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Yu L, Chen Z, Wu Y, Xu M, Zhong D, Xu H, Zhu W. Unraveling role of ubiquitination in drug resistance of gynecological cancer. Am J Cancer Res 2024; 14:2523-2537. [PMID: 38859858 PMCID: PMC11162667 DOI: 10.62347/wykz9784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 05/15/2024] [Indexed: 06/12/2024] Open
Abstract
Chemotherapy is the principal treatment for advanced cancer patients. However, chemotherapeutic resistance, an important hallmark of cancer, is considered as a key impediment to effective therapy in cancer patients. Multiple signaling pathways and factors have been underscored to participate in governing drug resistance. Posttranslational modifications, including ubiquitination, glycosylation, acetylation and phosphorylation, have emerged as key players in modulating drug resistance in gynecological tumors, such as ovarian cancer, cervical cancer and endometrial cancer. In this review article, we summarize the role of ubiquitination in governing drug sensitivity in gynecological cancers. Moreover, we describe the numerous compounds that target ubiquitination in gynecological cancers to reverse chemotherapeutic resistance. In addition, we provide the future perspectives to fully elucidate the mechanisms by which ubiquitination controls drug resistance in gynecological tumors, contributing to restoring drug sensitivity. This review highlights the complex interplay between ubiquitination and drug resistance in gynecological tumors, providing novel insights into potential therapeutic targets and personalized treatment strategies to overcome the bottleneck of drug resistance.
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Affiliation(s)
- Li Yu
- Cancer Center, Department of Nursing, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical CollegeHangzhou, Zhejiang, China
| | - Zheling Chen
- Cancer Center, Department of Medical Oncology, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical CollegeHangzhou, Zhejiang, China
| | - Ying Wu
- Cancer Center, Department of Nursing, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical CollegeHangzhou, Zhejiang, China
| | - Meiliang Xu
- Cancer Center, Department of Nursing, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical CollegeHangzhou, Zhejiang, China
| | - Difei Zhong
- Cancer Center, Department of Nursing, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical CollegeHangzhou, Zhejiang, China
| | - Hongen Xu
- Cancer Center, Department of Radiation Oncology, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical CollegeHangzhou, Zhejiang, China
| | - Wei Zhu
- Cancer Center, Department of Nursing, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical CollegeHangzhou, Zhejiang, China
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2
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Alfano L, Iannuzzi CA, Barone D, Forte IM, Ragosta MC, Cuomo M, Mazzarotti G, Dell'Aquila M, Altieri A, Caporaso A, Roma C, Marra L, Boffo S, Indovina P, De Laurentiis M, Giordano A. CDK9-55 guides the anaphase-promoting complex/cyclosome (APC/C) in choosing the DNA repair pathway choice. Oncogene 2024; 43:1263-1273. [PMID: 38433256 DOI: 10.1038/s41388-024-02982-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 02/08/2024] [Accepted: 02/13/2024] [Indexed: 03/05/2024]
Abstract
DNA double-strand breaks (DSBs) contribute to genome instability, a key feature of cancer. DSBs are mainly repaired by homologous recombination (HR) and non-homologous end-joining (NHEJ). We investigated the role of an isoform of the multifunctional cyclin-dependent kinase 9, CDK9-55, in DNA repair, by generating CDK9-55-knockout HeLa clones (through CRISPR-Cas9), which showed potential HR dysfunction. A phosphoproteomic screening in these clones treated with camptothecin revealed that CDC23 (cell division cycle 23), a component of the E3-ubiquitin ligase APC/C (anaphase-promoting complex/cyclosome), is a new substrate of CDK9-55, with S588 being its putative phosphorylation site. Mutated non-phosphorylatable CDC23(S588A) affected the repair pathway choice by impairing HR and favouring error-prone NHEJ. This CDK9 role should be considered when designing CDK-inhibitor-based cancer therapies.
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Affiliation(s)
- Luigi Alfano
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)-Fondazione G. Pascale, Napoli, Italy.
| | - Carmelina Antonella Iannuzzi
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)-Fondazione G. Pascale, Napoli, Italy
| | - Daniela Barone
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)-Fondazione G. Pascale, Napoli, Italy
| | - Iris Maria Forte
- Breast Unit, Istituto Nazionale Tumori-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)-Fondazione G. Pascale, Napoli, Italy
| | | | - Maria Cuomo
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Giulio Mazzarotti
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Milena Dell'Aquila
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, USA
| | - Angela Altieri
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, USA
| | - Antonella Caporaso
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, USA
| | - Cristin Roma
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)-Fondazione G. Pascale, Napoli, Italy
| | - Laura Marra
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)-Fondazione G. Pascale, Napoli, Italy
| | - Silvia Boffo
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, USA
| | - Paola Indovina
- Sbarro Research Health Organization, Candiolo, Torino, Italy
| | - Michelino De Laurentiis
- Breast Unit, Istituto Nazionale Tumori-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)-Fondazione G. Pascale, Napoli, Italy
| | - Antonio Giordano
- Department of Medical Biotechnologies, University of Siena, Siena, Italy.
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, USA.
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3
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Koo SY, Park EJ, Noh HJ, Jo SM, Ko BK, Shin HJ, Lee CW. Ubiquitination Links DNA Damage and Repair Signaling to Cancer Metabolism. Int J Mol Sci 2023; 24:ijms24098441. [PMID: 37176148 PMCID: PMC10179089 DOI: 10.3390/ijms24098441] [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: 04/12/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023] Open
Abstract
Changes in the DNA damage response (DDR) and cellular metabolism are two important factors that allow cancer cells to proliferate. DDR is a set of events in which DNA damage is recognized, DNA repair factors are recruited to the site of damage, the lesion is repaired, and cellular responses associated with the damage are processed. In cancer, DDR is commonly dysregulated, and the enzymes associated with DDR are prone to changes in ubiquitination. Additionally, cellular metabolism, especially glycolysis, is upregulated in cancer cells, and enzymes in this metabolic pathway are modulated by ubiquitination. The ubiquitin-proteasome system (UPS), particularly E3 ligases, act as a bridge between cellular metabolism and DDR since they regulate the enzymes associated with the two processes. Hence, the E3 ligases with high substrate specificity are considered potential therapeutic targets for treating cancer. A number of small molecule inhibitors designed to target different components of the UPS have been developed, and several have been tested in clinical trials for human use. In this review, we discuss the role of ubiquitination on overall cellular metabolism and DDR and confirm the link between them through the E3 ligases NEDD4, APC/CCDH1, FBXW7, and Pellino1. In addition, we present an overview of the clinically important small molecule inhibitors and implications for their practical use.
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Affiliation(s)
- Seo-Young Koo
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Eun-Ji Park
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Hyun-Ji Noh
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Su-Mi Jo
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Bo-Kyoung Ko
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Hyun-Jin Shin
- Team of Radiation Convergence Research, Korea Institute of Radiological & Medical Sciences, Seoul 01812, Republic of Korea
| | - Chang-Woo Lee
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
- SKKU Institute for Convergence, Sungkyunkwan University, Suwon 16419, Republic of Korea
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4
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Ozmen Yaylaci A, Canbek M. The role of ubiquitin signaling pathway on liver regeneration in rats. Mol Cell Biochem 2023; 478:131-147. [PMID: 35750978 DOI: 10.1007/s11010-022-04482-5] [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: 09/20/2021] [Accepted: 05/18/2022] [Indexed: 01/17/2023]
Abstract
The ubiquitin signalling pathway is a large system associated with numerous intracellular mechanisms. However, its function in the liver regeneration process remains unknown. This particular study investigates the intracellular effect mechanisms of the ubiquitin signalling pathway. It also determines the differences in the expression of 88 genes belonging to the ubiquitin pathway using the RT-PCR array method. To conduct this research, three genes-that differed in the expression analysis were selected. Moreover, their proteins were analysed by western blot analysis while using Ki67 immunohistochemical analysis that determines proliferation rates by hour. It was determined that BRCA1 and BARD1, which are effective in DNA repair, play an active role at PH24. Similarly, Ube2t expression, which belongs to the Fanconi anaemia pathway associated with DNA repair, was also found to be high at PH12-72 h. In addition, it was revealed that the expressions of Anapc2, Anapc11, Cdc20 belonging to the APC/CCdc20 complex, which participate in cell cycle regulation, differed at different hours after PH. Expression of Mul1, which is involved in mitochondrial biogenesis and mitophagy mechanisms, peaked at PH12 under the observation. Considering the Mul1 gene expression difference, MUL1-mediated mitophagy and mitochondrial fission mechanism may be associated with liver regeneration. It was also determined that PARKIN-mediated mitophagy mechanisms are not active in 0-72 h of liver regeneration since PARKIN expression did not show a significant change in PH groups.
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Affiliation(s)
- Ayse Ozmen Yaylaci
- Department of Biology, Faculty of Arts and Science, Hitit University, 19030, Corum, Turkey.
| | - Mediha Canbek
- Department of Biology, Faculty of Arts and Science, Eskisehir Osmangazi University, 26480, Eskisehir, Turkey
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5
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Cao X, Shami Shah A, Sanford EJ, Smolka MB, Baskin JM. Proximity Labeling Reveals Spatial Regulation of the Anaphase-Promoting Complex/Cyclosome by a Microtubule Adaptor. ACS Chem Biol 2022; 17:2605-2618. [PMID: 35952650 PMCID: PMC9933862 DOI: 10.1021/acschembio.2c00527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The anaphase-promoting complex/cyclosome (APC/C) coordinates advancement through mitosis via temporally controlled polyubiquitination events. Despite the long-appreciated spatial organization of key events in mitosis mediated largely by cytoskeletal networks, the spatial regulation of APC/C, the major mitotic E3 ligase, is poorly understood. We describe a microtubule-resident protein, PLEKHA5, as an interactor of APC/C and spatial regulator of its activity in mitosis. Microtubule-localized proximity biotinylation tools revealed that PLEKHA5 depletion decreased APC/C association with the microtubule cytoskeleton, which prevented efficient loading of APC/C with its coactivator CDC20 and led to reduced APC/C E3 ligase activity. PLEKHA5 knockdown delayed mitotic progression, causing accumulation of APC/C substrates dependent upon the PLEKHA5-APC/C interaction in microtubules. We propose that PLEKHA5 functions as an adaptor of APC/C that promotes its subcellular localization to microtubules and facilitates its activation by CDC20, thus ensuring the timely turnover of key mitotic APC/C substrates and proper progression through mitosis.
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Affiliation(s)
- Xiaofu Cao
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14850, United States
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14850, United States
| | - Adnan Shami Shah
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14850, United States
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14850, United States
| | - Ethan J Sanford
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14850, United States
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, United States
| | - Marcus B Smolka
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14850, United States
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, United States
| | - Jeremy M Baskin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14850, United States
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14850, United States
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6
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Greil C, Engelhardt M, Wäsch R. The Role of the APC/C and Its Coactivators Cdh1 and Cdc20 in Cancer Development and Therapy. Front Genet 2022; 13:941565. [PMID: 35832196 PMCID: PMC9273091 DOI: 10.3389/fgene.2022.941565] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/08/2022] [Indexed: 12/03/2022] Open
Abstract
To sustain genomic stability by correct DNA replication and mitosis, cell cycle progression is tightly controlled by the cyclic activity of cyclin-dependent kinases, their binding to cyclins in the respective phase and the regulation of cyclin levels by ubiquitin-dependent proteolysis. The spindle assembly checkpoint plays an important role at the metaphase-anaphase transition to ensure a correct separation of sister chromatids before cytokinesis and to initiate mitotic exit, as an incorrect chromosome distribution may lead to genetically unstable cells and tumorigenesis. The ubiquitin ligase anaphase-promoting complex or cyclosome (APC/C) is essential for these processes by mediating the proteasomal destruction of cyclins and other important cell cycle regulators. To this end, it interacts with the two regulatory subunits Cdh1 and Cdc20. Both play a role in tumorigenesis with Cdh1 being a tumor suppressor and Cdc20 an oncogene. In this review, we summarize the current knowledge about the APC/C-regulators Cdh1 and Cdc20 in tumorigenesis and potential targeted therapeutic approaches.
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7
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Adult Neural Stem Cell Migration Is Impaired in a Mouse Model of Alzheimer's Disease. Mol Neurobiol 2021; 59:1168-1182. [PMID: 34894324 PMCID: PMC8857127 DOI: 10.1007/s12035-021-02620-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/26/2021] [Indexed: 12/18/2022]
Abstract
Neurogenesis in the adult brain takes place in two neurogenic niches: the ventricular-subventricular zone (V-SVZ) and the subgranular zone. After differentiation, neural precursor cells (neuroblasts) have to move to an adequate position, a process known as neuronal migration. Some studies show that in Alzheimer’s disease, the adult neurogenesis is impaired. Our main aim was to investigate some proteins involved both in the physiopathology of Alzheimer’s disease and in the neuronal migration process using the APP/PS1 Alzheimer’s mouse model. Progenitor migrating cells are accumulated in the V-SVZ of the APP/PS1 mice. Furthermore, we find an increase of Cdh1 levels and a decrease of Cdk5/p35 and cyclin B1, indicating that these cells have an alteration of the cell cycle, which triggers a senescence state. We find less cells in the rostral migratory stream and less mature neurons in the olfactory bulbs from APP/PS1 mice, leading to an impaired odour discriminatory ability compared with WT mice. Alzheimer’s disease mice present a deficit in cell migration from V-SVZ due to a senescent phenotype. Therefore, these results can contribute to a new approach of Alzheimer’s based on senolytic compounds or pro-neurogenic factors.
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8
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Lee SY, Kim IY, Heo MB, Moon JH, Son JG, Lee TG. Global Proteomics to Study Silica Nanoparticle-Induced Cytotoxicity and Its Mechanisms in HepG2 Cells. Biomolecules 2021; 11:biom11030375. [PMID: 33801561 PMCID: PMC8000044 DOI: 10.3390/biom11030375] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 12/20/2022] Open
Abstract
Silica nanoparticles (SiO2 NPs) are commonly used in medical and pharmaceutical fields. Research into the cytotoxicity and overall proteomic changes occurring during initial exposure to SiO2 NPs is limited. We investigated the mechanism of toxicity in human liver cells according to exposure time [0, 4, 10, and 16 h (h)] to SiO2 NPs through proteomic analysis using mass spectrometry. SiO2 NP-induced cytotoxicity through various pathways in HepG2 cells. Interestingly, when cells were exposed to SiO2 NPs for 4 h, the morphology of the cells remained intact, while the expression of proteins involved in mRNA splicing, cell cycle, and mitochondrial function was significantly downregulated. These results show that the toxicity of the nanoparticles affects protein expression even if there is no change in cell morphology at the beginning of exposure to SiO2 NPs. The levels of reactive oxygen species changed significantly after 10 h of exposure to SiO2 NPs, and the expression of proteins associated with oxidative phosphorylation, as well as the immune system, was upregulated. Eventually, these changes in protein expression induced HepG2 cell death. This study provides insights into cytotoxicity evaluation at early stages of exposure to SiO2 NPs through in vitro experiments.
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Affiliation(s)
- Sun Young Lee
- Bioimaging Team, Safety Measurement Institute, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Korea;
| | - In Young Kim
- Nano-Safety Team, Safety Measurement Institute, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Korea; (I.Y.K.); (M.B.H.)
| | - Min Beom Heo
- Nano-Safety Team, Safety Measurement Institute, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Korea; (I.Y.K.); (M.B.H.)
| | - Jeong Hee Moon
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea;
| | - Jin Gyeong Son
- Bioimaging Team, Safety Measurement Institute, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Korea;
- Correspondence: (J.G.S.); (T.G.L.); Tel.: +82-42-868-5751 (J.G.S.); +82-42-868-5003 (T.G.L.)
| | - Tae Geol Lee
- Bioimaging Team, Safety Measurement Institute, Korea Research Institute of Standards and Science (KRISS), Daejeon 34113, Korea;
- Correspondence: (J.G.S.); (T.G.L.); Tel.: +82-42-868-5751 (J.G.S.); +82-42-868-5003 (T.G.L.)
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VanGenderen C, Harkness TAA, Arnason TG. The role of Anaphase Promoting Complex activation, inhibition and substrates in cancer development and progression. Aging (Albany NY) 2020; 12:15818-15855. [PMID: 32805721 PMCID: PMC7467358 DOI: 10.18632/aging.103792] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/14/2020] [Indexed: 02/07/2023]
Abstract
The Anaphase Promoting Complex (APC), a multi-subunit ubiquitin ligase, facilitates mitotic and G1 progression, and is now recognized to play a role in maintaining genomic stability. Many APC substrates have been observed overexpressed in multiple cancer types, such as CDC20, the Aurora A and B kinases, and Forkhead box M1 (FOXM1), suggesting APC activity is important for cell health. We performed BioGRID analyses of the APC coactivators CDC20 and CDH1, which revealed that at least 69 proteins serve as APC substrates, with 60 of them identified as playing a role in tumor promotion and 9 involved in tumor suppression. While these substrates and their association with malignancies have been studied in isolation, the possibility exists that generalized APC dysfunction could result in the inappropriate stabilization of multiple APC targets, thereby changing tumor behavior and treatment responsiveness. It is also possible that the APC itself plays a crucial role in tumorigenesis through its regulation of mitotic progression. In this review the connections between APC activity and dysregulation will be discussed with regards to cell cycle dysfunction and chromosome instability in cancer, along with the individual roles that the accumulation of various APC substrates may play in cancer progression.
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Affiliation(s)
- Cordell VanGenderen
- Department of Anatomy, Physiology and Pharmacology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Troy Anthony Alan Harkness
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Terra Gayle Arnason
- Department of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada.,Department of Anatomy, Physiology and Pharmacology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
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Terhune SS, Jung Y, Cataldo KM, Dash RK. Network mechanisms and dysfunction within an integrated computational model of progression through mitosis in the human cell cycle. PLoS Comput Biol 2020; 16:e1007733. [PMID: 32251461 PMCID: PMC7162553 DOI: 10.1371/journal.pcbi.1007733] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 04/16/2020] [Accepted: 02/12/2020] [Indexed: 12/20/2022] Open
Abstract
The cellular protein-protein interaction network that governs cellular proliferation (cell cycle) is highly complex. Here, we have developed a novel computational model of human mitotic cell cycle, integrating diverse cellular mechanisms, for the purpose of generating new hypotheses and predicting new experiments designed to help understand complex diseases. The pathogenic state investigated is infection by a human herpesvirus. The model starts at mitotic entry initiated by the activities of Cyclin-dependent kinase 1 (CDK1) and Polo-like kinase 1 (PLK1), transitions through Anaphase-promoting complex (APC/C) bound to Cell division cycle protein 20 (CDC20), and ends upon mitotic exit mediated by APC/C bound to CDC20 homolog 1 (CDH1). It includes syntheses and multiple mechanisms of degradations of the mitotic proteins. Prior to this work, no such comprehensive model of the human mitotic cell cycle existed. The new model is based on a hybrid framework combining Michaelis-Menten and mass action kinetics for the mitotic interacting reactions. It simulates temporal changes in 12 different mitotic proteins and associated protein complexes in multiple states using 15 interacting reactions and 26 ordinary differential equations. We have defined model parameter values using both quantitative and qualitative data and using parameter values from relevant published models, and we have tested the model to reproduce the cardinal features of human mitosis determined experimentally by numerous laboratories. Like cancer, viruses create dysfunction to support infection. By simulating infection of the human herpesvirus, cytomegalovirus, we hypothesize that virus-mediated disruption of APC/C is necessary to establish a unique mitotic collapse with sustained CDK1 activity, consistent with known mechanisms of virus egress. With the rapid discovery of cellular protein-protein interaction networks and regulatory mechanisms, we anticipate that this model will be highly valuable in helping us to understand the network dynamics and identify potential points of therapeutic interventions.
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Affiliation(s)
- Scott S. Terhune
- Departments of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Yongwoon Jung
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Katie M. Cataldo
- Departments of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Ranjan K. Dash
- Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
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11
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Bansal S, Tiwari S. Mechanisms for the temporal regulation of substrate ubiquitination by the anaphase-promoting complex/cyclosome. Cell Div 2019; 14:14. [PMID: 31889987 PMCID: PMC6927175 DOI: 10.1186/s13008-019-0057-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 12/04/2019] [Indexed: 12/16/2022] Open
Abstract
The anaphase-promoting complex/cyclosome (APC/C) is a multi-subunit, multifunctional ubiquitin ligase that controls the temporal degradation of numerous cell cycle regulatory proteins to direct the unidirectional cell cycle phases. Several different mechanisms contribute to ensure the correct order of substrate modification by the APC/C complex. Recent advances in biochemical, biophysical and structural studies of APC/C have provided a deep mechanistic insight into the working of this complex ubiquitin ligase. This complex displays remarkable conformational flexibility in response to various binding partners and post-translational modifications, which together regulate substrate selection and catalysis of APC/C. Apart from this, various features and modifications of the substrates also influence their recognition and affinity to APC/C complex. Ultimately, temporal degradation of substrates depends on the kind of ubiquitin modification received, the processivity of APC/C, and other extrinsic mechanisms. This review discusses our current understanding of various intrinsic and extrinsic mechanisms responsible for ‘substrate ordering’ by the APC/C complex.
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Affiliation(s)
- Shivangee Bansal
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Swati Tiwari
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
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12
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Meyer SK, Dunn M, Vidler DS, Porter A, Blain PG, Jowsey PA. Phosphorylation of MCPH1 isoforms during mitosis followed by isoform-specific degradation by APC/C-CDH1. FASEB J 2019; 33:2796-2808. [PMID: 30303738 PMCID: PMC6338662 DOI: 10.1096/fj.201801353r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 09/17/2018] [Indexed: 11/11/2022]
Abstract
Microcephalin-1 (MCPH1) exists as 2 isoforms that regulate cyclin-dependent kinase-1 activation and chromosome condensation during mitosis, with MCPH1 mutations causing primary microcephaly. MCPH1 is also a tumor suppressor protein, with roles in DNA damage repair/checkpoints. Despite these important roles, there is little information on the cellular regulation of MCPH1. We show that both MCPH1 isoforms are phosphorylated in a cyclin-dependent kinase-1-dependent manner in mitosis and identify several novel phosphorylation sites. Upon mitotic exit, MCPH1 isoforms were degraded by the anaphase-promoting complex/cyclosome-CDH1 E3 ligase complex. Anaphase-promoting complex/cyclosome-CDH1 target proteins generally have D-Box or KEN-Box degron sequences. We found that MCPH1 isoforms are degraded independently, with the long isoform degradation being D-Box dependent, whereas the short isoform was KEN-Box dependent. Our research identifies several novel mechanisms regulating MCPH1 and also highlights important issues with several commercial MCPH1 antibodies, with potential relevance to previously published data.-Meyer, S. K., Dunn, M., Vidler, D. S., Porter, A., Blain, P. G., Jowsey, P. A. Phosphorylation of MCPH1 isoforms during mitosis followed by isoform-specific degradation by APC/C-CDH1.
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Affiliation(s)
- Stephanie K. Meyer
- National Intitute for Health Research (NIHR) Health Protection Research Unit for Chemical and Radiation Threats and Hazards, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom; and
| | - Michael Dunn
- National Intitute for Health Research (NIHR) Health Protection Research Unit for Chemical and Radiation Threats and Hazards, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom; and
| | - Daniel S. Vidler
- National Intitute for Health Research (NIHR) Health Protection Research Unit for Chemical and Radiation Threats and Hazards, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom; and
| | - Andrew Porter
- Newcastle University Protein and Proteome Analysis, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Peter G. Blain
- National Intitute for Health Research (NIHR) Health Protection Research Unit for Chemical and Radiation Threats and Hazards, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom; and
| | - Paul A. Jowsey
- National Intitute for Health Research (NIHR) Health Protection Research Unit for Chemical and Radiation Threats and Hazards, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom; and
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13
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Curtis NL, Bolanos-Garcia VM. The Anaphase Promoting Complex/Cyclosome (APC/C): A Versatile E3 Ubiquitin Ligase. Subcell Biochem 2019; 93:539-623. [PMID: 31939164 DOI: 10.1007/978-3-030-28151-9_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
In the present chapter we discuss the essential roles of the human E3 ubiquitin ligase Anaphase Promoting Complex/Cyclosome (APC/C) in mitosis as well as the emerging evidence of important APC/C roles in cellular processes beyond cell division control such as regulation of genomic integrity and cell differentiation of the nervous system. We consider the potential incipient role of APC/C dysregulation in the pathophysiology of the neurological disorder Alzheimer's disease (AD). We also discuss how certain Deoxyribonucleic Acid (DNA) and Ribonucleic Acid (RNA) viruses take control of the host's cell division regulatory system through harnessing APC/C ubiquitin ligase activity and hypothesise the plausible molecular mechanisms underpinning virus manipulation of the APC/C. We also examine how defects in the function of this multisubunit protein assembly drive abnormal cell proliferation and lastly argue the potential of APC/C as a promising therapeutic target for the development of innovative therapies for the treatment of chronic malignancies such as cancer.
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Affiliation(s)
- Natalie L Curtis
- Faculty of Health and Life Sciences, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, England, UK
| | - Victor M Bolanos-Garcia
- Faculty of Health and Life Sciences, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, England, UK.
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14
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A review of radiation genomics: integrating patient radiation response with genomics for personalised and targeted radiation therapy. JOURNAL OF RADIOTHERAPY IN PRACTICE 2018. [DOI: 10.1017/s1460396918000547] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
AbstractBackgroundThe success of radiation therapy for cancer patients is dependent on the ability to deliver a total tumouricidal radiation dose capable of eradicating all cancer cells within the clinical target volume, however, the radiation dose tolerance of the surrounding healthy tissues becomes the main dose-limiting factor. The normal tissue adverse effects following radiotherapy are common and significantly impact the quality of life of patients. The likelihood of developing these adverse effects following radiotherapy cannot be predicted based only on the radiation treatment parameters. However, there is evidence to suggest that some common genetic variants are associated with radiotherapy response and the risk of developing adverse effects. Radiation genomics is a field that has evolved in recent years investigating the association between patient genomic data and the response to radiation therapy. This field aims to identify genetic markers that are linked to individual radiosensitivity with the potential to predict the risk of developing adverse effects due to radiotherapy using patient genomic information. It also aims to determine the relative radioresponse of patients using their genetic information for the potential prediction of patient radiation treatment response.Methods and materialsThis paper reports on a review of recent studies in the field of radiation genomics investigating the association between genomic data and patients response to radiation therapy, including the investigation of the role of genetic variants on an individual’s predisposition to enhanced radiotherapy radiosensitivity or radioresponse.ConclusionThe potential for early prediction of treatment response and patient outcome is critical in cancer patients to make decisions regarding continuation, escalation, discontinuation, and/or change in treatment options to maximise patient survival while minimising adverse effects and maintaining patients’ quality of life.
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15
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Khosravi A, Alizadeh S, Jalili A, Shirzad R, Saki N. The impact of Mir-9 regulation in normal and malignant hematopoiesis. Oncol Rev 2018; 12:348. [PMID: 29774136 PMCID: PMC5939831 DOI: 10.4081/oncol.2018.348] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Accepted: 03/01/2018] [Indexed: 12/19/2022] Open
Abstract
MicroRNA-9 (MiR-9) dysregulation has been observed in various cancers. Recently, MiR-9 is considered to have a part in hematopoiesis and hematologic malignancies. However, its importance in blood neoplasms is not yet well defined. Thus, this study was conducted in order to assess the significance of MiR-9 role in the development of hematologic neoplasia, prognosis, and treatment approaches. We have shown that a large number of MiR-9 targets (such as FOXOs, SIRT1, CCND1, ID2, CCNG1, Ets, and NFkB) play essential roles in leukemogenesis and that it is overexpressed in different leukemias. Our findings indicated MiR-9 downregulation in a majority of leukemias. However, its overexpression was reported in patients with dysregulated MiR-9 controlling factors (such as MLLr). Additionally, prognostic value of MiR-9 has been reported in some types of leukemia. This study generally emphasizes on the critical role of MiR-9 in hematologic malignancies as a prognostic factor and a therapeutic target.
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Affiliation(s)
- Abbas Khosravi
- Transfusion Research Center, High Institute for Research and Education in Transfusion Medi-cine, Tehran
| | - Shaban Alizadeh
- Hematology Department, Allied Medical School, Tehran University of Medical Sciences, Tehran
| | - Arsalan Jalili
- Department of Stem Cells and Developmental Biology at Cell Science Re-search Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran
| | - Reza Shirzad
- WHO Collaborating Center for Reference and Research on Rabies, Pasteur Institute of Iran, Tehran
| | - Najmaldin Saki
- Thalassemia & Hemoglobinopathy Research Center, Research Institute of Health, Ahvaz Jun-dishapur University of Medical Sciences, Ahvaz, Iran
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16
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Jaiswal H, Benada J, Müllers E, Akopyan K, Burdova K, Koolmeister T, Helleday T, Medema RH, Macurek L, Lindqvist A. ATM/Wip1 activities at chromatin control Plk1 re-activation to determine G2 checkpoint duration. EMBO J 2017; 36:2161-2176. [PMID: 28607002 PMCID: PMC5510006 DOI: 10.15252/embj.201696082] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 04/05/2017] [Accepted: 05/08/2017] [Indexed: 12/17/2022] Open
Abstract
After DNA damage, the cell cycle is arrested to avoid propagation of mutations. Arrest in G2 phase is initiated by ATM-/ATR-dependent signaling that inhibits mitosis-promoting kinases such as Plk1. At the same time, Plk1 can counteract ATR-dependent signaling and is required for eventual resumption of the cell cycle. However, what determines when Plk1 activity can resume remains unclear. Here, we use FRET-based reporters to show that a global spread of ATM activity on chromatin and phosphorylation of ATM targets including KAP1 control Plk1 re-activation. These phosphorylations are rapidly counteracted by the chromatin-bound phosphatase Wip1, allowing cell cycle restart despite persistent ATM activity present at DNA lesions. Combining experimental data and mathematical modeling, we propose a model for how the minimal duration of cell cycle arrest is controlled. Our model shows how cell cycle restart can occur before completion of DNA repair and suggests a mechanism for checkpoint adaptation in human cells.
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Affiliation(s)
- Himjyot Jaiswal
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Jan Benada
- Laboratory of Cancer Cell Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Erik Müllers
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Karen Akopyan
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Kamila Burdova
- Laboratory of Cancer Cell Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Tobias Koolmeister
- Department of Medical Biochemistry and Biophysics, and Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Thomas Helleday
- Department of Medical Biochemistry and Biophysics, and Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - René H Medema
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Libor Macurek
- Laboratory of Cancer Cell Biology, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Arne Lindqvist
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
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17
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Johnson BA, Aloor HL, Moody CA. The Rb binding domain of HPV31 E7 is required to maintain high levels of DNA repair factors in infected cells. Virology 2016; 500:22-34. [PMID: 27770701 DOI: 10.1016/j.virol.2016.09.029] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 09/20/2016] [Accepted: 09/26/2016] [Indexed: 01/12/2023]
Abstract
Human papillomaviruses (HPV) exhibit constitutive activation of ATM and ATR DNA damage response (DDR) pathways, which are required for productive viral replication. Expression of HPV31 E7 alone is sufficient to activate the DDR through an unknown mechanism. Here, we demonstrate that the E7 Rb binding domain is required to increase levels of many DDR proteins, including ATM, Chk2, Chk1, the MRN components MRE11, Rad50, and NBS1, as well as the homologous recombination repair proteins BRCA1 and Rad51. Interestingly, we have found that the increase in these DNA repair proteins does not occur solely at the level of transcription, but that E7 broadly increases the half-life of these DDR factors, a phenotype that is lost in the E7 Rb binding mutant. These data suggest that HPV-31 upregulates DNA repair factors necessary for replication by increasing protein half-life in a manner requiring the E7 Rb binding domain.
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Affiliation(s)
- Bryan A Johnson
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, NC, USA
| | - Heather L Aloor
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, NC, USA
| | - Cary A Moody
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, NC, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, NC, USA.
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18
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Zhou Z, He M, Shah AA, Wan Y. Insights into APC/C: from cellular function to diseases and therapeutics. Cell Div 2016; 11:9. [PMID: 27418942 PMCID: PMC4944252 DOI: 10.1186/s13008-016-0021-6] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 05/27/2016] [Indexed: 02/07/2023] Open
Abstract
Anaphase-promoting complex/cyclosome (APC/C) is a multifunctional ubiquitin-protein ligase that targets different substrates for ubiquitylation and therefore regulates a variety of cellular processes such as cell division, differentiation, genome stability, energy metabolism, cell death, autophagy as well as carcinogenesis. Activity of APC/C is principally governed by two WD-40 domain proteins, Cdc20 and Cdh1, in and beyond cell cycle. In the past decade, the results based on numerous biochemical, 3D structural, mouse genetic and small molecule inhibitor studies have largely attracted our attention into the emerging role of APC/C and its regulation in biological function, human diseases and potential therapeutics. This review will aim to summarize some recently reported insights into APC/C in regulating cellular function, connection of its dysfunction with human diseases and its implication of therapeutics.
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Affiliation(s)
- Zhuan Zhou
- Department of Cell Biology, University of Pittsburgh School of Medicine and University of Pittsburgh Cancer Institute, 5117 Centre Avenue, Hillman Cancer Center, HCC2.6c, Pittsburgh, PA 15213 USA
| | - Mingjing He
- Department of Cell Biology, University of Pittsburgh School of Medicine and University of Pittsburgh Cancer Institute, 5117 Centre Avenue, Hillman Cancer Center, HCC2.6c, Pittsburgh, PA 15213 USA ; State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041 Sichuan People's Republic of China
| | - Anil A Shah
- Department of Cell Biology, University of Pittsburgh School of Medicine and University of Pittsburgh Cancer Institute, 5117 Centre Avenue, Hillman Cancer Center, HCC2.6c, Pittsburgh, PA 15213 USA
| | - Yong Wan
- Department of Cell Biology, University of Pittsburgh School of Medicine and University of Pittsburgh Cancer Institute, 5117 Centre Avenue, Hillman Cancer Center, HCC2.6c, Pittsburgh, PA 15213 USA
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