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Zhang Y, Zhang Y, Song C, Zhao X, Ai B, Wang Y, Zhou L, Zhu J, Feng C, Xu L, Wang Q, Sun H, Fang Q, Xu X, Li E, Li C. CRdb: a comprehensive resource for deciphering chromatin regulators in human. Nucleic Acids Res 2023; 51:D88-D100. [PMID: 36318256 PMCID: PMC9825595 DOI: 10.1093/nar/gkac960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 10/04/2022] [Accepted: 10/12/2022] [Indexed: 11/05/2022] Open
Abstract
Chromatin regulators (CRs) regulate epigenetic patterns on a partial or global scale, playing a critical role in affecting multi-target gene expression. As chromatin immunoprecipitation sequencing (ChIP-seq) data associated with CRs are rapidly accumulating, a comprehensive resource of CRs needs to be built urgently for collecting, integrating, and processing these data, which can provide abundant annotated information on CR upstream and downstream regulatory analyses as well as CR-related analysis functions. This study established an integrative CR resource, named CRdb (http://cr.liclab.net/crdb/), with the aim of curating a large number of available resources for CRs and providing extensive annotations and analyses of CRs to help biological researchers clarify the regulation mechanism and function of CRs. The CRdb database comprised a total of 647 CRs and 2,591 ChIP-seq samples from more than 300 human tissues and cell types. These samples have been manually curated from NCBI GEO/SRA and ENCODE. Importantly, CRdb provided the abundant and detailed genetic annotations in CR-binding regions based on ChIP-seq. Furthermore, CRdb supported various functional annotations and upstream regulatory information on CRs. In particular, it embedded four types of CR regulatory analyses: CR gene set enrichment, CR-binding genomic region annotation, CR-TF co-occupancy analysis, and CR regulatory axis analysis. CRdb is a useful and powerful resource that can help in exploring the potential functions of CRs and their regulatory mechanism in diseases and biological processes.
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Affiliation(s)
- Yimeng Zhang
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, China
| | | | | | - Xilong Zhao
- School of Medical Informatics, Daqing Campus, Harbin Medical University.Daqing 163319, China
| | - Bo Ai
- School of Medical Informatics, Daqing Campus, Harbin Medical University.Daqing 163319, China
| | - Yuezhu Wang
- School of Medical Informatics, Daqing Campus, Harbin Medical University.Daqing 163319, China
| | - Liwei Zhou
- School of Medical Informatics, Daqing Campus, Harbin Medical University.Daqing 163319, China
| | - Jiang Zhu
- School of Medical Informatics, Daqing Campus, Harbin Medical University.Daqing 163319, China
| | - Chenchen Feng
- School of Medical Informatics, Daqing Campus, Harbin Medical University.Daqing 163319, China
| | - Liyan Xu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Institute of Oncologic Pathology, Cancer Research Center, Shantou University Medical College, Shantou 515041, China
| | - Qiuyu Wang
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- School of Computer, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- Hunan Provincial Base for Scientific and Technological Innovation Cooperation, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Hong Sun
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China
| | - Qiaoli Fang
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- School of Computer, University of South China, Hengyang, Hunan 421001, China
| | - Xiaozheng Xu
- School of Medical Informatics, Daqing Campus, Harbin Medical University.Daqing 163319, China
| | - Enmin Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, China
| | - Chunquan Li
- The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- School of Computer, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
- Hunan Provincial Base for Scientific and Technological Innovation Cooperation, University of South China, Hengyang, Hunan 421001, China
- The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South
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2
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Kim S, Kim Y, Kim Y, Yoon S, Lee KY, Lee Y, Kang S, Myung K, Oh CK. PCNA Ser46-Leu47 residues are crucial in preserving genomic integrity. PLoS One 2023; 18:e0285337. [PMID: 37205694 DOI: 10.1371/journal.pone.0285337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/19/2023] [Indexed: 05/21/2023] Open
Abstract
Proliferating cell nuclear antigen (PCNA) is a maestro of DNA replication. PCNA forms a homotrimer and interacts with various proteins, such as DNA polymerases, DNA ligase I (LIG1), and flap endonuclease 1 (FEN1) for faithful DNA replication. Here, we identify the crucial role of Ser46-Leu47 residues of PCNA in maintaining genomic integrity using in vitro, and cell-based assays and structural prediction. The predicted PCNAΔSL47 structure shows the potential distortion of the central loop and reduced hydrophobicity. PCNAΔSL47 shows a defective interaction with PCNAWT leading to defects in homo-trimerization in vitro. PCNAΔSL47 is defective in the FEN1 and LIG1 interaction. PCNA ubiquitination and DNA-RNA hybrid processing are defective in PCNAΔSL47-expressing cells. Accordingly, PCNAΔSL47-expressing cells exhibit an increased number of single-stranded DNA gaps and higher levels of γH2AX, and sensitivity to DNA-damaging agents, highlighting the importance of PCNA Ser46-Leu47 residues in maintaining genomic integrity.
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Affiliation(s)
- Sangin Kim
- Institute for Basic Science, Center for Genomic Integrity, Ulsan, Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, College of Information-Bio Convergence Engineering, Ulsan, Korea
| | - Yeongjae Kim
- Institute for Basic Science, Center for Genomic Integrity, Ulsan, Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, College of Information-Bio Convergence Engineering, Ulsan, Korea
| | - Youyoung Kim
- Institute for Basic Science, Center for Genomic Integrity, Ulsan, Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, College of Information-Bio Convergence Engineering, Ulsan, Korea
| | - Suhyeon Yoon
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Integrated Data Sciences Section, Research Technologies Branch, Bethesda, MD, United States of America
| | - Kyoo-Young Lee
- Institute for Basic Science, Center for Genomic Integrity, Ulsan, Korea
- Department of Biochemistry, College of Medicine, Hallym University, Chuncheon, Gangwon-do, Korea
| | - Yoonsung Lee
- Clinical Research Institute, Kyung Hee University Hospital at Gangdong, College of Medicine, Kyung Hee University, Seoul, Korea
| | - Sukhyun Kang
- Institute for Basic Science, Center for Genomic Integrity, Ulsan, Korea
| | - Kyungjae Myung
- Institute for Basic Science, Center for Genomic Integrity, Ulsan, Korea
- Ulsan National Institute of Science and Technology, Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan, Korea
| | - Chang-Kyu Oh
- Department of Biochemistry, Pusan National University, School of Medicine, Yangsan, Korea
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3
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Hwang IJ, Park J, Seo SB. Non-canonical transcriptional regulation of INHAT subunit SET/TAF-Iβ by EZH2. Biochem Biophys Res Commun 2022; 635:136-143. [DOI: 10.1016/j.bbrc.2022.10.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 10/10/2022] [Indexed: 11/26/2022]
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4
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Post-Translational Modifications of PCNA: Guiding for the Best DNA Damage Tolerance Choice. J Fungi (Basel) 2022; 8:jof8060621. [PMID: 35736104 PMCID: PMC9225081 DOI: 10.3390/jof8060621] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 02/01/2023] Open
Abstract
The sliding clamp PCNA is a multifunctional homotrimer mainly linked to DNA replication. During this process, cells must ensure an accurate and complete genome replication when constantly challenged by the presence of DNA lesions. Post-translational modifications of PCNA play a crucial role in channeling DNA damage tolerance (DDT) and repair mechanisms to bypass unrepaired lesions and promote optimal fork replication restart. PCNA ubiquitination processes trigger the following two main DDT sub-pathways: Rad6/Rad18-dependent PCNA monoubiquitination and Ubc13-Mms2/Rad5-mediated PCNA polyubiquitination, promoting error-prone translation synthesis (TLS) or error-free template switch (TS) pathways, respectively. However, the fork protection mechanism leading to TS during fork reversal is still poorly understood. In contrast, PCNA sumoylation impedes the homologous recombination (HR)-mediated salvage recombination (SR) repair pathway. Focusing on Saccharomyces cerevisiae budding yeast, we summarized PCNA related-DDT and repair mechanisms that coordinately sustain genome stability and cell survival. In addition, we compared PCNA sequences from various fungal pathogens, considering recent advances in structural features. Importantly, the identification of PCNA epitopes may lead to potential fungal targets for antifungal drug development.
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Zhang Q, Yang H, Feng Q, Cao J, Zhang Y, Li L, Yu L. Focus on the classical and non-classical functions of EZH2: Guide the development of inhibitors and degraders. Pharmacol Res 2022; 178:106159. [DOI: 10.1016/j.phrs.2022.106159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 02/28/2022] [Accepted: 03/03/2022] [Indexed: 12/16/2022]
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Adibfar S, Elveny M, Kashikova HS, Mikhailova MV, Farhangnia P, Vakili-Samiani S, Tarokhian H, Jadidi-Niaragh F. The molecular mechanisms and therapeutic potential of EZH2 in breast cancer. Life Sci 2021; 286:120047. [PMID: 34653429 DOI: 10.1016/j.lfs.2021.120047] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/30/2021] [Accepted: 10/07/2021] [Indexed: 02/08/2023]
Abstract
Due to its high occurrence and mortality rate, breast cancer has been studied from various aspects as one of the cancer field's hot topics in the last decade. Epigenetic alterations are spoused to be highly effective in breast cancer development. Enhancer of zeste homolog 2 (EZH2) is an enzymatic epi-protein that takes part in most vital cell functions by its different action modes. EZH2 is suggested to be dysregulated in specific breast cancer types, particularly in advanced stages. Mounting evidence revealed that EZH2 overexpression or dysfunction affects the pathophysiology of breast cancer. In this review, we discuss biological aspects of the EZH2 molecule with a focus on its newly identified action mechanisms. We also highlight how EZH2 plays an essential role in breast cancer initiation, progression, metastasis, and invasion, which emerged as a worthy target for treating breast cancer in different approaches.
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Affiliation(s)
- Sara Adibfar
- Department of Immunology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran; Student Research Committee, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Marischa Elveny
- DS & CI Research Group, Universitas Sumatera Utara, Medan, Indonesia
| | | | | | - Pooya Farhangnia
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran; Network of Immunity in Infection, Malignancy, and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran; Immunology Board for Transplantation and Advanced Cellular Therapeutics (ImmunoTACT), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Sajjad Vakili-Samiani
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hanieh Tarokhian
- Department of Immunology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Farhad Jadidi-Niaragh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; Integrated Medicine and Aging Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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7
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Zhang S, Zhou T, Wang Z, Yi F, Li C, Guo W, Xu H, Cui H, Dong X, Liu J, Song X, Cao L. Post-Translational Modifications of PCNA in Control of DNA Synthesis and DNA Damage Tolerance-the Implications in Carcinogenesis. Int J Biol Sci 2021; 17:4047-4059. [PMID: 34671219 PMCID: PMC8495385 DOI: 10.7150/ijbs.64628] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/19/2021] [Indexed: 11/05/2022] Open
Abstract
The faithful DNA replication is a critical event for cell survival and inheritance. However, exogenous or endogenous sources of damage challenge the accurate synthesis of DNA, which causes DNA lesions. The DNA lesions are obstacles for replication fork progression. However, the prolonged replication fork stalling leads to replication fork collapse, which may cause DNA double-strand breaks (DSB). In order to maintain genomic stability, eukaryotic cells evolve translesion synthesis (TLS) and template switching (TS) to resolve the replication stalling. Proliferating cell nuclear antigen (PCNA) trimer acts as a slide clamp and encircles DNA to orchestrate DNA synthesis and DNA damage tolerance (DDT). The post-translational modifications (PTMs) of PCNA regulate these functions to ensure the appropriate initiation and termination of replication and DDT. The aberrant regulation of PCNA PTMs will result in DSB, which causes mutagenesis and poor response to chemotherapy. Here, we review the roles of the PCNA PTMs in DNA duplication and DDT. We propose that clarifying the regulation of PCNA PTMs may provide insights into understanding the development of cancers.
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Affiliation(s)
- Siyi Zhang
- Institute of Health Sciences, China Medical University, Shenyang, Liaoning Province, 110122, PR China
| | - Tingting Zhou
- Institute of Health Sciences, China Medical University, Shenyang, Liaoning Province, 110122, PR China
| | - Zhuo Wang
- Institute of Health Sciences, China Medical University, Shenyang, Liaoning Province, 110122, PR China
| | - Fei Yi
- Institute of Health Sciences, China Medical University, Shenyang, Liaoning Province, 110122, PR China
| | - Chunlu Li
- Institute of Health Sciences, China Medical University, Shenyang, Liaoning Province, 110122, PR China
| | - Wendong Guo
- Institute of Health Sciences, China Medical University, Shenyang, Liaoning Province, 110122, PR China
| | - Hongde Xu
- Institute of Health Sciences, China Medical University, Shenyang, Liaoning Province, 110122, PR China
| | - Hongyan Cui
- Institute of Health Sciences, China Medical University, Shenyang, Liaoning Province, 110122, PR China
| | - Xiang Dong
- Institute of Health Sciences, China Medical University, Shenyang, Liaoning Province, 110122, PR China
| | - Jingwei Liu
- Institute of Health Sciences, China Medical University, Shenyang, Liaoning Province, 110122, PR China
| | - Xiaoyu Song
- Institute of Health Sciences, China Medical University, Shenyang, Liaoning Province, 110122, PR China
| | - Liu Cao
- College of Basic Medical Science, Key Laboratory of Cell Biology of Ministry of Public Health, Key Laboratory of Medical Cell Biology of Ministry of Education, Liaoning Province Collaborative Innovation Center of Aging Related Disease Diagnosis and Treatment and Prevention, China Medical University, Shenyang, Liaoning Province, 110122, PR China
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8
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Shen M, Young A, Autexier C. PCNA, a focus on replication stress and the alternative lengthening of telomeres pathway. DNA Repair (Amst) 2021; 100:103055. [PMID: 33581499 DOI: 10.1016/j.dnarep.2021.103055] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/25/2021] [Indexed: 12/16/2022]
Abstract
The maintenance of telomeres, which are specialized stretches of DNA found at the ends of linear chromosomes, is a crucial step for the immortalization of cancer cells. Approximately 10-15 % of cancer cells use a homologous recombination-based mechanism known as the Alternative Lengthening of Telomeres (ALT) pathway to maintain their telomeres. Telomeres in general pose a challenge to DNA replication owing to their repetitive nature and potential for forming secondary structures. Telomeres in ALT+ cells especially are subject to elevated levels of replication stress compared to telomeres that are maintained by the enzyme telomerase, in part due to the incorporation of telomeric variant repeats at ALT+ telomeres, their on average longer lengths, and their modified chromatin states. Many DNA metabolic strategies exist to counter replication stress and to protect stalled replication forks. The role of proliferating cell nuclear antigen (PCNA) as a platform for recruiting protein partners that participate in several of these DNA replication and repair pathways has been well-documented. We propose that many of these pathways may be active at ALT+ telomeres, either to facilitate DNA replication, to manage replication stress, or during telomere extension. Here, we summarize recent evidence detailing the role of PCNA in pathways including DNA secondary structure resolution, DNA damage bypass, replication fork restart, and DNA damage synthesis. We propose that an examination of PCNA and its post-translational modifications (PTMs) may offer a unique lens by which we might gain insight into the DNA metabolic landscape that is distinctively present at ALT+ telomeres.
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Affiliation(s)
- Michelle Shen
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, H3A 0C7, Canada; Jewish General Hospital, Lady Davis Institute, Montreal, Quebec, H3T 1E2, Canada
| | - Adrian Young
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, H3A 0C7, Canada; Jewish General Hospital, Lady Davis Institute, Montreal, Quebec, H3T 1E2, Canada
| | - Chantal Autexier
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, H3A 0C7, Canada; Jewish General Hospital, Lady Davis Institute, Montreal, Quebec, H3T 1E2, Canada.
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No Easy Way Out for EZH2: Its Pleiotropic, Noncanonical Effects on Gene Regulation and Cellular Function. Int J Mol Sci 2020; 21:ijms21249501. [PMID: 33327550 PMCID: PMC7765048 DOI: 10.3390/ijms21249501] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/04/2020] [Accepted: 12/08/2020] [Indexed: 12/14/2022] Open
Abstract
Enhancer of zeste homolog 2 (EZH2) plays critical roles in a range of biological processes including organ development and homeostasis, epigenomic and transcriptomic regulation, gene repression and imprinting, and DNA damage repair. A widely known function of EZH2 is to serve as an enzymatic subunit of Polycomb repressive complex 2 (PRC2) and catalyze trimethylation of histone H3 lysine 27 (H3K27me3) for repressing target gene expression. However, an increasing body of evidence demonstrates that EZH2 has many "non-conventional" functions that go beyond H3K27 methylation as a Polycomb factor. First, EZH2 can methylate a number of nonhistone proteins, thereby regulating cellular processes in an H3K27me3-independent fashion. Furthermore, EZH2 relies on both methyltransferase-dependent and methyltransferase-independent mechanisms for modulating gene-expression programs and/or epigenomic patterns of cells. Importantly, independent of PRC2, EZH2 also forms physical interactions with a number of DNA-binding factors and transcriptional coactivators to context-dependently influence gene expression. The purpose of this review is to detail the complex, noncanonical roles of EZH2, which are generally less appreciated in gene and (epi)genome regulation. Because EZH2 deregulation is prevalent in human diseases such as cancer, there is increased dependency on its noncanonical function, which shall have important implications in developing more effective therapeutics.
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Huang R, Chen Z, Li W, Fan C, Liu J. Immune system‑associated genes increase malignant progression and can be used to predict clinical outcome in patients with hepatocellular carcinoma. Int J Oncol 2020; 56:1199-1211. [PMID: 32319580 PMCID: PMC7115743 DOI: 10.3892/ijo.2020.4998] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 02/07/2020] [Indexed: 02/05/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most malignant types of cancer, and is associated with high recurrence rates and a poor response to chemotherapy. Immune signatures in the microenvironment of HCC have not been well explored systematically. The aim of the present study was to identify prognostic immune signatures and build a nomogram for use in clinical evaluation. Using bioinformatics analysis, RNA‑seq data and overall survival (OS) information on 370 HCC cases from TCGA and 232 HCC cases from ICGC were analyzed. The differential expression of select immune genes, based on previously published studies, between HCC and adjacent tissue were analyzed using the limma package in R. Enrichment of pathways and gene ontology analysis was performed using clusterProfiler. Subsequently, univariate Cox regression analysis, Lasso penalty linear regression and multivariate Cox regression models were used to construct a model for immune risk score (IRS). The R packages, survival and survivalROC, were used to plot survival and the associated receiver operating characteristic curves. Infiltration of immune cells was calculated using Tumor IMmune Estimation Resource, with significance examined using a Pearson's correlation test. P<0.05 was considered significant. Based on the analysis, expression of 200 immune genes were upregulated and 47 immune genes were downregulated immune genes. In the multivariate Cox model, 5 genes (enhancer of zest homology 2, ferritin light chain, complement factor H related 3, isthmin 2, cyclin dependent kinase 5) were used to generate the IRS. By stratifying according to the median IRS, it was shown that patients with a high IRS had poor OS rates after 1, 2, 3 and 5 years, and this result was consistent across the testing, training and independent validation cohorts. Additionally, the IRS was correlated with the abundance of infiltrating immune cells. The nomogram built using IRS and clinical characteristics, was able to predict 1, 3 and 5 year OS with area under the curve values of >0.8. These results suggest that the model developed to calculate the IRS may be used to monitor the effectiveness of treatment strategies and for prognostic prediction.
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Affiliation(s)
- Rongfu Huang
- Department of Clinical Laboratory, The Second Affiliated Hospital, Fujian Medical University, Quanzhou, Fujian 362000
| | - Zheng Chen
- Liver Cancer Institute, Zhongshan Hospital, Fudan University and Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200000
| | | | - Chunmei Fan
- Department of Clinical Laboratory, The Second Affiliated Hospital, Fujian Medical University, Quanzhou, Fujian 362000
| | - Jun Liu
- Department of Clinical Laboratory, Yue Bei People's Hospital, Shantou University Medical College, Shaoguan, Guangdong 512026, P.R. China
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González-Magaña A, Blanco FJ. Human PCNA Structure, Function and Interactions. Biomolecules 2020; 10:biom10040570. [PMID: 32276417 PMCID: PMC7225939 DOI: 10.3390/biom10040570] [Citation(s) in RCA: 147] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/01/2020] [Accepted: 04/03/2020] [Indexed: 12/13/2022] Open
Abstract
Proliferating cell nuclear antigen (PCNA) is an essential factor in DNA replication and repair. It forms a homotrimeric ring that embraces the DNA and slides along it, anchoring DNA polymerases and other DNA editing enzymes. It also interacts with regulatory proteins through a sequence motif known as PCNA Interacting Protein box (PIP-box). We here review the latest contributions to knowledge regarding the structure-function relationships in human PCNA, particularly the mechanism of sliding, and of the molecular recognition of canonical and non-canonical PIP motifs. The unique binding mode of the oncogene p15 is described in detail, and the implications of the recently discovered structure of PCNA bound to polymerase δ are discussed. The study of the post-translational modifications of PCNA and its partners may yield therapeutic opportunities in cancer treatment, in addition to illuminating the way PCNA coordinates the dynamic exchange of its many partners in DNA replication and repair.
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Affiliation(s)
- Amaia González-Magaña
- CIC bioGUNE, Bizkaia Science and Technology Park, bld 800, 48160 Derio, Bizkaia, Spain;
| | - Francisco J. Blanco
- CIC bioGUNE, Bizkaia Science and Technology Park, bld 800, 48160 Derio, Bizkaia, Spain;
- IKERBASQUE, Basque Foundation for Science, Maria Diaz de Haro 3, 6 solairua, 48013 Bilbao, Bizkaia, Spain
- Correspondence:
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Cheng H, Cao X, Min X, Zhang X, Kong Q, Mao Q, Li R, Xue B, Fang L, Liu L, Ding Z. Heat-Shock protein A12A is a novel PCNA-binding protein and promotes hepatocellular carcinoma growth. FEBS J 2020; 287:5464-5477. [PMID: 32128976 DOI: 10.1111/febs.15276] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 02/03/2020] [Accepted: 03/02/2020] [Indexed: 12/24/2022]
Abstract
Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death. Proliferating cell nuclear antigen (PCNA) plays a pivotal role in cancer development and progression. However, the long-term dismal prognosis of HCC mandates more investigation to identify novel regulators in HCC pathogenesis. Heat-shock protein A12A (HSPA12A) encodes a novel member of the HSP70 family. Here, we report that HCC cells showed increased HSPA12A expression, and overexpression of HSPA12A promoted HCC growth and angiogenesis in mice. Gain- and loss-of-functional studies demonstrated that the proliferation of HCC HepG2 cells, as well as β-catenin expression and nuclear translocation, was promoted by HSPA12A overexpression, but in turn suppressed by HSPA12A knockdown. HSPA12A did not impact PCNA expression; however, mass spectrometry and co-immunoprecipitation immunoblotting analysis revealed that HSPA12A directly binds to PCNA and promotes its trimerization, which is an essential functional conformation of PCNA for carcinogenesis. Importantly, PCNA inhibition by PCNA-I1 reversed the HSPA12A-mediated HepG2 cell differentiation. These findings indicate that HSPA12A is a novel regulator of HCC cell proliferation and tumor growth through binding to PCNA for its trimerization. HSPA12A inhibition might represent a viable strategy for the management of HCC in humans.
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Affiliation(s)
- Hao Cheng
- Department of Anesthesiology, First Affiliated Hospital of Nanjing Medical University, China
| | - Xiaofei Cao
- Department of Anesthesiology, First Affiliated Hospital of Nanjing Medical University, China
| | - Xinxu Min
- Department of Anesthesiology, First Affiliated Hospital of Nanjing Medical University, China
| | - Xiaojin Zhang
- Department of Geriatrics, Jiangsu Provincial Key Laboratory of Geriatrics, the First Affiliated Hospital of Nanjing Medical University, China
| | - Qiuyue Kong
- Department of Anesthesiology, First Affiliated Hospital of Nanjing Medical University, China
| | - Qian Mao
- Department of Anesthesiology, First Affiliated Hospital of Nanjing Medical University, China
| | - Rongrong Li
- Department of Anesthesiology, First Affiliated Hospital of Nanjing Medical University, China
| | - Bin Xue
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine, School of Medicine, Nanjing University, China
| | - Lei Fang
- Medical School, Nanjing University, China
| | - Li Liu
- Department of Geriatrics, Jiangsu Provincial Key Laboratory of Geriatrics, the First Affiliated Hospital of Nanjing Medical University, China.,Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, China
| | - Zhengnian Ding
- Department of Anesthesiology, First Affiliated Hospital of Nanjing Medical University, China
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Levy D. Lysine methylation signaling of non-histone proteins in the nucleus. Cell Mol Life Sci 2019; 76:2873-2883. [PMID: 31123776 PMCID: PMC11105312 DOI: 10.1007/s00018-019-03142-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 05/10/2019] [Indexed: 12/18/2022]
Abstract
Lysine methylation, catalyzed by protein lysine methyltransferases (PKMTs), is a central post-translational modification regulating many signaling pathways. It has direct and indirect effects on chromatin structure and transcription. Accumulating evidence suggests that dysregulation of PKMT activity has a fundamental impact on the development of many pathologies. While most of these works involve in-depth analysis of methylation events in the context of histones, in recent years, it has become evident that methylation of non-histone proteins also plays a pivotal role in cell processes. This review highlights the importance of non-histone methylation, with focus on methylation events taking place in the nucleus. Known experimental platforms which were developed to identify new methylation events, as well as examples of specific lysine methylation signaling events which regulate key transcription factors, are presented. In addition, the role of these methylation events in normal and disease states is emphasized.
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Affiliation(s)
- Dan Levy
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, 84105, Beersheba, Israel.
- The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, P.O.B. 653, 84105, Beersheba, Israel.
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14
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Advances in epigenetics link genetics to the environment and disease. Nature 2019; 571:489-499. [DOI: 10.1038/s41586-019-1411-0] [Citation(s) in RCA: 566] [Impact Index Per Article: 113.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 06/14/2019] [Indexed: 12/16/2022]
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15
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ATXR5/6 Forms Alternative Protein Complexes with PCNA and the Nucleosome Core Particle. J Mol Biol 2019; 431:1370-1379. [PMID: 30826376 DOI: 10.1016/j.jmb.2019.02.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/15/2019] [Accepted: 02/15/2019] [Indexed: 12/11/2022]
Abstract
The proliferating cell nuclear antigen (PCNA) is a sliding clamp associated with DNA polymerases and serves as a binding platform for the recruitment of regulatory proteins linked to DNA damage repair, cell cycle regulation, and epigenetic signaling. The histone H3 lysine-27 (H3K27) mono-methyltransferase Arabidopsis trithorax-related protein 5/6 (ATXR5/6) associates with PCNA, and this interaction has been proposed to act as a key determinant controlling the reestablishment of H3K27 mono-methylation following replication. In this study, we provide biochemical evidence showing that PCNA inhibits ATXR6 enzymatic activity. The structure of the ATXR6 PCNA-interacting peptide (PIP) in complex with PCNA indicates that a trio of hydrophobic residues contributes to the binding of the enzyme to the sliding clamp. Finally, despite the presence of three PIP binding clefts, only two molecules of ATXR6 bind to PCNA likely enabling the recruitment of a third protein to the sliding clamp. Collectively, these results rule out the model wherein PCNA-bound ATXR6 actively reestablishes H3K27 mono-methylation following DNA replication and provides insights into the role of ATXR6 PIP motif in its interaction with PCNA.
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16
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Zhang CJ, Liu C, Wang YX, Zhu N, Hu ZY, Liao DF, Qin L. Long non-coding RNA-SRA promotes neointimal hyperplasia and vascular smooth muscle cells proliferation via MEK-ERK-CREB pathway. Vascul Pharmacol 2019; 116:16-23. [PMID: 30822571 DOI: 10.1016/j.vph.2019.02.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 02/23/2019] [Accepted: 02/25/2019] [Indexed: 12/18/2022]
Abstract
Long noncoding RNA-steroid receptor RNA activator (LncRNA-SRA) is transcribed from a class of noncoding genes, and plays a critical role in regulating cell proliferation. However, the effect of lncRNA-SRA remains unclear in vascular proliferative diseases. In the present study, we overexpressed lncRNA-SRA in vitro, then investigated the biological consequences. A vascular damage mice model was constructed by performing femoral artery wire injury. LncRNA-SRA was overexpressed in the injured arteries, and significantly promoted the expression of ki67, thereby caused an overall increase in neointima formation. LncRNA-SRA overexpression led to the proliferation and migration of vascular smooth muscle cells (VSMCs). By stimulating the phosphorylation of MEK, ERK and CREB (cyclic nucleotide responsive element binding protein), lncRNA-SRA promoted VSMC proliferation. Meanwhile, these effects were blocked by the MEK inhibitor U0126. Therefore, lncRNA-SRA promoted VSMC proliferation by activating the MEK-ERK-CREB pathway. LncRNA-SRA could be a promising therapeutic target in vascular diseases characterized by neointimal hyperplasia.
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Affiliation(s)
- Chan-Juan Zhang
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, Hunan, China; Division of Stem Cell Regulation and Application, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Chan Liu
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, Hunan, China; Liuyang People's Hospital, Liuyang, Hunan, China
| | - Yu-Xiang Wang
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, Hunan, China; Division of Stem Cell Regulation and Application, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Neng Zhu
- The First Affiliated Hospital, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Zhe-Yu Hu
- Department of Breast Medical Oncology, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Duan-Fang Liao
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, Hunan, China; Division of Stem Cell Regulation and Application, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Li Qin
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, Hunan, China; Division of Stem Cell Regulation and Application, Hunan University of Chinese Medicine, Changsha, Hunan, China.
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17
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Leung W, Baxley RM, Moldovan GL, Bielinsky AK. Mechanisms of DNA Damage Tolerance: Post-Translational Regulation of PCNA. Genes (Basel) 2018; 10:genes10010010. [PMID: 30586904 PMCID: PMC6356670 DOI: 10.3390/genes10010010] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 12/18/2018] [Accepted: 12/19/2018] [Indexed: 12/12/2022] Open
Abstract
DNA damage is a constant source of stress challenging genomic integrity. To ensure faithful duplication of our genomes, mechanisms have evolved to deal with damage encountered during replication. One such mechanism is referred to as DNA damage tolerance (DDT). DDT allows for replication to continue in the presence of a DNA lesion by promoting damage bypass. Two major DDT pathways exist: error-prone translesion synthesis (TLS) and error-free template switching (TS). TLS recruits low-fidelity DNA polymerases to directly replicate across the damaged template, whereas TS uses the nascent sister chromatid as a template for bypass. Both pathways must be tightly controlled to prevent the accumulation of mutations that can occur from the dysregulation of DDT proteins. A key regulator of error-prone versus error-free DDT is the replication clamp, proliferating cell nuclear antigen (PCNA). Post-translational modifications (PTMs) of PCNA, mainly by ubiquitin and SUMO (small ubiquitin-like modifier), play a critical role in DDT. In this review, we will discuss the different types of PTMs of PCNA and how they regulate DDT in response to replication stress. We will also cover the roles of PCNA PTMs in lagging strand synthesis, meiotic recombination, as well as somatic hypermutation and class switch recombination.
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Affiliation(s)
- Wendy Leung
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Ryan M Baxley
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
| | - Anja-Katrin Bielinsky
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
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