen He
- Princess Margaret Cancer Centre and
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Li Zhang
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada; and
- Department of Laboratory Medicine and Pathobiology
- Department of Immunology, and
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28
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Kosinsky RL, Saul D, Ammer-Herrmenau C, Faubion WA, Neesse A, Johnsen SA. USP22 Suppresses SPARC Expression in Acute Colitis and Inflammation-Associated Colorectal Cancer. Cancers (Basel) 2021; 13:cancers13081817. [PMID: 33920268 PMCID: PMC8070211 DOI: 10.3390/cancers13081817] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/06/2021] [Accepted: 04/08/2021] [Indexed: 11/18/2022] Open
Abstract
Simple Summary Intestinal inflammation leads to an increased risk of developing colorectal cancer (CRC) and incidences are expected to rise. Therefore, it is crucial to identify molecular factors contributing to these medical conditions. In an earlier study, we identified USP22 as a tumor suppressor in CRC since the loss of Usp22 resulted in severe tumor burden in mice. Moreover, Usp22-deficient mice displayed inflammation-associated symptoms. Therefore, we aimed to elucidate the function of USP22 in intestinal inflammation and inflammation-associated CRC. Indeed, mice with an intestine-specific loss of Usp22 displayed more severe colitis compared to wild type controls. In addition, the loss of Usp22 in a mouse model for CRC resulted in increased numbers of inflammation-associated tumors. Finally, we observed that the loss of USP22 induces the expression of Sparc, a factor previously linked to inflammation. Together, our results suggest that USP22 suppresses Sparc expression in acute colitis and inflammation-associated CRC. Abstract As a member of the 11-gene “death-from-cancer” gene expression signature, ubiquitin-specific protease 22 (USP22) has been considered an oncogene in various human malignancies, including colorectal cancer (CRC). We recently identified an unexpected tumor-suppressive function of USP22 in CRC and detected intestinal inflammation after Usp22 deletion in mice. We aimed to investigate the function of USP22 in intestinal inflammation as well as inflammation-associated CRC. We evaluated the effects of a conditional, intestine-specific knockout of Usp22 during dextran sodium sulfate (DSS)-induced colitis and in a model for inflammation-associated CRC. Mice were analyzed phenotypically and histologically. Differentially regulated genes were identified in USP22-deficient human CRC cells and the occupancy of active histone markers was determined using chromatin immunoprecipitation. The knockout of Usp22 increased inflammation-associated symptoms after DSS treatment locally and systemically. In addition, Usp22 deletion resulted in increased inflammation-associated colorectal tumor growth. Mechanistically, USP22 depletion in human CRC cells induced a profound upregulation of secreted protein acidic and rich in cysteine (SPARC) by affecting H3K27ac and H2Bub1 occupancy on the SPARC gene. The induction of SPARC was confirmed in vivo in our intestinal Usp22-deficient mice. Together, our findings uncover that USP22 controls SPARC expression and inflammation intensity in colitis and CRC.
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Affiliation(s)
- Robyn Laura Kosinsky
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA;
- Department of General, Visceral and Pediatric Surgery, University Medical Center Goettingen, Robert-Koch-Str. 40, 37075 Goettingen, Germany
- Correspondence: ; Tel.: +1-507-293-2386
| | - Dominik Saul
- Kogod Center on Aging and Division of Endocrinology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA;
- Department of Trauma, Orthopedics and Reconstructive Surgery, Georg-August-University Goettingen, 37075 Goettingen, Germany
| | - Christoph Ammer-Herrmenau
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center Goettingen, Robert-Koch-Str. 40, 37075 Goettingen, Germany; (C.A.-H.); (A.N.)
| | - William A. Faubion
- Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA;
| | - Albrecht Neesse
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center Goettingen, Robert-Koch-Str. 40, 37075 Goettingen, Germany; (C.A.-H.); (A.N.)
| | - Steven A. Johnsen
- Gene Regulatory Mechanisms and Molecular Epigenetics Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA;
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Zhou S, Cai Y, Liu X, Jin L, Wang X, Ma W, Zhang T. Role of H2B mono-ubiquitination in the initiation and progression of cancer. Bull Cancer 2021; 108:385-398. [PMID: 33685627 DOI: 10.1016/j.bulcan.2020.12.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/04/2020] [Accepted: 12/11/2020] [Indexed: 01/07/2023]
Abstract
Numerous epigenetic alterations are observed in cancer cells, and dysregulation of mono-ubiquitination of histone H2B (H2Bub1) has often been linked to tumorigenesis. H2Bub1 is a dynamic post-translational histone modification associated with transcriptional elongation and DNA damage response. Histone H2B monoubiquitination occurs in the site of lysine 120, written predominantly by E3 ubiquitin ligases RNF20/RNF40 and deubiquitinated by ubiquitin specific peptidase 22 (USP22). RNF20/40 is often altered in the primary tumors including colorectal cancer, breast cancer, ovarian cancer, prostate cancer, and lung cancer, and the loss of H2Bub1 is usually associated with poor prognosis in tumor patients. The purpose of this review is to summarize the current knowledge of H2Bub1 in transcription, DNA damage response and primary tumors. This review also provides novel options for exploiting the potential therapeutic target H2Bub1 in personalized cancer therapy.
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Affiliation(s)
- Sa Zhou
- Tianjin University of Science and Technology, College of Biotechnology, Tianjin 300457, PR China
| | - Yuqiao Cai
- Tianjin University of Science and Technology, College of Biotechnology, Tianjin 300457, PR China
| | - Xinyi Liu
- Tianjin University of Science and Technology, College of Biotechnology, Tianjin 300457, PR China
| | - Lijun Jin
- Tianjin University of Science and Technology, College of Biotechnology, Tianjin 300457, PR China
| | - Xiaoqin Wang
- Beijing University of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing 102206, PR China
| | - Wenjian Ma
- Tianjin University of Science and Technology, College of Biotechnology, Tianjin 300457, PR China; Qilu Institute of Technology, Shandong 250200, PR China.
| | - Tongcun Zhang
- Tianjin University of Science and Technology, College of Biotechnology, Tianjin 300457, PR China; Wuhan University of Science and Technology, Institute of Biology and Medicine, Wuhan 430081, PR China.
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30
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Jeusset LM, Guppy BJ, Lichtensztejn Z, McDonald D, McManus KJ. Reduced USP22 Expression Impairs Mitotic Removal of H2B Monoubiquitination, Alters Chromatin Compaction and Induces Chromosome Instability That May Promote Oncogenesis. Cancers (Basel) 2021; 13:cancers13051043. [PMID: 33801331 PMCID: PMC7958346 DOI: 10.3390/cancers13051043] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 12/19/2022] Open
Abstract
Chromosome instability (CIN) is an enabling feature of oncogenesis associated with poor patient outcomes, whose genetic determinants remain largely unknown. As mitotic chromatin compaction defects can compromise the accuracy of chromosome segregation into daughter cells and drive CIN, characterizing the molecular mechanisms ensuring accurate chromatin compaction may identify novel CIN genes. In vitro, histone H2B monoubiquitination at lysine 120 (H2Bub1) impairs chromatin compaction, while in vivo H2Bub1 is rapidly depleted from chromatin upon entry into mitosis, suggesting that H2Bub1 removal may be a pre-requisite for mitotic fidelity. The deubiquitinating enzyme USP22 catalyzes H2Bub1 removal in interphase and may also be required for H2Bub1 removal in early mitosis to maintain chromosome stability. In this study, we demonstrate that siRNA-mediated USP22 depletion increases H2Bub1 levels in early mitosis and induces CIN phenotypes associated with mitotic chromatin compaction defects revealed by super-resolution microscopy. Moreover, USP22-knockout models exhibit continuously changing chromosome complements over time. These data identify mitotic removal of H2Bub1 as a critical determinant of chromatin compaction and faithful chromosome segregation. We further demonstrate that USP22 is a CIN gene, indicating that USP22 deletions, which are frequent in many tumor types, may drive genetic heterogeneity and contribute to cancer pathogenesis.
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Affiliation(s)
- Lucile M. Jeusset
- Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, MB R3E0V9, Canada; (L.M.J.); (B.J.G.); (Z.L.)
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3E0J9, Canada
| | - Brent J. Guppy
- Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, MB R3E0V9, Canada; (L.M.J.); (B.J.G.); (Z.L.)
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3E0J9, Canada
| | - Zelda Lichtensztejn
- Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, MB R3E0V9, Canada; (L.M.J.); (B.J.G.); (Z.L.)
| | - Darin McDonald
- Department of Oncology, University of Alberta, Edmonton, AB T6G2H7, Canada;
| | - Kirk J. McManus
- Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, MB R3E0V9, Canada; (L.M.J.); (B.J.G.); (Z.L.)
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3E0J9, Canada
- Correspondence: ; Tel.: +1-(204)-787-2833
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31
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Erez N, Israitel L, Bitman-Lotan E, Wong WH, Raz G, Cornelio-Parra DV, Danial S, Flint Brodsly N, Belova E, Maksimenko O, Georgiev P, Druley T, Mohan RD, Orian A. A Non-stop identity complex (NIC) supervises enterocyte identity and protects from premature aging. eLife 2021; 10:62312. [PMID: 33629655 PMCID: PMC7936876 DOI: 10.7554/elife.62312] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 02/17/2021] [Indexed: 02/06/2023] Open
Abstract
A hallmark of aging is loss of differentiated cell identity. Aged Drosophila midgut differentiated enterocytes (ECs) lose their identity, impairing tissue homeostasis. To discover identity regulators, we performed an RNAi screen targeting ubiquitin-related genes in ECs. Seventeen genes were identified, including the deubiquitinase Non-stop (CG4166). Lineage tracing established that acute loss of Non-stop in young ECs phenocopies aged ECs at cellular and tissue levels. Proteomic analysis unveiled that Non-stop maintains identity as part of a Non-stop identity complex (NIC) containing E(y)2, Sgf11, Cp190, (Mod) mdg4, and Nup98. Non-stop ensured chromatin accessibility, maintaining the EC-gene signature, and protected NIC subunit stability. Upon aging, the levels of Non-stop and NIC subunits declined, distorting the unique organization of the EC nucleus. Maintaining youthful levels of Non-stop in wildtype aged ECs safeguards NIC subunits, nuclear organization, and suppressed aging phenotypes. Thus, Non-stop and NIC, supervise EC identity and protects from premature aging.
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Affiliation(s)
- Neta Erez
- Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Lena Israitel
- Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Eliya Bitman-Lotan
- Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Wing H Wong
- Division of Pediatric Hematology and Oncology, Washington University, Saint-Louis, United States
| | - Gal Raz
- Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Dayanne V Cornelio-Parra
- Department of Genetics, Developmental & Evolutionary Biology, School of Biological and Chemical Sciences University of Missouri, Kansas City, United States
| | - Salwa Danial
- Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Na'ama Flint Brodsly
- Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Elena Belova
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russian Federation
| | - Oksana Maksimenko
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russian Federation
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russian Federation
| | - Todd Druley
- Division of Pediatric Hematology and Oncology, Washington University, Saint-Louis, United States
| | - Ryan D Mohan
- Department of Genetics, Developmental & Evolutionary Biology, School of Biological and Chemical Sciences University of Missouri, Kansas City, United States
| | - Amir Orian
- Rappaport Research Institute and Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
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Hu X, Wang J, Chu M, Liu Y, Wang ZW, Zhu X. Emerging Role of Ubiquitination in the Regulation of PD-1/PD-L1 in Cancer Immunotherapy. Mol Ther 2021; 29:908-919. [PMID: 33388422 DOI: 10.1016/j.ymthe.2020.12.032] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/09/2020] [Accepted: 12/22/2020] [Indexed: 12/11/2022] Open
Abstract
A growing amount of evidence suggests that ubiquitination and deubiquitination of programmed death 1 (PD-1)/programmed death-ligand 1 (PD-L1) play crucial roles in the regulation of PD-1 and PD-L1 protein stabilization and dynamics. PD-1/PD-L1 is a major coinhibitory checkpoint pathway that modulates immune escape in cancer patients, and its engagement and inhibition has significantly reshaped the landscape of tumor clearance. The abnormal ubiquitination and deubiquitination of PD-1/PD-L1 influence PD-1/PD-L1-mediated immunosuppression. In this review, we describe the ubiquitination- and deubiquitination-mediated modulation of PD-1/PD-L1 signaling through a variety of E3 ligases and deubiquitinating enzymes (DUBs). Moreover, we briefly expound on the anticancer potential of some agents that target related E3 ligases, which further modulate the ubiquitination of PD-1/PD-L1 in cancers. Therefore, this review reveals the development of a highly promising therapeutic approach for cancer immunotherapy by targeting PD-1/PD-L1 ubiquitination.
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Affiliation(s)
- Xiaoli Hu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Jing Wang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Man Chu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Yi Liu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China; Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Zhi-Wei Wang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China.
| | - Xueqiong Zhu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325027, China.
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Marsh DJ, Ma Y, Dickson KA. Histone Monoubiquitination in Chromatin Remodelling: Focus on the Histone H2B Interactome and Cancer. Cancers (Basel) 2020; 12:E3462. [PMID: 33233707 PMCID: PMC7699835 DOI: 10.3390/cancers12113462] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 11/13/2020] [Accepted: 11/17/2020] [Indexed: 12/21/2022] Open
Abstract
Chromatin remodelling is a major mechanism by which cells control fundamental processes including gene expression, the DNA damage response (DDR) and ensuring the genomic plasticity required by stem cells to enable differentiation. The post-translational modification of histone H2B resulting in addition of a single ubiquitin, in humans at lysine 120 (K120; H2Bub1) and in yeast at K123, has key roles in transcriptional elongation associated with the RNA polymerase II-associated factor 1 complex (PAF1C) and in the DDR. H2Bub1 itself has been described as having tumour suppressive roles and a number of cancer-related proteins and/or complexes are recognised as part of the H2Bub1 interactome. These include the RING finger E3 ubiquitin ligases RNF20, RNF40 and BRCA1, the guardian of the genome p53, the PAF1C member CDC73, subunits of the switch/sucrose non-fermenting (SWI/SNF) chromatin remodelling complex and histone methyltransferase complexes DOT1L and COMPASS, as well as multiple deubiquitinases including USP22 and USP44. While globally depleted in many primary human malignancies, including breast, lung and colorectal cancer, H2Bub1 is selectively enriched at the coding region of certain highly expressed genes, including at p53 target genes in response to DNA damage, functioning to exercise transcriptional control of these loci. This review draws together extensive literature to cement a significant role for H2Bub1 in a range of human malignancies and discusses the interplay between key cancer-related proteins and H2Bub1-associated chromatin remodelling.
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Affiliation(s)
- Deborah J. Marsh
- Translational Oncology Group, Faculty of Science, School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia; (Y.M.); (K.-A.D.)
- Kolling Institute, Faculty of Medicine and Health, Northern Clinical School, University of Sydney, Camperdown, NSW 2006, Australia
| | - Yue Ma
- Translational Oncology Group, Faculty of Science, School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia; (Y.M.); (K.-A.D.)
| | - Kristie-Ann Dickson
- Translational Oncology Group, Faculty of Science, School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia; (Y.M.); (K.-A.D.)
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Gatti V, Bernassola F, Talora C, Melino G, Peschiaroli A. The Impact of the Ubiquitin System in the Pathogenesis of Squamous Cell Carcinomas. Cancers (Basel) 2020; 12:cancers12061595. [PMID: 32560247 PMCID: PMC7352818 DOI: 10.3390/cancers12061595] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/11/2020] [Accepted: 06/13/2020] [Indexed: 02/07/2023] Open
Abstract
The ubiquitin system is a dynamic regulatory pathway controlling the activity, subcellular localization and stability of a myriad of cellular proteins, which in turn affects cellular homeostasis through the regulation of a variety of signaling cascades. Aberrant activity of key components of the ubiquitin system has been functionally linked with numerous human diseases including the initiation and progression of human tumors. In this review, we will contextualize the importance of the two main components of the ubiquitin system, the E3 ubiquitin ligases (E3s) and deubiquitinating enzymes (DUBs), in the etiology of squamous cell carcinomas (SCCs). We will discuss the signaling pathways regulated by these enzymes, emphasizing the genetic and molecular determinants underlying their deregulation in SCCs.
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Affiliation(s)
- Veronica Gatti
- National Research Council of Italy, Institute of Translational Pharmacology, 00133 Rome, Italy;
| | - Francesca Bernassola
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133 Rome, Italy; (F.B.); (G.M.)
| | - Claudio Talora
- Department of Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy;
| | - Gerry Melino
- Department of Experimental Medicine, TOR, University of Rome Tor Vergata, 00133 Rome, Italy; (F.B.); (G.M.)
| | - Angelo Peschiaroli
- National Research Council of Italy, Institute of Translational Pharmacology, 00133 Rome, Italy;
- Correspondence:
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Interaction of Deubiquitinase 2A-DUB/MYSM1 with DNA Repair and Replication Factors. Int J Mol Sci 2020; 21:ijms21113762. [PMID: 32466590 PMCID: PMC7312997 DOI: 10.3390/ijms21113762] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/07/2020] [Accepted: 05/19/2020] [Indexed: 01/09/2023] Open
Abstract
The deubiquitination of histone H2A on lysine 119 by 2A-DUB/MYSM1, BAP1, USP16, and other enzymes is required for key cellular processes, including transcriptional activation, apoptosis, and cell cycle control, during normal hematopoiesis and tissue development, and in tumor cells. Based on our finding that MYSM1 colocalizes with γH2AX foci in human peripheral blood mononuclear cells, leukemia cells, and melanoma cells upon induction of DNA double-strand breaks with topoisomerase inhibitor etoposide, we applied a mass spectrometry-based proteomics approach to identify novel 2A-DUB/MYSM1 interaction partners in DNA-damage responses. Differential display of MYSM1 binding proteins significantly enriched after exposure of 293T cells to etoposide revealed an interacting network of proteins involved in DNA damage and replication, including factors associated with poor melanoma outcome. In the context of increased DNA-damage in a variety of cell types in Mysm1-deficient mice, in bone marrow cells upon aging and in UV-exposed Mysm1-deficient skin, our current mass spectrometry data provide additional evidence for an interaction between MYSM1 and key DNA replication and repair factors, and indicate a potential function of 2A-DUB/MYSM1 in DNA repair processes.
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36
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Zhang K, Yang L, Wang J, Sun T, Guo Y, Nelson R, Tong TR, Pangeni R, Salgia R, Raz DJ. Ubiquitin-specific protease 22 is critical to in vivo angiogenesis, growth and metastasis of non-small cell lung cancer. Cell Commun Signal 2019; 17:167. [PMID: 31842906 PMCID: PMC6916027 DOI: 10.1186/s12964-019-0480-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 11/11/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Loss of monoubiquitination of histone H2B (H2Bub1) was found to be associated with poor differentiation, cancer stemness, and enhanced malignancy of non-small cell lung cancer (NSCLC). Herein, we investigated the biological significance and therapeutic implications of ubiquitin-specific protease 22 (USP22), an H2Bub1 deubiquitinase, in non-small cell lung cancer (NSCLC). METHODS USP22 expression and its clinical relevance were assessed in NSCLC patients. The effects of USP22 knockout on sensitivity to cisplatin and irradiation, and growth, metastasis of NSCLC xenografts, and survival of cancer-bearing mice were investigated. The underlying mechanisms of targeting USP22 were explored. RESULTS Overexpression of USP22 was observed in 49.0% (99/202) of NSCLC tissues; higher USP22 immunostaining was found to be associated with enhanced angiogenesis and recurrence of NSCLC. Notably, USP22 knockout dramatically suppressed in vitro proliferation, colony formation; and angiogenesis, growth, metastasis of A549 and H1299 in mouse xenograft model, and significantly prolonged survival of metastatic cancer-bearing mice. Furthermore, USP22 knockout significantly impaired non-homologous DNA damage repair capacity, enhanced cisplatin and irradiation-induced apoptosis in these cells. In terms of underlying mechanisms, RNA sequencing and gene ontology enrichment analysis demonstrated that USP22 knockout significantly suppressed angiogenesis, proliferation, EMT, RAS, c-Myc pathways, concurrently enhanced oxidative phosphorylation and tight junction pathways in A549 and H1299 NSCLC cells. Immunoblot analysis confirmed that USP22 knockout upregulated E-cadherin, p16; reduced ALDH1A3, Cyclin E1, c-Myc, and attenuated activation of AKT and ERK pathways in these cells. CONCLUSIONS Our findings suggest USP22 plays critical roles in the malignancy and progression of NSCLC and provide rationales for targeting USP22, which induces broad anti-cancer activities, as a novel therapeutic strategy for NSCLC patient.
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Affiliation(s)
- Keqiang Zhang
- Division of Thoracic Surgery, City of Hope National Medical Center, Duarte, California, USA.
| | - Lu Yang
- Department of System Biology, City of Hope National Medical Center, Duarte, California, USA
| | - Jinhui Wang
- The Integrative Genomics Core Laboratory of Department of Molecular Medicine, City of Hope National Medical Center, Duarte, California, USA
| | - Ting Sun
- Division of Thoracic Surgery, City of Hope National Medical Center, Duarte, California, USA.,Department of Surgery, the General Hospital of Ningxia Medical University, Yinchuan, China
| | - Yuming Guo
- Division of Comparative Medicine, City of Hope National Medical Center, Duarte, CA, USA
| | - Rebecca Nelson
- Department of Pathology, City of Hope National Medical Center, Duarte, California, USA
| | - Tommy R Tong
- Division of Biostatistics, City of Hope National Medical Center, Duarte, California, USA
| | - Rajendra Pangeni
- Division of Thoracic Surgery, City of Hope National Medical Center, Duarte, California, USA
| | - Ravi Salgia
- Department of Medical Oncology & Therapeutics Research, City of Hope National Medical Center, Duarte, California, USA
| | - Dan J Raz
- Division of Thoracic Surgery, City of Hope National Medical Center, Duarte, California, USA.
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37
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USP22-dependent HSP90AB1 expression promotes resistance to HSP90 inhibition in mammary and colorectal cancer. Cell Death Dis 2019; 10:911. [PMID: 31801945 PMCID: PMC6892875 DOI: 10.1038/s41419-019-2141-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/30/2019] [Accepted: 11/11/2019] [Indexed: 12/11/2022]
Abstract
As a member of the 11-gene “death-from-cancer” gene expression signature, overexpression of the Ubiquitin-Specific Protease 22 (USP22) was associated with poor prognosis in various human malignancies. To investigate the function of USP22 in cancer development and progression, we sought to detect common USP22-dependent molecular mechanisms in human colorectal and breast cancer cell lines. We performed mRNA-seq to compare gene expression profiles of various colorectal (SW837, SW480, HCT116) and mammary (HCC1954 and MCF10A) cell lines upon siRNA-mediated knockdown of USP22. Intriguingly, while USP22 depletion had highly heterogeneous effects across the cell lines, all cell lines displayed a common reduction in the expression of Heat Shock Protein 90 Alpha Family Class B Member 1 (HSP90AB1). The downregulation of HSP90AB1 was confirmed at the protein level in these cell lines as well as in colorectal and mammary tumors in mice with tissue-specific Usp22 deletions. Mechanistically, we detected a significant reduction of H3K9ac on the HSP90AB1 gene in USP22-deficient cells. Interestingly, USP22-deficient cells displayed a high dependence on HSP90AB1 expression and diminishing HSP90 activity further using the HSP90 inhibitor Ganetespib resulted in increased therapeutic vulnerability in both colorectal and breast cancer cells in vitro. Accordingly, subcutaneously transplanted CRC cells deficient in USP22 expression displayed increased sensitivity towards Ganetespib treatment in vivo. Together, we discovered that HSP90AB1 is USP22-dependent and that cooperative targeting of USP22 and HSP90 may provide an effective approach to the treatment of colorectal and breast cancer.
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38
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Kosinsky RL, Zerche M, Saul D, Wang X, Wohn L, Wegwitz F, Begus-Nahrmann Y, Johnsen SA. USP22 exerts tumor-suppressive functions in colorectal cancer by decreasing mTOR activity. Cell Death Differ 2019; 27:1328-1340. [PMID: 31527800 DOI: 10.1038/s41418-019-0420-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 08/01/2019] [Accepted: 09/02/2019] [Indexed: 11/09/2022] Open
Abstract
USP22, the deubiquitinating subunit of the SAGA transcriptional cofactor complex, is a member of an 11-gene "death-from-cancer" signature. USP22 has been considered an attractive therapeutic target since high levels of its expression were associated with distant metastasis, poor survival, and high recurrence rates in a wide variety of solid tumors, including colorectal cancer (CRC). We sought to investigate the role of Usp22 during tumorigenesis in vivo using a mouse model for intestinal carcinogenesis with a tissue-specific Usp22 ablation. In addition, we assessed the effects of USP22 depletion in human CRC cells on tumorigenic potential and identified underlying molecular mechanisms. For the first time, we report that USP22 has an unexpected tumor-suppressive function in vivo. Intriguingly, intestine-specific Usp22 deletion exacerbated the tumor phenotype caused by Apc mutation, resulting in significantly decreased survival and higher intestinal tumor incidence. Accordingly, human CRC cells showed increased tumorigenic properties upon USP22 reduction in vitro and in vivo and induced gene expression signatures associated with an unfavorable outcome in CRC patients. Notably, USP22 loss resulted in increased mTOR activity with the tumorigenic properties elicited by the loss of USP22 being reversible by mTOR inhibitor treatment in vitro and in vivo. Here, we demonstrate that USP22 can exert tumor-suppressive functions in CRC where its loss increases CRC burden by modulating mTOR activity. Importantly, our data uncover a tumor- and context-specific role of USP22, suggesting that USP22 expression could serve as a marker for therapeutic stratification of cancer patients.
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Affiliation(s)
- Robyn Laura Kosinsky
- Department of General, Visceral and Pediatric Surgery, Göttingen Center of Molecular Biosciences (GZMB), University Medical Center Göttingen, Göttingen, Germany.
| | - Maria Zerche
- Department of General, Visceral and Pediatric Surgery, Göttingen Center of Molecular Biosciences (GZMB), University Medical Center Göttingen, Göttingen, Germany
| | - Dominik Saul
- Department of Trauma, Orthopedics and Reconstructive Surgery, University Medical Center Göttingen, Göttingen, Germany
| | - Xin Wang
- Department of General, Visceral and Pediatric Surgery, Göttingen Center of Molecular Biosciences (GZMB), University Medical Center Göttingen, Göttingen, Germany
| | - Luisa Wohn
- Department of General, Visceral and Pediatric Surgery, Göttingen Center of Molecular Biosciences (GZMB), University Medical Center Göttingen, Göttingen, Germany
| | - Florian Wegwitz
- Department of General, Visceral and Pediatric Surgery, Göttingen Center of Molecular Biosciences (GZMB), University Medical Center Göttingen, Göttingen, Germany
| | - Yvonne Begus-Nahrmann
- Institute of Molecular Oncology, Göttingen Center of Molecular Biosciences (GZMB), University Medical Center Göttingen, Göttingen, Germany
| | - Steven A Johnsen
- Department of General, Visceral and Pediatric Surgery, Göttingen Center of Molecular Biosciences (GZMB), University Medical Center Göttingen, Göttingen, Germany. .,Gene Regulatory Mechanisms and Molecular Epigenetics Lab, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA.
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Bourbousse C, Barneche F. A Dynamic Signaling Path to Chromatin-Level Control of Plant Drought Response. MOLECULAR PLANT 2019; 12:292-294. [PMID: 30738193 DOI: 10.1016/j.molp.2019.01.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 01/18/2019] [Accepted: 01/28/2019] [Indexed: 06/09/2023]
Affiliation(s)
- Clara Bourbousse
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005 Paris, France.
| | - Fredy Barneche
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL University, 75005 Paris, France.
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40
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Jeusset LMP, McManus KJ. Developing Targeted Therapies That Exploit Aberrant Histone Ubiquitination in Cancer. Cells 2019; 8:cells8020165. [PMID: 30781493 PMCID: PMC6406838 DOI: 10.3390/cells8020165] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 02/12/2019] [Accepted: 02/13/2019] [Indexed: 12/13/2022] Open
Abstract
Histone ubiquitination is a critical epigenetic mechanism regulating DNA-driven processes such as gene transcription and DNA damage repair. Importantly, the cellular machinery regulating histone ubiquitination is frequently altered in cancers. Moreover, aberrant histone ubiquitination can drive oncogenesis by altering the expression of tumor suppressors and oncogenes, misregulating cellular differentiation and promoting cancer cell proliferation. Thus, targeting aberrant histone ubiquitination may be a viable strategy to reprogram transcription in cancer cells, in order to halt cellular proliferation and induce cell death, which is the basis for the ongoing development of therapies targeting histone ubiquitination. In this review, we present the normal functions of histone H2A and H2B ubiquitination and describe the role aberrant histone ubiquitination has in oncogenesis. We also describe the key benefits and challenges associated with current histone ubiquitination targeting strategies. As these strategies are predicted to have off-target effects, we discuss additional efforts aimed at developing synthetic lethal strategies and epigenome editing tools, which may prove pivotal in achieving effective and selective therapies targeting histone ubiquitination, and ultimately improving the lives and outcomes of those living with cancer.
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Affiliation(s)
- Lucile M-P Jeusset
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada.
| | - Kirk J McManus
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada.
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada.
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41
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Nassrallah A, Rougée M, Bourbousse C, Drevensek S, Fonseca S, Iniesto E, Ait-Mohamed O, Deton-Cabanillas AF, Zabulon G, Ahmed I, Stroebel D, Masson V, Lombard B, Eeckhout D, Gevaert K, Loew D, Genovesio A, Breyton C, De Jaeger G, Bowler C, Rubio V, Barneche F. DET1-mediated degradation of a SAGA-like deubiquitination module controls H2Bub homeostasis. eLife 2018; 7:37892. [PMID: 30192741 PMCID: PMC6128693 DOI: 10.7554/elife.37892] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 08/22/2018] [Indexed: 12/11/2022] Open
Abstract
DE-ETIOLATED 1 (DET1) is an evolutionarily conserved component of the ubiquitination machinery that mediates the destabilization of key regulators of cell differentiation and proliferation in multicellular organisms. In this study, we provide evidence from Arabidopsis that DET1 is essential for the regulation of histone H2B monoubiquitination (H2Bub) over most genes by controlling the stability of a deubiquitination module (DUBm). In contrast with yeast and metazoan DUB modules that are associated with the large SAGA complex, the Arabidopsis DUBm only comprises three proteins (hereafter named SGF11, ENY2 and UBP22) and appears to act independently as a major H2Bub deubiquitinase activity. Our study further unveils that DET1-DDB1-Associated-1 (DDA1) protein interacts with SGF11 in vivo, linking the DET1 complex to light-dependent ubiquitin-mediated proteolytic degradation of the DUBm. Collectively, these findings uncover a signaling path controlling DUBm availability, potentially adjusting H2Bub turnover capacity to the cell transcriptional status.
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Affiliation(s)
- Amr Nassrallah
- Centro Nacional de Biotecnología, CNB-CSIC, Madrid, Spain
| | - Martin Rougée
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France.,Université Paris-Sud, Orsay, France
| | - Clara Bourbousse
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France.,Université Paris-Sud, Orsay, France
| | - Stephanie Drevensek
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Sandra Fonseca
- Centro Nacional de Biotecnología, CNB-CSIC, Madrid, Spain
| | - Elisa Iniesto
- Centro Nacional de Biotecnología, CNB-CSIC, Madrid, Spain
| | - Ouardia Ait-Mohamed
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Anne-Flore Deton-Cabanillas
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Gerald Zabulon
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Ikhlak Ahmed
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - David Stroebel
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Vanessa Masson
- Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie PSL Research University, 75005 Paris, France
| | - Berangere Lombard
- Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie PSL Research University, 75005 Paris, France
| | - Dominique Eeckhout
- Department of Plant Systems Biology, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Kris Gevaert
- Department of Biochemistry, Ghent University, Ghent, Belgium.,VIB Center for Medical Biotechnology, Ghent, Belgium
| | - Damarys Loew
- Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie PSL Research University, 75005 Paris, France
| | - Auguste Genovesio
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Cecile Breyton
- Université Grenoble Alpes, Institut de Biologie Structurale, Grenoble, France
| | - Geert De Jaeger
- Department of Plant Systems Biology, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Chris Bowler
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Vicente Rubio
- Centro Nacional de Biotecnología, CNB-CSIC, Madrid, Spain
| | - Fredy Barneche
- Institut de biologie de l'Ecole normale supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, Paris, France
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