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Hu X, Jin X, Cao X, Liu B. The Anaphase-Promoting Complex/Cyclosome Is a Cellular Ageing Regulator. Int J Mol Sci 2022; 23:ijms232315327. [PMID: 36499653 PMCID: PMC9740938 DOI: 10.3390/ijms232315327] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/11/2022] Open
Abstract
The anaphase-promoting complex/cyclosome (APC/C) is a complicated cellular component that plays significant roles in regulating the cell cycle process of eukaryotic organisms. The spatiotemporal regulation mechanisms of APC/C in distinct cell cycle transitions are no longer mysterious, and the components of this protein complex are gradually identified and characterized. Given the close relationship between the cell cycle and lifespan, it is urgent to understand the roles of APC/C in lifespan regulation, but this field still seems to have not been systematically summarized. Furthermore, although several reviews have reported the roles of APC/C in cancer, there are still gaps in the summary of its roles in other age-related diseases. In this review, we propose that the APC/C is a novel cellular ageing regulator based on its indispensable role in the regulation of lifespan and its involvement in age-associated diseases. This work provides an extensive review of aspects related to the underlying mechanisms of APC/C in lifespan regulation and how it participates in age-associated diseases. More comprehensive recognition and understanding of the relationship between APC/C and ageing and age-related diseases will increase the development of targeted strategies for human health.
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Affiliation(s)
- Xiangdong Hu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Xuejiao Jin
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Xiuling Cao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
- Correspondence: (X.C.); (B.L.)
| | - Beidong Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden
- Correspondence: (X.C.); (B.L.)
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2
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Luminescence complementation technology for the identification of MYC:TRRAP inhibitors. Oncotarget 2021; 12:2147-2157. [PMID: 34676047 PMCID: PMC8522838 DOI: 10.18632/oncotarget.28078] [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: 05/15/2021] [Accepted: 09/04/2021] [Indexed: 11/25/2022] Open
Abstract
Mechanism-based targeted therapies have exhibited remarkable success in treating otherwise untreatable or unresectable cancers. Novel targeted therapies that correct dysregulated transcriptional programs in cancer are an unmet medical need. The transcription factor MYC is the most frequently amplified gene in human cancer and is overexpressed because of mutations in an array of oncogenic signaling pathways. The fact that many cancer cells cannot survive without MYC – a phenomenon termed “MYC addiction” – provides a compelling case for the development of MYC-specific targeted therapies. We propose a new strategy to inhibit MYC function by disrupting its essential interaction with TRRAP using small molecules. To achieve our goal, we developed a platform using luminescence complementation for identifying small molecules as inhibitors of the MYC:TRRAP interaction. Here we present validation of this assay by measuring the disruption of TRRAP binding caused by substitutions to the invariant and essential MYC homology 2 region of MYC.
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3
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Li Z, Chen S, Jhong JH, Pang Y, Huang KY, Li S, Lee TY. UbiNet 2.0: a verified, classified, annotated and updated database of E3 ubiquitin ligase-substrate interactions. Database (Oxford) 2021; 2021:baab010. [PMID: 33693667 PMCID: PMC7947570 DOI: 10.1093/database/baab010] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/14/2021] [Accepted: 02/25/2021] [Indexed: 12/13/2022]
Abstract
Ubiquitination is an important post-translational modification, which controls protein turnover by labeling malfunctional and redundant proteins for proteasomal degradation, and also serves intriguing non-proteolytic regulatory functions. E3 ubiquitin ligases, whose substrate specificity determines the recognition of target proteins of ubiquitination, play crucial roles in ubiquitin-proteasome system. UbiNet 2.0 is an updated version of the database UbiNet. It contains 3332 experimentally verified E3-substrate interactions (ESIs) in 54 organisms and rich annotations useful for investigating the regulation of ubiquitination and the substrate specificity of E3 ligases. Based on the accumulated ESIs data, the recognition motifs in substrates for each E3 were also identified and a functional enrichment analysis was conducted on the collected substrates. To facilitate the research on ESIs with different categories of E3 ligases, UbiNet 2.0 performed strictly evidence-based classification of the E3 ligases in the database based on their mechanisms of ubiquitin transfer and substrate specificity. The platform also provides users with an interactive tool that can visualize the ubiquitination network of a group of self-defined proteins, displaying ESIs and protein-protein interactions in a graphical manner. The tool can facilitate the exploration of inner regulatory relationships mediated by ubiquitination among proteins of interest. In summary, UbiNet 2.0 is a user-friendly web-based platform that provides comprehensive as well as updated information about experimentally validated ESIs and a visualized tool for the construction of ubiquitination regulatory networks available at http://awi.cuhk.edu.cn/~ubinet/index.php.
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Affiliation(s)
- Zhongyan Li
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, P.R.China
| | - Siyu Chen
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, P.R.China
| | - Jhih-Hua Jhong
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, P.R.China
| | - Yuxuan Pang
- School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, P.R.China
| | - Kai-Yao Huang
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, P.R.China
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, P.R.China
| | - Shangfu Li
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, P.R.China
| | - Tzong-Yi Lee
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, P.R.China
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, P.R. China
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4
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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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5
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Adam AHB, de Haan LHJ, Estruch IM, Hooiveld GJEJ, Louisse J, Rietjens IMCM. Estrogen receptor alpha (ERα)-mediated coregulator binding and gene expression discriminates the toxic ERα agonist diethylstilbestrol (DES) from the endogenous ERα agonist 17β-estradiol (E2). Cell Biol Toxicol 2020; 36:417-435. [PMID: 32088792 PMCID: PMC7505815 DOI: 10.1007/s10565-020-09516-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 01/28/2020] [Indexed: 12/29/2022]
Abstract
Diethylstilbestrol (DES) is a synthetic estrogen and proven human teratogen and carcinogen reported to act via the estrogen receptor α (ERα). Since the endogenous ERα ligand 17β-estradiol (E2) does not show these adverse effects to a similar extent, we hypothesized that DES' interaction with the ERα differs from that of E2. The current study aimed to investigate possible differences between DES and E2 using in vitro assays that detect ERα-mediated effects, including ERα-mediated reporter gene expression, ERα-mediated breast cancer cell (T47D) proliferation and ERα-coregulator interactions and gene expression in T47D cells. Results obtained indicate that DES and E2 activate ERα-mediated reporter gene transcription and T47D cell proliferation in a similar way. However, significant differences between DES- and E2-induced binding of the ERα to 15 coregulator motifs and in transcriptomic signatures obtained in the T47D cells were observed. It is concluded that differences observed in binding of the ERα with several co-repressor motifs, in downregulation of genes involved in histone deacetylation and DNA methylation and in upregulation of CYP26A1 and CYP26B1 contribute to the differential effects reported for DES and E2.
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Affiliation(s)
- Aziza Hussein Bakheit Adam
- Division of Toxicology, Wageningen University and Research, PO Box 8000, 6700 EA, Wageningen, The Netherlands.
| | - Laura H J de Haan
- Division of Toxicology, Wageningen University and Research, PO Box 8000, 6700 EA, Wageningen, The Netherlands
| | - Ignacio Miro Estruch
- Division of Toxicology, Wageningen University and Research, PO Box 8000, 6700 EA, Wageningen, The Netherlands
| | - Guido J E J Hooiveld
- Division of Human Nutrition and Health, Wageningen University and Research, PO Box 17, 6700 AA, Wageningen, The Netherlands
| | - Jochem Louisse
- Division of Toxicology, Wageningen University and Research, PO Box 8000, 6700 EA, Wageningen, The Netherlands
| | - Ivonne M C M Rietjens
- Division of Toxicology, Wageningen University and Research, PO Box 8000, 6700 EA, Wageningen, The Netherlands
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6
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Chi JJ, Li H, Zhou Z, Izquierdo-Ferrer J, Xue Y, Wavelet CM, Schiltz GE, Zhang B, Cristofanilli M, Lu X, Bahar I, Wan Y. A novel strategy to block mitotic progression for targeted therapy. EBioMedicine 2019; 49:40-54. [PMID: 31669221 PMCID: PMC6945239 DOI: 10.1016/j.ebiom.2019.10.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 10/07/2019] [Accepted: 10/08/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Blockade of mitotic progression is an ideal approach to induce mitotic catastrophe that suppresses cancer cell expansion. Cdc20 is a critical mitotic factor governing anaphase initiation and the exit from mitosis through recruiting substrates to APC/C for degradation. Results from recent TCGA (The Cancer Genome Atlas) and pathological studies have demonstrated a pivotal oncogenic role for Cdc20-APC/C in tumor progression as well as drug resistance. Thus, deprivation of the mitotic role for Cdc20-APC/C by either inhibition of Cdc20-APC/C activity or elimination of Cdc20 protein via induced protein degradation emerges as an effective therapeutic strategy to control cancer. METHODS We designed a proteolysis targeting chimera, called CP5V, which comprises a Cdc20 ligand and VHL binding moiety bridged by a PEG5 linker that induces Cdc20 degradation. We characterized the effect of CP5V in destroying Cdc20, arresting mitosis, and inhibiting tumor progression by measuring protein degradation, 3D structure dynamics, cell cycle control, tumor cell killing and tumor inhibition using human breast cancer xenograft mouse model. FINDINGS Results from our study demonstrate that CP5V can specifically degrade Cdc20 by linking Cdc20 to the VHL/VBC complex for ubiquitination followed by proteasomal degradation. Induced degradation of Cdc20 by CP5V leads to significant inhibition of breast cancer cell proliferation and resensitization of Taxol-resistant cell lines. Results based on a human breast cancer xenograft mouse model show a significant role for CP5V in suppressing breast tumor progression. INTERPRETATION CP5V-mediated degradation of Cdc20 could be an effective therapeutic strategy for anti-mitotic therapy.
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Affiliation(s)
- Junlong Jack Chi
- Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, USA; Department of Biomedical Engineering, Northwestern University, USA
| | - Hongchun Li
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, USA
| | - Zhuan Zhou
- Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, USA
| | | | - Yifan Xue
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, USA
| | - Cindy M Wavelet
- Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, USA
| | - Gary E Schiltz
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, USA; Center for Molecular Innovation and Drug Discovery, Northwestern University, USA
| | - Bin Zhang
- Department of Medicine-Hematology and Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, USA
| | - Massimo Cristofanilli
- Department of Medicine-Hematology and Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, USA
| | - Xinghua Lu
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, USA
| | - Ivet Bahar
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, USA
| | - Yong Wan
- Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, USA; Department of Pharmacology, Northwestern University Feinberg School of Medicine, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, USA; Chemical of Life Processes Institute, Northwestern University, USA.
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7
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Pseudokinases: From Allosteric Regulation of Catalytic Domains and the Formation of Macromolecular Assemblies to Emerging Drug Targets. Catalysts 2019. [DOI: 10.3390/catal9090778] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Pseudokinases are a member of the kinase superfamily that lack one or more of the canonical residues required for catalysis. Protein pseudokinases are widely distributed across species and are present in proteins that perform a great diversity of roles in the cell. They represent approximately 10% to 40% of the kinome of a multicellular organism. In the human, the pseudokinase subfamily consists of approximately 60 unique proteins. Despite their lack of one or more of the amino acid residues typically required for the productive interaction with ATP and metal ions, which is essential for the phosphorylation of specific substrates, pseudokinases are important functional molecules that can act as dynamic scaffolds, competitors, or modulators of protein–protein interactions. Indeed, pseudokinase misfunctions occur in diverse diseases and represent a new therapeutic window for the development of innovative therapeutic approaches. In this contribution, we describe the structural features of pseudokinases that are used as the basis of their classification; analyse the interactome space of human pseudokinases and discuss their potential as suitable drug targets for the treatment of various diseases, including metabolic, neurological, autoimmune, and cell proliferation disorders.
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8
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Kang KT, Kwon YW, Kim DK, Lee SI, Kim KH, Suh DS, Kim JH. TRRAP stimulates the tumorigenic potential of ovarian cancer stem cells. BMB Rep 2019. [PMID: 29936929 PMCID: PMC6235085 DOI: 10.5483/bmbrep.2018.51.10.042] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Ovarian cancer is the most fatal gynecological malignancy in women and identification of new therapeutic targets is essential for the continued development of therapy for ovarian cancer. TRRAP (transformation/transcription domain-associated protein) is an adaptor protein and a component of histone acetyltransferase complex. The present study was undertaken to investigate the roles played by TRRAP in the proliferation and tumorigenicity of ovarian cancer stem cells. TRRAP expression was found to be up-regulated in the sphere cultures of A2780 ovarian cancer cells. Knockdown of TRRAP significantly decreased cell proliferation and the number of A2780 spheroids. In addition, TRRAP knockdown induced cell cycle arrest and increased apoptotic percentages of A2780 sphere cells. Notably, the mRNA levels of stemness-associated markers, that is, OCT4, SOX2, and NANOG, were suppressed in TRRAP-silenced A2780 sphere cells. In addition, TRRAP overexpression increased the mRNA level of NANOG and the transcriptional activity of NANOG promoter in these cells. Furthermore, TRRAP knockdown significantly reduced tumor growth in a murine xenograft transplantation model. Taken together, the findings of the present study suggest that TRRAP plays an important role in the regulation of the proliferation and stemness of ovarian cancer stem cells.
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Affiliation(s)
- Kyung Taek Kang
- Departments of Physiology, School of Medicine, Pusan National University, Yangsan 50612, Korea
| | - Yang Woo Kwon
- Departments of Physiology, School of Medicine, Pusan National University, Yangsan 50612, Korea
| | - Dae Kyoung Kim
- Departments of Physiology, School of Medicine, Pusan National University, Yangsan 50612, Korea
| | - Su In Lee
- Departments of Physiology, School of Medicine, Pusan National University, Yangsan 50612, Korea
| | - Ki-Hyung Kim
- Obstetrics and Gynecology, School of Medicine, Pusan National University, Yangsan 50612, Korea
| | - Dong-Soo Suh
- Obstetrics and Gynecology, School of Medicine, Pusan National University, Yangsan 50612, Korea
| | - Jae Ho Kim
- Departments of Physiology, School of Medicine, Pusan National University, Yangsan 50612, Korea; Research Institute of Convergence Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan 50612, Korea
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9
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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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10
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Elbarbary RA, Miyoshi K, Myers JR, Du P, Ashton JM, Tian B, Maquat LE. Tudor-SN-mediated endonucleolytic decay of human cell microRNAs promotes G 1/S phase transition. Science 2018; 356:859-862. [PMID: 28546213 DOI: 10.1126/science.aai9372] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 11/16/2016] [Accepted: 04/21/2017] [Indexed: 12/22/2022]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression. The pathways that mediate mature miRNA decay are less well understood than those that mediate miRNA biogenesis. We found that functional miRNAs are degraded in human cells by the endonuclease Tudor-SN (TSN). In vitro, recombinant TSN initiated the decay of both protein-free and Argonaute 2-loaded miRNAs via endonucleolytic cleavage at CA and UA dinucleotides, preferentially at scissile bonds located more than five nucleotides away from miRNA ends. Cellular targets of TSN-mediated decay defined using microRNA sequencing followed this rule. Inhibiting TSN-mediated miRNA decay by CRISPR-Cas9 knockout of TSN inhibited cell cycle progression by up-regulating a cohort of miRNAs that down-regulates mRNAs that encode proteins critical for the G1-to-S phase transition. Our study indicates that targeting TSN nuclease activity could inhibit pathological cell proliferation.
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Affiliation(s)
- Reyad A Elbarbary
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA.,Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
| | - Keita Miyoshi
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA.,Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
| | - Jason R Myers
- Genomics Research Center, University of Rochester, Rochester, NY 14642, USA
| | - Peicheng Du
- Office of Advanced Research Computing, Rutgers University, Piscataway, NJ 08854, USA
| | - John M Ashton
- Genomics Research Center, University of Rochester, Rochester, NY 14642, USA
| | - Bin Tian
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA. .,Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA.,Department of Oncology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA
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11
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The secret life of kinases: insights into non-catalytic signalling functions from pseudokinases. Biochem Soc Trans 2017; 45:665-681. [PMID: 28620028 DOI: 10.1042/bst20160331] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 03/08/2017] [Accepted: 03/09/2017] [Indexed: 12/31/2022]
Abstract
Over the past decade, our understanding of the mechanisms by which pseudokinases, which comprise ∼10% of the human and mouse kinomes, mediate signal transduction has advanced rapidly with increasing structural, biochemical, cellular and genetic studies. Pseudokinases are the catalytically defective counterparts of conventional, active protein kinases and have been attributed functions as protein interaction domains acting variously as allosteric modulators of conventional protein kinases and other enzymes, as regulators of protein trafficking or localisation, as hubs to nucleate assembly of signalling complexes, and as transmembrane effectors of such functions. Here, by categorising mammalian pseudokinases based on their known functions, we illustrate the mechanistic diversity among these proteins, which can be viewed as a window into understanding the non-catalytic functions that can be exerted by conventional protein kinases.
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12
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Yamashita S, Iida N, Takeshima H, Hattori N, Maeda M, Kishino T, Nagano R, Shimazu T, Tsugane S, Ushijima T. A novel method to quantify base substitution mutations at the 10 -6 per bp level in DNA samples. Cancer Lett 2017. [PMID: 28642169 DOI: 10.1016/j.canlet.2017.06.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Somatic base substitution mutations of frequencies at the 10-6/bp level are expected to be present in many biomedical samples, such as tissues exposed to carcinogenic factors and exhausted stem cells. However, measurement of such rare mutations has been very difficult in human DNA samples. Here, we invented the use of 100 copies of genomic DNA as a template for amplicon deep sequencing so that a real mutation in a single DNA molecule would be detected at a variant allele frequency of 1% while sequencing errors have less frequency. In addition, we selected 15,552 error-resistant base positions whose mutation frequency was expected to reflect that of base positions that can drive carcinogenesis or potentially even of the entire genome. The validity of the method was first confirmed by the successful detection of mutations premixed at the frequency of 0.1%. Second, increasing mutation frequencies (4-60 × 10-6/bp) were successfully detected in cells treated with increasing doses of one of two mutagens, and their signature mutations were detected. The ratio of non-synonymous mutations to synonymous mutations time-dependently decreased after treatment with a mutagen, supporting the neutral theory of molecular evolution for somatic mutations. Importantly, gastric mucosae exposed to Helicobacter pylori infection was shown to have significantly higher mutation frequency than those without. These results demonstrated that our new method can be used to measure rare base substitution mutations at the 10-6/bp level, and is now ready for a wide range of applications.
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Affiliation(s)
- Satoshi Yamashita
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Naoko Iida
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Hideyuki Takeshima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Naoko Hattori
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Masahiro Maeda
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Takayoshi Kishino
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Reiko Nagano
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Taichi Shimazu
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Shoichiro Tsugane
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan.
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14
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van Dam PA, van Dam PJHH, Rolfo C, Giallombardo M, van Berckelaer C, Trinh XB, Altintas S, Huizing M, Papadimitriou K, Tjalma WAA, van Laere S. In silico pathway analysis in cervical carcinoma reveals potential new targets for treatment. Oncotarget 2016; 7:2780-95. [PMID: 26701206 PMCID: PMC4823071 DOI: 10.18632/oncotarget.6667] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 11/21/2015] [Indexed: 11/25/2022] Open
Abstract
An in silico pathway analysis was performed in order to improve current knowledge on the molecular drivers of cervical cancer and detect potential targets for treatment. Three publicly available Affymetrix gene expression data-sets (GSE5787, GSE7803, GSE9750) were retrieved, vouching for a total of 9 cervical cancer cell lines (CCCLs), 39 normal cervical samples, 7 CIN3 samples and 111 cervical cancer samples (CCSs). Predication analysis of microarrays was performed in the Affymetrix sets to identify cervical cancer biomarkers. To select cancer cell-specific genes the CCSs were compared to the CCCLs. Validated genes were submitted to a gene set enrichment analysis (GSEA) and Expression2Kinases (E2K). In the CCSs a total of 1,547 probe sets were identified that were overexpressed (FDR < 0.1). Comparing to CCCLs 560 probe sets (481 unique genes) had a cancer cell-specific expression profile, and 315 of these genes (65%) were validated. GSEA identified 5 cancer hallmarks enriched in CCSs (P < 0.01 and FDR < 0.25) showing that deregulation of the cell cycle is a major component of cervical cancer biology. E2K identified a protein-protein interaction (PPI) network of 162 nodes (including 20 drugable kinases) and 1626 edges. This PPI-network consists of 5 signaling modules associated with MYC signaling (Module 1), cell cycle deregulation (Module 2), TGFβ-signaling (Module 3), MAPK signaling (Module 4) and chromatin modeling (Module 5). Potential targets for treatment which could be identified were CDK1, CDK2, ABL1, ATM, AKT1, MAPK1, MAPK3 among others. The present study identified important driver pathways in cervical carcinogenesis which should be assessed for their potential therapeutic drugability.
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Affiliation(s)
- Peter A van Dam
- Antwerp University Hospital, Centre of Oncologic Research (CORE) Antwerp University, Edegem, Belgium.,Multidisciplinary Oncologic Centre Antwerp (MOCA), Edegem, Belgium
| | - Pieter-Jan H H van Dam
- Antwerp University Hospital, Centre of Oncologic Research (CORE) Antwerp University, Edegem, Belgium
| | - Christian Rolfo
- Antwerp University Hospital, Centre of Oncologic Research (CORE) Antwerp University, Edegem, Belgium.,Multidisciplinary Oncologic Centre Antwerp (MOCA), Edegem, Belgium.,Phase I - Early Clinical Trials Unit, Oncology Department, University Hospital Antwerp UZA, Edegem, Belgium
| | - Marco Giallombardo
- Antwerp University Hospital, Centre of Oncologic Research (CORE) Antwerp University, Edegem, Belgium.,Phase I - Early Clinical Trials Unit, Oncology Department, University Hospital Antwerp UZA, Edegem, Belgium
| | - Christophe van Berckelaer
- Antwerp University Hospital, Centre of Oncologic Research (CORE) Antwerp University, Edegem, Belgium
| | - Xuan Bich Trinh
- Multidisciplinary Oncologic Centre Antwerp (MOCA), Edegem, Belgium
| | - Sevilay Altintas
- Multidisciplinary Oncologic Centre Antwerp (MOCA), Edegem, Belgium
| | - Manon Huizing
- Multidisciplinary Oncologic Centre Antwerp (MOCA), Edegem, Belgium
| | | | - Wiebren A A Tjalma
- Antwerp University Hospital, Centre of Oncologic Research (CORE) Antwerp University, Edegem, Belgium.,Multidisciplinary Oncologic Centre Antwerp (MOCA), Edegem, Belgium
| | - Steven van Laere
- Antwerp University Hospital, Centre of Oncologic Research (CORE) Antwerp University, Edegem, Belgium
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15
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Targeting Cdc20 as a novel cancer therapeutic strategy. Pharmacol Ther 2015; 151:141-51. [PMID: 25850036 DOI: 10.1016/j.pharmthera.2015.04.002] [Citation(s) in RCA: 166] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 03/31/2015] [Indexed: 12/25/2022]
Abstract
The Anaphase Promoting Complex (APC, also called APC/C) regulates cell cycle progression by forming two closely related, but functionally distinct E3 ubiquitin ligase sub-complexes, APC(Cdc20) and APC(Cdh1), respectively. Emerging evidence has begun to reveal that Cdc20 and Cdh1 have opposing functions in tumorigenesis. Specifically, Cdh1 functions largely as a tumor suppressor, whereas Cdc20 exhibits an oncogenic function, suggesting that Cdc20 could be a promising therapeutic target for combating human cancer. However, the exact underlying molecular mechanisms accounting for their differences in tumorigenesis remain largely unknown. Therefore, in this review, we summarize the downstream substrates of Cdc20 and the critical functions of Cdc20 in cell cycle progression, apoptosis, ciliary disassembly and brain development. Moreover, we briefly describe the upstream regulators of Cdc20 and the oncogenic role of Cdc20 in a variety of human malignancies. Furthermore, we summarize multiple pharmacological Cdc20 inhibitors including TAME and Apcin, and their potential clinical benefits. Taken together, development of specific Cdc20 inhibitors could be a novel strategy for the treatment of human cancers with elevated Cdc20 expression.
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16
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Re A, Workman CT, Waldron L, Quattrone A, Brunak S. Lineage-specific interface proteins match up the cell cycle and differentiation in embryo stem cells. Stem Cell Res 2014; 13:316-28. [PMID: 25173649 DOI: 10.1016/j.scr.2014.07.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 07/25/2014] [Accepted: 07/26/2014] [Indexed: 11/25/2022] Open
Abstract
The shortage of molecular information on cell cycle changes along embryonic stem cell (ESC) differentiation prompts an in silico approach, which may provide a novel way to identify candidate genes or mechanisms acting in coordinating the two programs. We analyzed germ layer specific gene expression changes during the cell cycle and ESC differentiation by combining four human cell cycle transcriptome profiles with thirteen in vitro human ESC differentiation studies. To detect cross-talk mechanisms we then integrated the transcriptome data that displayed differential regulation with protein interaction data. A new class of non-transcriptionally regulated genes was identified, encoding proteins which interact systematically with proteins corresponding to genes regulated during the cell cycle or cell differentiation, and which therefore can be seen as interface proteins coordinating the two programs. Functional analysis gathered insights in fate-specific candidates of interface functionalities. The non-transcriptionally regulated interface proteins were found to be highly regulated by post-translational ubiquitylation modification, which may synchronize the transition between cell proliferation and differentiation in ESCs.
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Affiliation(s)
- Angela Re
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Via delle Regole 101, I38123 Trento, Italy; Center for Biological Sequence Analysis, Technical University of Denmark, Kemitorvet, DK2800 Lyngby, Denmark
| | - Christopher T Workman
- Center for Biological Sequence Analysis, Technical University of Denmark, Kemitorvet, DK2800 Lyngby, Denmark
| | - Levi Waldron
- City University of New York School of Public Health, Hunter College, 2180 3rd Avenue, NY 10035, USA
| | - Alessandro Quattrone
- Laboratory of Translational Genomics, Centre for Integrative Biology, University of Trento, Via delle Regole 101, I38123 Trento, Italy.
| | - Søren Brunak
- Center for Biological Sequence Analysis, Technical University of Denmark, Kemitorvet, DK2800 Lyngby, Denmark; Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, DK2200 Copenhagen, Denmark.
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17
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Leduc C, Chemin G, Puget N, Sawan C, Moutahir M, Herceg Z, Khamlichi AA. Tissue-specific inactivation of HAT cofactor TRRAP reveals its essential role in B cells. Cell Cycle 2014; 13:1583-9. [PMID: 24675885 PMCID: PMC4050163 DOI: 10.4161/cc.28560] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 03/11/2014] [Accepted: 03/17/2014] [Indexed: 11/19/2022] Open
Abstract
The transformation/transcription domain-associated protein (TRRAP) is a common component of many histone acetyltransferase (HAT) complexes. Targeted-deletion of the Trrap gene led to early embryonic lethality and revealed a critical function of TRRAP in cell proliferation. Here, we investigate the function of TRRAP in murine B cells. To this end, we ablated Trrap gene in a B cell-restricted manner and studied its impact on B-cell development and proliferation, a pre-requisite for class switch recombination (CSR), the process that allows IgM-expressing B lymphocytes to switch to the expression of IgG, IgE, or IgA isotypes. We show that TRRAP deficiency impairs B-cell development but does not directly affect CSR. Instead, cells induced to proliferate undergo apoptosis. Our findings demonstrate a central and general role of TRRAP in cell proliferation.
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Affiliation(s)
- Claire Leduc
- CNRS UMR5089; IPBS (Institut de Pharmacologie et de Biologie Structurale); Toulouse, France
- Université de Toulouse; UPS; IPBS; Toulouse, France
| | - Guillaume Chemin
- CNRS UMR5089; IPBS (Institut de Pharmacologie et de Biologie Structurale); Toulouse, France
- Université de Toulouse; UPS; IPBS; Toulouse, France
| | - Nadine Puget
- CNRS UMR5089; IPBS (Institut de Pharmacologie et de Biologie Structurale); Toulouse, France
- Université de Toulouse; UPS; IPBS; Toulouse, France
| | - Carla Sawan
- International Agency for Research on Cancer (IARC); Lyon, France
| | - Mohammed Moutahir
- CNRS UMR5089; IPBS (Institut de Pharmacologie et de Biologie Structurale); Toulouse, France
- Université de Toulouse; UPS; IPBS; Toulouse, France
| | - Zdenko Herceg
- International Agency for Research on Cancer (IARC); Lyon, France
| | - Ahmed Amine Khamlichi
- CNRS UMR5089; IPBS (Institut de Pharmacologie et de Biologie Structurale); Toulouse, France
- Université de Toulouse; UPS; IPBS; Toulouse, France
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18
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Zhang J, Wan L, Dai X, Sun Y, Wei W. Functional characterization of Anaphase Promoting Complex/Cyclosome (APC/C) E3 ubiquitin ligases in tumorigenesis. Biochim Biophys Acta Rev Cancer 2014; 1845:277-93. [PMID: 24569229 DOI: 10.1016/j.bbcan.2014.02.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Revised: 02/09/2014] [Accepted: 02/12/2014] [Indexed: 12/25/2022]
Abstract
The Anaphase Promoting Complex/Cyclosome (APC/C) is a multi-subunit E3 ubiquitin ligase that primarily governs cell cycle progression. APC/C is composed of at least 14 core subunits and recruits its substrates for ubiquitination via one of the two adaptor proteins, Cdc20 or Cdh1, in M or M/early G1 phase, respectively. Furthermore, recent studies have shed light on crucial functions for APC/C in maintaining genomic integrity, neuronal differentiation, cellular metabolism and tumorigenesis. To gain better insight into the in vivo physiological functions of APC/C in regulating various cellular processes, particularly development and tumorigenesis, a number of mouse models of APC/C core subunits, coactivators or inhibitors have been established and characterized. However, due to their essential role in cell cycle regulation, most of the germline knockout mice targeting the APC/C pathway are embryonic lethal, indicating the need for generating conditional knockout mouse models to assess the role in tumorigenesis for each APC/C signaling component in specific tissues. In this review, we will first provide a brief introduction of the ubiquitin-proteasome system (UPS) and the biochemical activities and cellular functions of the APC/C E3 ligase. We will then focus primarily on characterizing genetic mouse models used to understand the physiological roles of each APC/C signaling component in embryogenesis, cell proliferation, development and carcinogenesis. Finally, we discuss future research directions to further elucidate the physiological contributions of APC/C components during tumorigenesis and validate their potentials as a novel class of anti-cancer targets.
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Affiliation(s)
- Jinfang Zhang
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Lixin Wan
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Xiangpeng Dai
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Yi Sun
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
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19
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Abstract
Epigenetic modifications constitute the next frontier in tumor biology research. Post-translation modification of histones dynamically influences gene expression independent of alterations to the DNA sequence. These mechanisms are often mediated by histone linkers or by proteins associated with the recruitment of DNA-binding proteins, HDAC I and II interacting proteins and transcriptional activators, coactivators or corepressors. Early evidence suggested that histones and their modifiers are involved in sophisticated processes that modulate tumor behavior and cellular phenotype. In this review, we discuss how recent discoveries about chromatin modifications, particularly histone acetylation, are shaping our knowledge of cell biology and our understanding of the molecular circuitry governing tumor progression and consider whether recent insights may extend to novel therapeutic approaches. Furthermore, we discuss the latest oncogenomic findings in Head and Neck Squamous Cell Carcinoma (HNSCC) from studies using Next Generation Sequencing (NGS) technology and highlight the impact of mutations identified in histones and their modifiers.
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Affiliation(s)
- Manoela D Martins
- Department of Oral Pathology, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Rogerio M Castilho
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, MI, USA
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