1
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Si LH, Sun GC, Liu ZW, Gu SY, Yan CH, Xu JY, Jia Y. High expression levels of centromere protein O participates in cell proliferation of human ovarian cancer. J Ovarian Res 2024; 17:126. [PMID: 38890751 PMCID: PMC11184697 DOI: 10.1186/s13048-024-01452-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 06/10/2024] [Indexed: 06/20/2024] Open
Abstract
Ovarian cancer is a common malignant tumor in women, with a high mortality rate ranking first among gynecological tumors. Currently, there is insufficient understanding of the causes, pathogenesis, recurrence and metastasis of ovarian cancer, and early diagnosis and treatment still face great challenges. The sensitivity and specificity of existing ovarian cancer screening methods are still unsatisfactory. Centromere protein O (CENP-O) is a recently discovered structural centromere protein that is involved in cell death and is essential for spindle assembly, chromosome separation, and checkpoint signaling during mitosis. The abnormal high expression of CENP-O was detected in various tumors such as bladder cancer and gastric cancer, and it participates in the regulation of tumor cell proliferation. In this study, we detect the expression abundance of CENP-O mRNA in different ovarian cancer cells ( ES-2, A2780, Caov-3, OVCAR-3 and SK-OV-3). The biological function changes of cell proliferation and apoptosis were detected and the role of CENP-O in ovarian cancer cell proliferation and apoptosis was explored by knocking down the expression of CENP-O gene. The results showed that CENP-O gene was significantly expressed in 5 types of ovarian cancer cell lines. After knocking down the CENP-O gene, the proliferation and cloning ability of ovarian cancer cells decreased, and the apoptosis increased. This study indicates that CENP-O has the potential to be a molecular therapeutic target, and downregulating the expression of CENP-O gene can break the unlimited proliferation ability of cancer cells and promote their apoptosis, providing a foundation and new ideas for subsequent molecular mechanism research and targeted therapy.
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Affiliation(s)
- Li-Hui Si
- Department of Obstetrics and Gynecology, The second Hospital of Jilin University, Changchun, Jilin, China
| | - Guang-Chao Sun
- Department of Neurosurgery, The Second Hospital of Jilin University, Changchun, Jilin, China
| | - Zi-Wei Liu
- Department of Obstetrics and Gynecology, The second Hospital of Jilin University, Changchun, Jilin, China
| | - Shi-Yu Gu
- Department of Obstetrics and Gynecology, The second Hospital of Jilin University, Changchun, Jilin, China
| | - Chu-Han Yan
- Department of Obstetrics and Gynecology, The second Hospital of Jilin University, Changchun, Jilin, China
| | - Jin-Yuan Xu
- Department of Obstetrics and Gynecology, The second Hospital of Jilin University, Changchun, Jilin, China
| | - Yan Jia
- Department of Obstetrics and Gynecology, The second Hospital of Jilin University, Changchun, Jilin, China.
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2
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Bui M, Baek S, Bentahar RS, Melters DP, Dalal Y. Native and tagged CENP-A histones are functionally inequivalent. Epigenetics Chromatin 2024; 17:19. [PMID: 38825690 PMCID: PMC11145777 DOI: 10.1186/s13072-024-00543-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 05/22/2024] [Indexed: 06/04/2024] Open
Abstract
BACKGROUND Over the past several decades, the use of biochemical and fluorescent tags has elucidated mechanistic and cytological processes that would otherwise be impossible. The challenging nature of certain nuclear proteins includes low abundancy, poor antibody recognition, and transient dynamics. One approach to get around those issues is the addition of a peptide or larger protein tag to the target protein to improve enrichment, purification, and visualization. However, many of these studies were done under the assumption that tagged proteins can fully recapitulate native protein function. RESULTS We report that when C-terminally TAP-tagged CENP-A histone variant is introduced, it undergoes altered kinetochore protein binding, differs in post-translational modifications (PTMs), utilizes histone chaperones that differ from that of native CENP-A, and can partially displace native CENP-A in human cells. Additionally, these tagged CENP-A-containing nucleosomes have reduced centromeric incorporation at early G1 phase and poorly associates with linker histone H1.5 compared to native CENP-A nucleosomes. CONCLUSIONS These data suggest expressing tagged versions of histone variant CENP-A may result in unexpected utilization of non-native pathways, thereby altering the biological function of the histone variant.
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Affiliation(s)
- Minh Bui
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, 41 Medlars Drive, Bldg 41/Rm B1300, Bethesda, MD, 20892, USA.
| | - Songjoon Baek
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, 41 Medlars Drive, Bldg 41/Rm B1300, Bethesda, MD, 20892, USA
| | - Reda S Bentahar
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, 41 Medlars Drive, Bldg 41/Rm B1300, Bethesda, MD, 20892, USA
| | - Daniël P Melters
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, 41 Medlars Drive, Bldg 41/Rm B1300, Bethesda, MD, 20892, USA
| | - Yamini Dalal
- Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, 41 Medlars Drive, Bldg 41/Rm B1300, Bethesda, MD, 20892, USA.
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3
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Balachandra V, Shrestha RL, Hammond CM, Lin S, Hendriks IA, Sethi SC, Chen L, Sevilla S, Caplen NJ, Chari R, Karpova TS, McKinnon K, Todd MA, Koparde V, Cheng KCC, Nielsen ML, Groth A, Basrai MA. DNAJC9 prevents CENP-A mislocalization and chromosomal instability by maintaining the fidelity of histone supply chains. EMBO J 2024; 43:2166-2197. [PMID: 38600242 PMCID: PMC11148058 DOI: 10.1038/s44318-024-00093-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 03/20/2024] [Accepted: 03/25/2024] [Indexed: 04/12/2024] Open
Abstract
The centromeric histone H3 variant CENP-A is overexpressed in many cancers. The mislocalization of CENP-A to noncentromeric regions contributes to chromosomal instability (CIN), a hallmark of cancer. However, pathways that promote or prevent CENP-A mislocalization remain poorly defined. Here, we performed a genome-wide RNAi screen for regulators of CENP-A localization which identified DNAJC9, a J-domain protein implicated in histone H3-H4 protein folding, as a factor restricting CENP-A mislocalization. Cells lacking DNAJC9 exhibit mislocalization of CENP-A throughout the genome, and CIN phenotypes. Global interactome analysis showed that DNAJC9 depletion promotes the interaction of CENP-A with the DNA-replication-associated histone chaperone MCM2. CENP-A mislocalization upon DNAJC9 depletion was dependent on MCM2, defining MCM2 as a driver of CENP-A deposition at ectopic sites when H3-H4 supply chains are disrupted. Cells depleted for histone H3.3, also exhibit CENP-A mislocalization. In summary, we have defined novel factors that prevent mislocalization of CENP-A, and demonstrated that the integrity of H3-H4 supply chains regulated by histone chaperones such as DNAJC9 restrict CENP-A mislocalization and CIN.
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Grants
- 75N91019D00024 NCI NIH HHS
- HHSN261201500003I NCI NIH HHS
- ZIA BC 010822 HHS | NIH | NCI | Center for Cancer Research (CCR)
- ZIA BC 011704 HHS | NIH | NCI | Center for Cancer Research (CCR)
- 75N91019D00024 NCI NIH HHS
- HHSN261201500003I NCI NIH HHS
- 0135-00096B and 8020-00220B,EPIC-XS-823839,R146-A9159-16-S2 Independent Research Fund Denmark, European Union's Horizon 2020 research and innovation program, Danish Cancer Society
- ERC CoG 724436,R198-2015-269 and R313-2019-448,7016-00042B,NNF21OC0067425,NNF14CC0001 European Research Council, Lund-beck Foundation, Independent Research Fund Denmark, Novo Nordisk Foundation
- HHS | NIH | National Cancer Institute (NCI)
- Independent Research Fund Denmark, European Union’s Horizon 2020 research and innovation program, Danish Cancer Society
- NIH Intramural Research Program, Intramural Research Program of the National Center for Advancing Translational Sciences (NCATS)
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Affiliation(s)
- Vinutha Balachandra
- Yeast Genome Stability Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Roshan L Shrestha
- Yeast Genome Stability Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Colin M Hammond
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.
| | - Shinjen Lin
- Functional Genomics Laboratory, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Ivo A Hendriks
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Subhash Chandra Sethi
- Yeast Genome Stability Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lu Chen
- Functional Genomics Laboratory, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Samantha Sevilla
- Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Natasha J Caplen
- Functional Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Raj Chari
- Genome Modification Core (GMC), Frederick National Lab for Cancer Research, Frederick, MD, USA
| | - Tatiana S Karpova
- Optical Microscopy Core, Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Katherine McKinnon
- Flow Cytometry Core, Vaccine Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Matthew Am Todd
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Vishal Koparde
- Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Ken Chih-Chien Cheng
- Functional Genomics Laboratory, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Michael L Nielsen
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anja Groth
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Munira A Basrai
- Yeast Genome Stability Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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4
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Renaud-Pageot C, Almouzni G. Tipping the balance in histone supply puts genome stability at stake. EMBO J 2024; 43:2091-2093. [PMID: 38698217 PMCID: PMC11148134 DOI: 10.1038/s44318-024-00112-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 04/18/2024] [Indexed: 05/05/2024] Open
Abstract
New work identifying an H3-H4 chaperone as factor restricting localization of CENP-A underscores the importance of balanced histone levels for maintaining proper chromosome segregation.
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Affiliation(s)
- Charlène Renaud-Pageot
- Institut Curie, CNRS, PSL Research University, Sorbonne University, Nuclear Dynamics Unit, Équipe Labellisée Ligue contre le Cancer, Paris, France
| | - Geneviève Almouzni
- Institut Curie, CNRS, PSL Research University, Sorbonne University, Nuclear Dynamics Unit, Équipe Labellisée Ligue contre le Cancer, Paris, France.
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5
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Khurana S, Varma D, Foltz DR. Contribution of CENP-F to FOXM1-Mediated Discordant Centromere and Kinetochore Transcriptional Regulation. Mol Cell Biol 2024:1-17. [PMID: 38779933 DOI: 10.1080/10985549.2024.2350543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/28/2024] [Indexed: 05/25/2024] Open
Abstract
Proper chromosome segregation is required to ensure chromosomal stability. The centromere (CEN) is a unique chromatin domain defined by CENP-A and is responsible for recruiting the kinetochore (KT) during mitosis, ultimately regulating microtubule spindle attachment and mitotic checkpoint function. Upregulation of many CEN/KT genes is commonly observed in cancer. Here, we show that although FOXM1 occupies promoters of many CEN/KT genes with MYBL2, FOXM1 overexpression alone is insufficient to drive the FOXM1-correlated transcriptional program. CENP-F is canonically an outer kinetochore component; however, it functions with FOXM1 to coregulate G2/M transcription and proper chromosome segregation. Loss of CENP-F results in altered chromatin accessibility at G2/M genes and reduced FOXM1-MBB complex formation. We show that coordinated CENP-FFOXM1 transcriptional regulation is a cancer-specific function. We observe a small subset of CEN/KT genes including CENP-C, that are not regulated by FOXM1. Upregulation of CENP-C in the context of CENP-A overexpression leads to increased chromosome missegregation and cell death suggesting that escape of CENP-C from FOXM1 regulation is a cancer survival mechanism. Together, we show that FOXM1 and CENP-F coordinately regulate G2/M genes, and this coordination is specific to a subset of genes to allow for maintenance of chromosome instability levels and subsequent cell survival.
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Affiliation(s)
- Sakshi Khurana
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Dileep Varma
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Department of Cellular and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Daniel R Foltz
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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6
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Serafim RB, Cardoso C, Storti CB, da Silva P, Qi H, Parasuram R, Navegante G, Peron JPS, Silva WA, Espreafico EM, Paçó-Larson ML, Price BD, Valente V. HJURP is recruited to double-strand break sites and facilitates DNA repair by promoting chromatin reorganization. Oncogene 2024; 43:804-820. [PMID: 38279062 DOI: 10.1038/s41388-024-02937-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 12/21/2023] [Accepted: 01/04/2024] [Indexed: 01/28/2024]
Abstract
HJURP is overexpressed in several cancer types and strongly correlates with patient survival. However, the mechanistic basis underlying the association of HJURP with cancer aggressiveness is not well understood. HJURP promotes the loading of the histone H3 variant, CENP-A, at the centromeric chromatin, epigenetically defining the centromeres and supporting proper chromosome segregation. In addition, HJURP is associated with DNA repair but its function in this process is still scarcely explored. Here, we demonstrate that HJURP is recruited to DSBs through a mechanism requiring chromatin PARylation and promotes epigenetic alterations that favor the execution of DNA repair. Incorporation of HJURP at DSBs promotes turnover of H3K9me3 and HP1, facilitating DNA damage signaling and DSB repair. Moreover, HJURP overexpression in glioma cell lines also affected global structure of heterochromatin independently of DNA damage induction, promoting genome-wide reorganization and assisting DNA damage response. HJURP overexpression therefore extensively alters DNA damage signaling and DSB repair, and also increases radioresistance of glioma cells. Importantly, HJURP expression levels in tumors are also associated with poor response of patients to radiation. Thus, our results enlarge the understanding of HJURP involvement in DNA repair and highlight it as a promising target for the development of adjuvant therapies that sensitize tumor cells to irradiation.
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Affiliation(s)
- Rodolfo B Serafim
- Department of Cellular and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo (USP), Avenida Bandeirantes, 3900, Ribeirão Preto, 14049-900, Brazil
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Rodovia Araraquara - Jaú, Km 01 - s/n, Campos Ville, Araraquara, SP, 14800-903, Brazil
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for Cell-Based Therapy-CEPID/FAPESP, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, 14051-140, Brazil
| | - Cibele Cardoso
- Department of Cellular and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo (USP), Avenida Bandeirantes, 3900, Ribeirão Preto, 14049-900, Brazil
- Center for Cell-Based Therapy-CEPID/FAPESP, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, 14051-140, Brazil
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), Avenida Bandeirantes, 3900, Ribeirão Preto, 14049-900, Brazil
| | - Camila B Storti
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), Avenida Bandeirantes, 3900, Ribeirão Preto, 14049-900, Brazil
| | - Patrick da Silva
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Hongyun Qi
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Ramya Parasuram
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Geovana Navegante
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Rodovia Araraquara - Jaú, Km 01 - s/n, Campos Ville, Araraquara, SP, 14800-903, Brazil
| | - Jean Pierre S Peron
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Wilson A Silva
- Center for Cell-Based Therapy-CEPID/FAPESP, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, 14051-140, Brazil
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo (USP), Avenida Bandeirantes, 3900, Ribeirão Preto, 14049-900, Brazil
| | - Enilza M Espreafico
- Department of Cellular and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo (USP), Avenida Bandeirantes, 3900, Ribeirão Preto, 14049-900, Brazil
| | - Maria L Paçó-Larson
- Department of Cellular and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo (USP), Avenida Bandeirantes, 3900, Ribeirão Preto, 14049-900, Brazil
| | - Brendan D Price
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
| | - Valeria Valente
- Department of Cellular and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo (USP), Avenida Bandeirantes, 3900, Ribeirão Preto, 14049-900, Brazil.
- São Paulo State University (UNESP), School of Pharmaceutical Sciences, Rodovia Araraquara - Jaú, Km 01 - s/n, Campos Ville, Araraquara, SP, 14800-903, Brazil.
- Center for Cell-Based Therapy-CEPID/FAPESP, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, 14051-140, Brazil.
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7
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Ohkuni K, Au WC, Kazi A, Villamil M, Kaiser P, Basrai M. Interaction of histone H4 with Cse4 facilitates conformational changes in Cse4 for its sumoylation and mislocalization. Nucleic Acids Res 2024; 52:643-659. [PMID: 38038247 PMCID: PMC10810195 DOI: 10.1093/nar/gkad1133] [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] [Received: 08/23/2023] [Revised: 10/27/2023] [Accepted: 11/09/2023] [Indexed: 12/02/2023] Open
Abstract
Mislocalization of overexpressed CENP-A (Cse4 in budding yeast, Cnp1 in fission yeast, CID in flies) contributes to chromosomal instability (CIN) in yeasts, flies, and human cells. Mislocalization of CENP-A is observed in many cancers and this correlates with poor prognosis. Structural mechanisms that contribute to mislocalization of CENP-A are poorly defined. Here, we show that interaction of histone H4 with Cse4 facilitates an in vivo conformational change in Cse4 promoting its mislocalization in budding yeast. We determined that Cse4 Y193A mutant exhibits reduced sumoylation, mislocalization, interaction with histone H4, and lethality in psh1Δ and cdc48-3 strains; all these phenotypes are suppressed by increased gene dosage of histone H4. We developed a new in vivo approach, antibody accessibility (AA) assay, to examine the conformation of Cse4. AA assay showed that wild-type Cse4 with histone H4 is in an 'open' state, while Cse4 Y193A predominantly exhibits a 'closed' state. Increased gene dosage of histone H4 contributes to a shift of Cse4 Y193A to an 'open' state with enhanced sumoylation and mislocalization. We provide molecular insights into how Cse4-H4 interaction changes the conformational state of Cse4 in vivo. These studies advance our understanding for mechanisms that promote mislocalization of CENP-A in human cancers.
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Affiliation(s)
- Kentaro Ohkuni
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wei-Chun Au
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amira Z Kazi
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark Villamil
- Department of Biological Chemistry, School of Medicine, Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California, Irvine, CA 92697-1700, USA
| | - Peter Kaiser
- Department of Biological Chemistry, School of Medicine, Center for Epigenetics and Metabolism, Chao Family Comprehensive Cancer Center, University of California, Irvine, CA 92697-1700, USA
| | - Munira A Basrai
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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8
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Sissoko GB, Tarasovetc EV, Marescal O, Grishchuk EL, Cheeseman IM. Higher-order protein assembly controls kinetochore formation. Nat Cell Biol 2024; 26:45-56. [PMID: 38168769 PMCID: PMC10842828 DOI: 10.1038/s41556-023-01313-7] [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] [Received: 04/23/2023] [Accepted: 11/13/2023] [Indexed: 01/05/2024]
Abstract
To faithfully segregate chromosomes during vertebrate mitosis, kinetochore-microtubule interactions must be restricted to a single site on each chromosome. Prior work on pair-wise kinetochore protein interactions has been unable to identify the mechanisms that prevent outer kinetochore formation in regions with a low density of CENP-A nucleosomes. To investigate the impact of higher-order assembly on kinetochore formation, we generated oligomers of the inner kinetochore protein CENP-T using two distinct, genetically engineered systems in human cells. Although individual CENP-T molecules interact poorly with outer kinetochore proteins, oligomers that mimic centromeric CENP-T density trigger the robust formation of functional, cytoplasmic kinetochore-like particles. Both in cells and in vitro, each molecule of oligomerized CENP-T recruits substantially higher levels of outer kinetochore components than monomeric CENP-T molecules. Our work suggests that the density dependence of CENP-T restricts outer kinetochore recruitment to centromeres, where densely packed CENP-A recruits a high local concentration of inner kinetochore proteins.
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Affiliation(s)
- Gunter B Sissoko
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ekaterina V Tarasovetc
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Océane Marescal
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ekaterina L Grishchuk
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Iain M Cheeseman
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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9
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Ólafsson G, Haase MAB, Boeke JD. Humanization reveals pervasive incompatibility of yeast and human kinetochore components. G3 (BETHESDA, MD.) 2023; 14:jkad260. [PMID: 37962556 PMCID: PMC10755175 DOI: 10.1093/g3journal/jkad260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 06/29/2023] [Accepted: 11/06/2023] [Indexed: 11/15/2023]
Abstract
Kinetochores assemble on centromeres to drive chromosome segregation in eukaryotic cells. Humans and budding yeast share most of the structural subunits of the kinetochore, whereas protein sequences have diverged considerably. The conserved centromeric histone H3 variant, CenH3 (CENP-A in humans and Cse4 in budding yeast), marks the site for kinetochore assembly in most species. A previous effort to complement Cse4 in yeast with human CENP-A was unsuccessful; however, co-complementation with the human core nucleosome was not attempted. Previously, our lab successfully humanized the core nucleosome in yeast; however, this severely affected cellular growth. We hypothesized that yeast Cse4 is incompatible with humanized nucleosomes and that the kinetochore represented a limiting factor for efficient histone humanization. Thus, we argued that including the human CENP-A or a Cse4-CENP-A chimera might improve histone humanization and facilitate kinetochore function in humanized yeast. The opposite was true: CENP-A expression reduced histone humanization efficiency, was toxic to yeast, and disrupted cell cycle progression and kinetochore function in wild-type (WT) cells. Suppressors of CENP-A toxicity included gene deletions of subunits of 3 conserved chromatin remodeling complexes, highlighting their role in CenH3 chromatin positioning. Finally, we attempted to complement the subunits of the NDC80 kinetochore complex, individually and in combination, without success, in contrast to a previous study indicating complementation by the human NDC80/HEC1 gene. Our results suggest that limited protein sequence similarity between yeast and human components in this very complex structure leads to failure of complementation.
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Affiliation(s)
- Guðjón Ólafsson
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Max A B Haase
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
- Vilcek Institute of Graduate Biomedical Sciences, NYU School of Medicine, New York, NY 10016, USA
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 14 11201, USA
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10
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Yang Z, Wu H, Dai D, Yuan Y, Shao X. ZNF692 Promotes the Progression of Colon Adenocarcinoma by Regulating HSF4 Expression. IRANIAN JOURNAL OF PUBLIC HEALTH 2023; 52:2601-2610. [PMID: 38435777 PMCID: PMC10903307 DOI: 10.18502/ijph.v52i12.14321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 07/18/2023] [Indexed: 03/05/2024]
Abstract
Background Colon adenocarcinoma (COAD) is one of the most common cancer happened in gastrointestinal tract, with the overall incidence rate of 4%-5% among human beings. Like most malignancies, we uncovered the exact mechanisms of the pathogenesis of colorectal cancer yet. Therefore, there is an urgent need to explore the molecules that can be used as diagnostic maker at early stage. In addition, we also need to define the essential factors that related to the prognosis and treatment of the colon carcinoma. Methods The study was conducted at the Third Affiliated Hospital of Qiqihar Medical University, Qiqihar, China in September 2020. The R language was used to identify the differentially expressed genes. We performed receiver operating characteristic curve analysis to determine the diagnostic markers for COAD. The machine learning strategy was used to assess the effectiveness of genes in the diagnosis of COAD. The molecular mechanism and prognostic value of genes were explored by bioinformatics analysis and molecular experiments. Results The expression level of heat shock factor 4 (HSF4) was significantly elevated in COAD patients (P=1.89×10-29), according to The Cancer Genome Atlas (TCGA) database. Additionally, survival analysis showed the higher expression level of the HSF4 was correlated with the poor prognosis in COAD. Conclusion The HSF4 was the target gene of zinc finger protein 692(ZNF692). HSF4 might promote the progression of COAD through the apoptosis pathway. It was diagnostic and prognosis maker of COAD. Furthermore, the upstream gene of HSF4, ZNF692, promotes the progression of colorectal cancer by regulating HSF4 expression.
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Affiliation(s)
- Zhengpeng Yang
- Department of General Surgery, the Third Affiliated Hospital of Qiqihar Medical University, Qiqihar 161002, China
| | - Hao Wu
- Department of General Surgery, the Third Affiliated Hospital of Qiqihar Medical University, Qiqihar 161002, China
| | - Defu Dai
- Department of General Surgery, the Third Affiliated Hospital of Qiqihar Medical University, Qiqihar 161002, China
| | - Yufeng Yuan
- Department of General Surgery, the Third Affiliated Hospital of Qiqihar Medical University, Qiqihar 161002, China
| | - Xueqian Shao
- Department of General Surgery, the Third Affiliated Hospital of Qiqihar Medical University, Qiqihar 161002, China
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11
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Delaney K, Weiss N, Almouzni G. The cell-cycle choreography of H3 variants shapes the genome. Mol Cell 2023; 83:3773-3786. [PMID: 37734377 PMCID: PMC10621666 DOI: 10.1016/j.molcel.2023.08.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/07/2023] [Accepted: 08/29/2023] [Indexed: 09/23/2023]
Abstract
Histone variants provide versatility in the basic unit of chromatin, helping to define dynamic landscapes and cell fates. Maintaining genome integrity is paramount for the cell, and it is intimately linked with chromatin dynamics, assembly, and disassembly during DNA transactions such as replication, repair, recombination, and transcription. In this review, we focus on the family of H3 variants and their dynamics in space and time during the cell cycle. We review the distinct H3 variants' specific features along with their escort partners, the histone chaperones, compiled across different species to discuss their distinct importance considering evolution. We place H3 dynamics at different times during the cell cycle with the possible consequences for genome stability. Finally, we examine how their mutation and alteration impact disease. The emerging picture stresses key parameters in H3 dynamics to reflect on how when they are perturbed, they become a source of stress for genome integrity.
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Affiliation(s)
- Kamila Delaney
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, Equipe Labellisée Ligue contre le Cancer, 26 rue d'Ulm, 75005 Paris, France
| | - Nicole Weiss
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, Equipe Labellisée Ligue contre le Cancer, 26 rue d'Ulm, 75005 Paris, France
| | - Geneviève Almouzni
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, Equipe Labellisée Ligue contre le Cancer, 26 rue d'Ulm, 75005 Paris, France.
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12
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Kale S, Boopathi R, Belotti E, Lone IN, Graies M, Schröder M, Petrova M, Papin C, Bednar J, Ugrinova I, Hamiche A, Dimitrov S. The CENP-A nucleosome: where and when it happens during the inner kinetochore's assembly. Trends Biochem Sci 2023; 48:849-859. [PMID: 37596196 DOI: 10.1016/j.tibs.2023.07.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/19/2023] [Accepted: 07/19/2023] [Indexed: 08/20/2023]
Abstract
CENP-A is an essential histone variant that replaces the canonical H3 at the centromeres and marks these regions epigenetically. The CENP-A nucleosome is the specific building block of centromeric chromatin, and it is recognized by CENP-C and CENP-N, two components of the constitutive centromere-associated network (CCAN), the first protein layer of the kinetochore. Recent proposals of the yeast and human (h)CCAN structures position the assembly on exposed DNA, suggesting an elusive spatiotemporal recognition. We summarize the data on the structural organization of the CENP-A nucleosome and the binding of CENP-C and CENP-N. The latter posits an apparent contradiction in engaging the CENP-A nucleosome versus the CCAN. We propose a reconciliatory model for the assembly of CCAN on centromeric chromatin.
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Affiliation(s)
- Seyit Kale
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Balcova, Izmir 35330, Turkey.
| | - Ramachandran Boopathi
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000 Grenoble, France; Laboratoire de Biologie et de Modelisation de la Cellule (LBMC), CNRS/ENSL/UCBL, Ecole Normale Supérieure de Lyon, 69007 Lyon, France
| | - Edwige Belotti
- Laboratoire Physiopathologie et Génétique du Neurone et du Muscle (PGNM), Institut NeuroMyoGène, Université Claude Bernard Lyon 1, INSERM U1315, CNRS UMR5261, 8 avenue Rockefeller, 69008 Lyon, France
| | - Imtiaz Nisar Lone
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Balcova, Izmir 35330, Turkey
| | - Mohamed Graies
- Institute for Advanced Biosciences, INSERM U1209, CNRS, UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France
| | - Maria Schröder
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Maria Petrova
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Christophe Papin
- Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), UdS, CNRS, INSERM, Illkirch-Graffenstaden, France
| | - Jan Bednar
- Institute for Advanced Biosciences, INSERM U1209, CNRS, UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France
| | - Iva Ugrinova
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Ali Hamiche
- Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), UdS, CNRS, INSERM, Illkirch-Graffenstaden, France.
| | - Stefan Dimitrov
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Balcova, Izmir 35330, Turkey; Institute for Advanced Biosciences, INSERM U1209, CNRS, UMR 5309, Université Grenoble Alpes, 38000 Grenoble, France; Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria.
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13
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Shi YX, Dai PH, Jiang YF, Wang YQ, Liu W. A pan-cancer landscape of centromere proteins in tumorigenesis and anticancer drug sensitivity. Transl Oncol 2023; 31:101658. [PMID: 36944275 PMCID: PMC10036944 DOI: 10.1016/j.tranon.2023.101658] [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: 12/06/2022] [Revised: 02/21/2023] [Accepted: 03/10/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND During mitosis and meiosis, centromere proteins (CENPs) play a key role in proper chromosome segregation. Abnormal expression of CENPs leads to chromosome instability, which is the main cause of tumorigenesis. METHODS To elucidate the functional characteristics of CENPs in pan-cancer, we comprehensively analyzed the expression landscape of CENPs and their relationships with patient survival, genomic alterations, tumor immunity, tumor microenvironment, and anticancer drug sensitivity. The expression patterns and signaling pathways of CENPs were identified through multiple bioinformatics mining and experimental verification. GEPIA2 and PrognoScan were implemented to evaluate the prognostic value of CENPs. The molecular functions of CENPs in pan-cancer were comprehensively assessed using cBioPortal, GSCA, ImmuCellAI, CellMiner, the ROC plotter tool and TIDE. RESULTS The results showed that CENPs were upregulated in most tumors compared with normal tissues. We confirmed this conclusion by immunohistochemistry and real-time quantitative PCR. Survival analysis revealed a significant association between high CENP expression and a poor prognosis. CENP expression is related to genome alterations, copy number variation, single nucleotide variation and methylation. Among CENP family genes, CENPF and CENPE are mutated at high frequencies in various tumors, while CENPM and CENPA are less frequently mutated. Furthermore, CENPs regulate the tumor mutational burden, stemness, and microsatellite instability, and are associated with tumor immunity. Most importantly, we revealed that CENP family gene expression was correlated with chemosensitivity and immunotherapy responses. CONCLUSION These findings may clarify the role of CENPs in cancer progression and antitumor drug sensitivity and provide evidence for CENPs as a potential target in pan-cancer.
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Affiliation(s)
- Yuan-Xiang Shi
- Institute of Clinical Medicine, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan 410005, P.R. China.
| | - Peng-Hui Dai
- Department of Pathology, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan 410005, P.R. China
| | - Yu-Fei Jiang
- Faculty of Health Sciences, University of Macau, Macau 999078, P.R. China
| | - Yan-Qing Wang
- Department of Thoracic Surgery, Beijing Chest Hospital, Capital Medical University/ Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101149, P.R. China
| | - Wen Liu
- Department of Pharmacy, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan 410005, P.R. China
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14
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Yang Y, Duan M, Zha Y, Wu Z. CENP-A is a potential prognostic biomarker and correlated with immune infiltration levels in glioma patients. Front Genet 2022; 13:931222. [PMID: 36105094 PMCID: PMC9465177 DOI: 10.3389/fgene.2022.931222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 08/05/2022] [Indexed: 12/02/2022] Open
Abstract
Background: Centromeric protein A (CENP-A), an essential protein involved in chromosomal segregation during cell division, is associated with several cancer types. However, its role in gliomas remains unclear. This study examined the clinical and prognostic significance of CENP-A in gliomas. Methods: Data of patients with glioma were collected from the Cancer Genome Atlas. Logistic regression, the Kruskal–Wallis test, and the Wilcoxon signed-rank test were performed to assess the relationship between CENP-A expression and clinicopathological parameters. The Cox regression model and Kaplan–Meier curve were used to analyze the association between CENP-A and survival outcomes. A prognostic nomogram was constructed based on Cox multivariate analysis. Gene set enrichment analysis (GSEA) was conducted to identify key CENP-A-related pathways and biological processes. Results:CENP-A was upregulated in glioma samples. Increased CENP-A levels were significantly associated with the world health organization (WHO) grade [Odds ratio (OR) = 49.88 (23.52–129.06) for grade 4 vs. grades 2 and 3], primary therapy outcome [OR = 2.44 (1.64–3.68) for progressive disease (PD) and stable disease (SD) vs. partial response (PR) and complete response (CR)], isocitrate dehydrogenase (IDH) status [OR = 13.76 (9.25–20.96) for wild-type vs. mutant], 1p/19q co-deletion [OR = 5.91 (3.95–9.06) for no codeletion vs. co-deletion], and age [OR = 4.02 (2.68–6.18) for > 60 vs. ≤ 60]. Elevated CENP-A expression was correlated with shorter overall survival in both univariate [hazard ratio (HR): 5.422; 95% confidence interval (CI): 4.044–7.271; p < 0.001] and multivariate analyses (HR: 1.967; 95% CI: 1.280–3.025; p < 0.002). GSEA showed enrichment of numerous cell cycle-and tumor-related pathways in the CENP-A high expression phenotype. The calibration plot and C-index indicated the favorable performance of our nomogram for prognostic prediction in patients with glioma. Conclusion: We propose a role for CENP-A in glioma progression and its potential as a biomarker for glioma diagnosis and prognosis.
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Affiliation(s)
- Yuan Yang
- Department of Radiology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Mengyun Duan
- Health Science Center, Department of Medical Imaging, Yangtze University, Jingzhou, China
| | - Yunfei Zha
- Department of Radiology, Renmin Hospital of Wuhan University, Wuhan, China
- *Correspondence: Yunfei Zha, ; Zijun Wu,
| | - Zijun Wu
- Department of Radiology, Renmin Hospital of Wuhan University, Wuhan, China
- *Correspondence: Yunfei Zha, ; Zijun Wu,
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15
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Dibus N, Korinek V, Cermak L. FBXO38 Ubiquitin Ligase Controls Centromere Integrity via ZXDA/B Stability. Front Cell Dev Biol 2022; 10:929288. [PMID: 35813202 PMCID: PMC9260856 DOI: 10.3389/fcell.2022.929288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/02/2022] [Indexed: 11/13/2022] Open
Abstract
Alterations in the gene encoding the E3 ubiquitin ligase substrate receptor FBXO38 have been associated with several diseases, including early-onset motor neuronopathy. However, the cellular processes affected by the enzymatic action of FBXO38 are not yet known. Here, we identify the zinc finger proteins ZXDA/B as its interaction partners. FBXO38 controls the stability of ZXDA/B proteins via ubiquitination and proteasome-dependent degradation. We show that ZXDA/B proteins associate with the centromeric protein CENP-B and that the interaction between ZXDA/B and FBXO38 or CENP-B is mutually exclusive. Functionally, ZXDA/B factors control the protein level of chromatin-associated CENP-B. Furthermore, their inappropriate stabilization leads to upregulation of CENP-A and CENP-B positive centromeric chromatin. Thus we demonstrate a previously unknown role of cullin-dependent protein degradation in the control of centromeric chromatin integrity.
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Affiliation(s)
- Nikol Dibus
- Laboratory of Cancer Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czechia
| | - Vladimir Korinek
- Laboratory of Cell and Developmental Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Lukas Cermak
- Laboratory of Cancer Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czechia
- *Correspondence: Lukas Cermak,
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16
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Renaud-Pageot C, Quivy JP, Lochhead M, Almouzni G. CENP-A Regulation and Cancer. Front Cell Dev Biol 2022; 10:907120. [PMID: 35721491 PMCID: PMC9201071 DOI: 10.3389/fcell.2022.907120] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/11/2022] [Indexed: 11/13/2022] Open
Abstract
In mammals, CENP-A, a histone H3 variant found in the centromeric chromatin, is critical for faithful chromosome segregation and genome integrity maintenance through cell divisions. Specifically, it has dual functions, enabling to define epigenetically the centromere position and providing the foundation for building up the kinetochore. Regulation of its dynamics of synthesis and deposition ensures to propagate proper centromeres on each chromosome across mitosis and meiosis. However, CENP-A overexpression is a feature identified in many cancers. Importantly, high levels of CENP-A lead to its mislocalization outside the centromere. Recent studies in mammals have begun to uncover how CENP-A overexpression can affect genome integrity, reprogram cell fate and impact 3D nuclear organization in cancer. Here, we summarize the mechanisms that orchestrate CENP-A regulation. Then we review how, beyond its centromeric function, CENP-A overexpression is linked to cancer state in mammalian cells, with a focus on the perturbations that ensue at the level of chromatin organization. Finally, we review the clinical interest for CENP-A in cancer treatment.
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17
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Gonzalez PA, Nagy PD. The centromeric histone CenH3 is recruited into the tombusvirus replication organelles. PLoS Pathog 2022; 18:e1010653. [PMID: 35767596 PMCID: PMC9275711 DOI: 10.1371/journal.ppat.1010653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 07/12/2022] [Accepted: 06/07/2022] [Indexed: 11/19/2022] Open
Abstract
Tombusviruses, similar to other (+)RNA viruses, exploit the host cells by co-opting numerous host components and rewiring cellular pathways to build extensive virus-induced replication organelles (VROs) in the cytosol of the infected cells. Most molecular resources are suboptimal in susceptible cells and therefore, tomato bushy stunt virus (TBSV) drives intensive remodeling and subversion of many cellular processes. The authors discovered that the nuclear centromeric CenH3 histone variant (Cse4p in yeast, CENP-A in humans) plays a major role in tombusvirus replication in plants and in the yeast model host. We find that over-expression of CenH3 greatly interferes with tombusvirus replication, whereas mutation or knockdown of CenH3 enhances TBSV replication in yeast and plants. CenH3 binds to the viral RNA and acts as an RNA chaperone. Although these data support a restriction role of CenH3 in tombusvirus replication, we demonstrate that by partially sequestering CenH3 into VROs, TBSV indirectly alters selective gene expression of the host, leading to more abundant protein pool. This in turn helps TBSV to subvert pro-viral host factors into replication. We show this through the example of hypoxia factors, glycolytic and fermentation enzymes, which are exploited more efficiently by tombusviruses to produce abundant ATP locally within the VROs in infected cells. Altogether, we propose that subversion of CenH3/Cse4p from the nucleus into cytosolic VROs facilitates transcriptional changes in the cells, which ultimately leads to more efficient ATP generation in situ within VROs by the co-opted glycolytic enzymes to support the energy requirement of virus replication. In summary, CenH3 plays both pro-viral and restriction functions during tombusvirus replication. This is a surprising novel role for a nuclear histone variant in cytosolic RNA virus replication.
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Affiliation(s)
| | - Peter D. Nagy
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, United States of America
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18
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The ins and outs of CENP-A: Chromatin dynamics of the centromere-specific histone. Semin Cell Dev Biol 2022; 135:24-34. [PMID: 35422390 DOI: 10.1016/j.semcdb.2022.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/05/2022] [Accepted: 04/05/2022] [Indexed: 01/08/2023]
Abstract
Centromeres are highly specialised chromosome domains defined by the presence of an epigenetic mark, the specific histone H3 variant called CENP-A (centromere protein A). They constitute the genomic regions on which kinetochores form and when defective cause segregation defects that can lead to aneuploidy and cancer. Here, we discuss how CENP-A is established and maintained to propagate centromere identity while subjected to dynamic chromatin remodelling during essential cellular processes like DNA repair, replication, and transcription. We highlight parallels and identify conserved mechanisms between different model organism with a particular focus on 1) the establishment of CENP-A at centromeres, 2) CENP-A maintenance during transcription and replication, and 3) the mechanisms that help preventing CENP-A localization at non-centromeric sites. We then give examples of how timely loading of new CENP-A to the centromere, maintenance of old CENP-A during S-phase and transcription, and removal of CENP-A at non-centromeric sites are coordinated and controlled by an intricate network of factors whose identity is slowly being unravelled.
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19
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Ohkuni K, Gliford L, Au WC, Suva E, Kaiser P, Basrai M. Cdc48Ufd1/Npl4 segregase removes mislocalized centromeric histone H3 variant CENP-A from non-centromeric chromatin. Nucleic Acids Res 2022; 50:3276-3291. [PMID: 35234920 PMCID: PMC8989521 DOI: 10.1093/nar/gkac135] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/10/2022] [Accepted: 02/14/2022] [Indexed: 12/02/2023] Open
Abstract
Restricting the localization of CENP-A (Cse4 in Saccharomyces cerevisiae) to centromeres prevents chromosomal instability (CIN). Mislocalization of overexpressed CENP-A to non-centromeric chromatin contributes to CIN in budding and fission yeasts, flies, and humans. Overexpression and mislocalization of CENP-A is observed in cancers and is associated with increased invasiveness. Mechanisms that remove mislocalized CENP-A and target it for degradation have not been defined. Here, we report that Cdc48 and its cofactors Ufd1 and Npl4 facilitate the removal of mislocalized Cse4 from non-centromeric chromatin. Defects in removal of mislocalized Cse4 contribute to lethality of overexpressed Cse4 in cdc48,ufd1 andnpl4 mutants. High levels of polyubiquitinated Cse4 and mislocalization of Cse4 are observed in cdc48-3, ufd1-2 and npl4-1mutants even under normal physiological conditions, thereby defining polyubiquitinated Cse4 as the substrate of the ubiquitin directed segregase Cdc48Ufd1/Npl4. Accordingly, Npl4, the ubiquitin binding receptor, associates with mislocalized Cse4, and this interaction is dependent on Psh1-mediated polyubiquitination of Cse4. In summary, we provide the first evidence for a mechanism that facilitates the removal of polyubiquitinated and mislocalized Cse4 from non-centromeric chromatin. Given the conservation of Cdc48Ufd1/Npl4 in humans, it is likely that defects in such pathways may contribute to CIN in human cancers.
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Affiliation(s)
- Kentaro Ohkuni
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Loran Gliford
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wei-Chun Au
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Evelyn Suva
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter Kaiser
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697, USA
| | - Munira A Basrai
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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20
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Arunkumar G, Baek S, Sturgill D, Bui M, Dalal Y. Oncogenic lncRNAs alter epigenetic memory at a fragile chromosomal site in human cancer cells. SCIENCE ADVANCES 2022; 8:eabl5621. [PMID: 35235361 PMCID: PMC8890707 DOI: 10.1126/sciadv.abl5621] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Chromosome instability is a critical event in cancer progression. Histone H3 variant CENP-A plays a fundamental role in defining centromere identity, structure, and function but is innately overexpressed in several types of solid cancers. In the cancer background, excess CENP-A is deposited ectopically on chromosome arms, including 8q24/cMYC locus, by invading transcription-coupled H3.3 chaperone pathways. Up-regulation of lncRNAs in many cancers correlates with poor prognosis and recurrence in patients. We report that transcription of 8q24-derived oncogenic lncRNAs plays an unanticipated role in altering the 8q24 chromatin landscape by H3.3 chaperone-mediated deposition of CENP-A-associated complexes. Furthermore, a transgene cassette carrying specific 8q24-derived lncRNA integrated into a naïve chromosome locus recruits CENP-A to the new location in a cis-acting manner. These data provide a plausible mechanistic link between locus-specific oncogenic lncRNAs, aberrant local chromatin structure, and the generation of new epigenetic memory at a fragile site in human cancer cells.
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21
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Lou Y, Lu J, Zhang Y, Gu P, Wang H, Qian F, Zhou W, Zhang W, Zhong H, Han B. The centromere-associated protein CENPU promotes cell proliferation, migration, and invasiveness in lung adenocarcinoma. Cancer Lett 2022; 532:215599. [PMID: 35176420 DOI: 10.1016/j.canlet.2022.215599] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 01/19/2022] [Accepted: 02/13/2022] [Indexed: 12/01/2022]
Abstract
CENPU, encoding an important factor involved in kinetochore assembly during mitosis, is associated with shorter survival rates in lung adenocarcinoma (LUAD) patients. CENPU promotes growth rates and invasive behavior of LUAD cells; however, its mechanism of action in LUAD progression remains to be elucidated. CENPU mRNA and protein expression were elevated in LUAD tumors, and high CENPU gene expression was associated with inferior survival prognosis in LUAD patients. CENPU knockdown inhibited LUAD cell proliferation, clone formation, migration, invasion, and epithelial-mesenchymal transition (EMT) in addition to inducing cell cycle arrest and apoptosis in vitro and reduced LUAD xenograft tumor growth in vivo. Furthermore, we identified CENPU-regulated genes significantly enriched for proliferation and apoptosis pathways, and identified HSP Family Member C10 (DNAJC10) as putative effector of CENPU. CENPU knockdown produced DNAJC10 protein downregulation, and DNAJC10 overexpression partially rescued the phenotypic effects of CENPU knockdown in LUAD cells. Moreover, CENPU's coiled-coil domain was essential for CENPU's phenotypic effects in LUAD cells. In conclusion, the kinetochore component CENPU plays a critical role in LUAD cell proliferation and invasiveness. Targeting CENPU-DNAJC10 axis may inhibit LUAD tumor cell proliferation and metastasis.
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Affiliation(s)
- Yuqing Lou
- Department of Respiratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jun Lu
- Department of Respiratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yanwei Zhang
- Department of Respiratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Ping Gu
- Department of Respiratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Huimin Wang
- Department of Respiratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Fangfei Qian
- Department of Respiratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Wensheng Zhou
- Department of Respiratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Zhang
- Department of Respiratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China.
| | - Hua Zhong
- Department of Respiratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China.
| | - Baohui Han
- Department of Respiratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China.
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22
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Wen T, Chen QY. Dynamic Activity of Histone H3-Specific Chaperone Complexes in Oncogenesis. Front Oncol 2022; 11:806974. [PMID: 35087762 PMCID: PMC8786718 DOI: 10.3389/fonc.2021.806974] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/15/2021] [Indexed: 11/30/2022] Open
Abstract
Canonical histone H3.1 and variant H3.3 deposit at different sites of the chromatin via distinct histone chaperones. Histone H3.1 relies on chaperone CAF-1 to mediate replication-dependent nucleosome assembly during S-phase, while H3.3 variant is regulated and incorporated into the chromatin in a replication-independent manner through HIRA and DAXX/ATRX. Current literature suggests that dysregulated expression of histone chaperones may be implicated in tumor progression. Notably, ectopic expression of CAF-1 can promote a switch between canonical H3.1 and H3 variants in the chromatin, impair the chromatic state, lead to chromosome instability, and impact gene transcription, potentially contributing to carcinogenesis. This review focuses on the chaperone proteins of H3.1 and H3.3, including structure, regulation, as well as their oncogenic and tumor suppressive functions in tumorigenesis.
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Affiliation(s)
- Ting Wen
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, China
| | - Qiao Yi Chen
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, China
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23
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Li Z, Zhang L, Liu D, Yang Z, Xuan D, Zhang Y. Knockdown of NRMT enhances sensitivity of retinoblastoma cells to cisplatin through upregulation of the CENPA/Myc/Bcl2 axis. Cell Death Dis 2022; 8:14. [PMID: 35013138 PMCID: PMC8748520 DOI: 10.1038/s41420-021-00622-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 08/09/2021] [Accepted: 08/18/2021] [Indexed: 11/09/2022]
Abstract
Chemotherapy resistance of tumor cells causes failure in anti-tumor therapies. Recently, N-terminal regulator of chromatin condensation 1 methyltransferase (NRMT) is abnormally expressed in different cancers. Hence, we speculate that NRMT may pay a crucial role in the development of chemosensitivity in retinoblastoma. We characterized the upregulation of NRMT in the developed cisplatin (CDDP)-resistant retinoblastoma cell line relative to parental cells. Loss-of-function experiments demonstrated that NRMT silencing enhanced chemosensitivity of retinoblastoma cells to CDDP. Next, NRMT was identified to enrich histone-H3 lysine 4 trimethylation in the promoter of centromere protein A (CENPA) by chromatin immunoprecipitation assay. Rescue experiments suggested that CENPA reduced chemosensitivity by increasing the viability and proliferation and reducing apoptosis of CDDP-resistant retinoblastoma cells, which was reversed by NRMT. Subsequently, CENPA was witnessed to induce the transcription of Myc and to elevate the expression of B cell lymphoma-2. At last, in vivo experiments confirmed the promotive effect of NRMT knockdown on chemosensitivity of retinoblastoma cells to CDDP in tumor-bearing mice. Taken together, NRMT is an inhibitor of chemosensitivity in retinoblastoma. Those findings shed new light on NRMT-targeted therapies for retinoblastoma.
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Affiliation(s)
- Zhongrui Li
- Department of Ophthalmology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, P. R. China
| | - Lan Zhang
- Department of Cardiology, the Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, P. R. China
| | - Dongrui Liu
- Department of Ophthalmology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, P. R. China
| | - Zhanghui Yang
- Department of Ophthalmology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, P. R. China
| | - Di Xuan
- Department of Ophthalmology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, P. R. China
| | - Yi Zhang
- Department of Ophthalmology, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, P. R. China.
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24
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Jeffery D, Lochhead M, Almouzni G. CENP-A: A Histone H3 Variant with Key Roles in Centromere Architecture in Healthy and Diseased States. Results Probl Cell Differ 2022; 70:221-261. [PMID: 36348109 DOI: 10.1007/978-3-031-06573-6_7] [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: 06/16/2023]
Abstract
Centromeres are key architectural components of chromosomes. Here, we examine their construction, maintenance, and functionality. Focusing on the mammalian centromere- specific histone H3 variant, CENP-A, we highlight its coevolution with both centromeric DNA and its chaperone, HJURP. We then consider CENP-A de novo deposition and the importance of centromeric DNA recently uncovered with the added value from new ultra-long-read sequencing. We next review how to ensure the maintenance of CENP-A at the centromere throughout the cell cycle. Finally, we discuss the impact of disrupting CENP-A regulation on cancer and cell fate.
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Affiliation(s)
- Daniel Jeffery
- Equipe Labellisée Ligue contre le Cancer, Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, UMR3664, Paris, France
| | - Marina Lochhead
- Equipe Labellisée Ligue contre le Cancer, Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, UMR3664, Paris, France
| | - Geneviève Almouzni
- Equipe Labellisée Ligue contre le Cancer, Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, UMR3664, Paris, France.
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25
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Zhao J, Liu B, Li X. A transcription factor signature predicts the survival of patients with adrenocortical carcinoma. PeerJ 2021; 9:e12433. [PMID: 34966575 PMCID: PMC8667743 DOI: 10.7717/peerj.12433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/13/2021] [Indexed: 12/26/2022] Open
Abstract
Background Adrenocortical carcinoma (ACC) is a rare endocrine cancer that manifests as abdominal masses and excessive steroid hormone levels and is associated with poor clinical outcomes. Transcription factors (TFs) deregulation is found to be involved in adrenocortical tumorigenesis and cancer progression. This study aimed to construct a TF-based prognostic signature for the prediction of survival of ACC patients. Methods The gene expression profile and clinical information for ACC patients were downloaded from The Cancer Genome Atlas (TCGA, training set) and Gene Expression Omnibus (GEO, validation set) datasets after obtained 1,639 human TFs from a previously published study. The univariate Cox regression analysis was applied to identify the survival-related TFs and the LASSO Cox regression was conducted to construct the TF signature based on these survival-associated TFs candidates. Then, multivariate analysis was used to reveal the independent prognostic factors. Furthermore, Gene Set Enrichment Analysis (GSEA) was performed to analyze the significance of the TFs constituting the prognostic signature. Results LASSO Cox regression and multivariate Cox regression identified a 13-TF prognostic signature comprised of CREB3L3, NR0B1, CENPA, FOXM1, E2F2, MYBL2, HOXC11, ZIC2, ZNF282, DNMT1, TCF3, ELK4, and KLF6. The risk score based on the TF signature could classify patients into low- and high-risk groups. Kaplan-Meier analyses showed that patients in the high-risk group had significantly shorter overall survival (OS) compared to the low-risk patients. Receiver operating characteristic (ROC) curves showed that the prognostic signature predicted the OS of ACC patients with good sensitivity and specificity both in the training set (AUC > 0.9) and the validation set (AUC > 0.7). Furthermore, the TF-risk score was an independent prognostic factor. Conclusions Taken together, we identified a 13-TF prognostic marker to predict OS in ACC patients.
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Affiliation(s)
- Jianyu Zhao
- Department of Endocrinology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Bo Liu
- Department of Endocrinology, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
| | - Xiaoping Li
- Department of Pediatrics Endocrinology, The First Hospital of Jilin University, Changchun, Jilin, China, Jilin, China
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26
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Li Q, Liang J, Zhang S, an N, Xu L, Ye C. Overexpression of centromere protein K (CENPK) gene in Differentiated Thyroid Carcinoma promote cell Proliferation and Migration. Bioengineered 2021; 12:1299-1310. [PMID: 33904381 PMCID: PMC8806198 DOI: 10.1080/21655979.2021.1911533] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 03/29/2021] [Indexed: 02/07/2023] Open
Abstract
Differentiated thyroid carcinoma (DTC) is one of the most common malignant tumors. Increasing evidence indicates that centromere protein K(CENPK) may play a key role in promoting carcinogenesis. The expression, biological functions, and clinical significance of CENPK in DTC are still unclear. The CENPK expression in the DTC specimen was confirmed using quantitative real-time PCR and Western blot. The expression of CENPK was silenced and promoted by lentivirus-mediated transfection with shRNA sequences or CENPK plasmid targeting CENPK in TPC1 and FTC-133 cells, respectively. Colony formation, Cell Counting Kit-8 (CCK-8), Transwell invasion, and scratch assays were performed to assess the malignant biological properties of FTC-133 and TPC1 cells. Tumorigenicity assay was performed using C57BL/6 mice to explore the influence of CENPK on the growth of TPC1. The present work suggested that the expression of CENPK remarkably increased in follicular thyroid cancer and papillary thyroid cancer tissue samples at the mRNA level. Immunohistochemical staining also showed consistent results at the protein level. In addition, CENPK mRNA expression level showed great value in diagnosis of DTC. Knockdown of CENPK significantly inhibited the invasion and migration of TPC1 and FTC-133 cells. In contrast, CENPK overexpression promoted invasion and migration of TPC1 and FTC-133 cells. Knockdown and overexpression of CENPK showed consistent effect on DTC tumor growth and expression of Ki-67 invivo. Our results indicated that CENPK was evidently upregulated in DTC. Knocking down CENPK suppressed TPC1 cell proliferation, invasion and migration. Targeting the CENPK may be anovel therapeutic method for DTC.
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Affiliation(s)
- Qizhi Li
- Department of Head and Neck Surgery, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology,Wuhan, China
| | - Jiang Liang
- Department of Head and Neck Surgery, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology,Wuhan, China
| | - Shuai Zhang
- Department of Head and Neck Surgery, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology,Wuhan, China
| | - Ning an
- Department of Head and Neck Surgery, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology,Wuhan, China
| | - Lingfeng Xu
- Department of Head and Neck Surgery, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology,Wuhan, China
| | - Changhong Ye
- Department of Gynecology, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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27
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Kim T. Epigenetic control of centromere: what can we learn from neocentromere? Genes Genomics 2021; 44:317-325. [PMID: 34843088 DOI: 10.1007/s13258-021-01193-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 11/16/2021] [Indexed: 12/17/2022]
Abstract
BACKGROUND The centromere is the special region on a chromosome, which serves as the site for assembly of kinetochore complex and is essential for maintaining genomic integrity. Neocentromeres are new centromeres that form on the non-centromeric regions of the chromosome when the natural centromere is disrupted or inactivated. Although neocentromeres lack the typical features found in centromeres, cells with neocentromeres divide normally during mitosis and meiosis. Neocentromeres not only arise naturally but their formation can also be induced experimentally. Therefore, neocentromeres are a great tool for studying functions and formation of centromeres. OBJECTIVE To study neocentromeres and use that knowledge to gain insights into the epigenetic regulation of canonical centromeres. DISCUSSION Here, we review the characteristics of naturally occurring centromeres and neocentromeres and those of experimentally induced neocentromeres. We also discuss the mechanism of centromere formation and epigenetic regulation of centromere function, which we learned from studying the neocentromeres. Although neocentromeres lack main features of centromeres, such as presence of repetitive ⍺-satellite DNA and pericentric heterochromatin, they behave quite similar to the canonical centromere, indicating the epigenetic nature of the centromere. Still, further investigation will help to understand the formation and maintenance of the centromere, and the correlation to human diseases. CONCLUSION Neocentromeres helped us to understand the formation of canonical centromeres. Also, since neocentromeres are associated with certain cancer types, knowledge about them could be helpful to treat cancer.
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Affiliation(s)
- Taekyung Kim
- Department of Biology Education, Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan, 46241, Korea.
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28
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Wang K, Liu Y, Yu Z, Gu B, Hu J, Huang L, Ge X, Xu L, Zhang M, Zhao J, Hu M, Le R, Wu Q, Ye S, Gao S, Zhang X, Xu RM, Li G. Phosphorylation at Ser68 facilitates DCAF11-mediated ubiquitination and degradation of CENP-A during the cell cycle. Cell Rep 2021; 37:109987. [PMID: 34758320 DOI: 10.1016/j.celrep.2021.109987] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/11/2021] [Accepted: 10/19/2021] [Indexed: 12/28/2022] Open
Abstract
CENP-A (centromeric protein A), a histone H3 variant, specifies centromere identity and is essential to centromere maintenance. Little is known about how protein levels of CENP-A are controlled in mammalian cells. Here, we report that the phosphorylation of CENP-A Ser68 primes the ubiquitin-proteasome-mediated proteolysis of CENP-A during mitotic phase in human cultured cells. We identify two major polyubiquitination sites that are responsible for this phosphorylation-dependent degradation. Substituting the two residues, Lys49 and Lys124, with arginines abrogates proper CENP-A degradation and results in CENP-A mislocalization to non-centromeric regions. Furthermore, we find that DCAF11 (DDB1 and CUL4 associated factor 11/WDR23) is the E3 ligase that specifically mediates the observed polyubiquitination. Deletion of DCAF11 hampers CENP-A degradation and causes its mislocalization. We conclude that the Ser68 phosphorylation plays an important role in regulating cellular CENP-A homeostasis via DCAF11-mediated degradation to prevent ectopic localization of CENP-A during the cell cycle.
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Affiliation(s)
- Kehui Wang
- National Laboratory of Bio-macromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China
| | - Yuting Liu
- National Laboratory of Bio-macromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhouliang Yu
- National Laboratory of Bio-macromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bo Gu
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jie Hu
- National Laboratory of Bio-macromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Huang
- National Laboratory of Bio-macromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China
| | - Xiao Ge
- Center for Comparative Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lingyi Xu
- Department of Biophysics, Department of Pathology of Sir Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Department of Biophysics, Institute of Neuroscience, NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Mengyu Zhang
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Jicheng Zhao
- National Laboratory of Bio-macromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China
| | - Mingli Hu
- National Laboratory of Bio-macromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rongrong Le
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Qiang Wu
- Center for Comparative Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Sheng Ye
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, 92 Weijin Road, Nankai District, Tianjin 300072, China; Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Shaorong Gao
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xiaodong Zhang
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Rui-Ming Xu
- National Laboratory of Bio-macromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guohong Li
- National Laboratory of Bio-macromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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29
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Peng S, Petersen JL, Bellone RR, Kalbfleisch T, Kingsley NB, Barber AM, Cappelletti E, Giulotto E, Finno CJ. Decoding the Equine Genome: Lessons from ENCODE. Genes (Basel) 2021; 12:genes12111707. [PMID: 34828313 PMCID: PMC8625040 DOI: 10.3390/genes12111707] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/24/2021] [Accepted: 10/26/2021] [Indexed: 12/23/2022] Open
Abstract
The horse reference genome assemblies, EquCab2.0 and EquCab3.0, have enabled great advancements in the equine genomics field, from tools to novel discoveries. However, significant gaps of knowledge regarding genome function remain, hindering the study of complex traits in horses. In an effort to address these gaps and with inspiration from the Encyclopedia of DNA Elements (ENCODE) project, the equine Functional Annotation of Animal Genome (FAANG) initiative was proposed to bridge the gap between genome and gene expression, providing further insights into functional regulation within the horse genome. Three years after launching the initiative, the equine FAANG group has generated data from more than 400 experiments using over 50 tissues, targeting a variety of regulatory features of the equine genome. In this review, we examine how valuable lessons learned from the ENCODE project informed our decisions in the equine FAANG project. We report the current state of the equine FAANG project and discuss how FAANG can serve as a template for future expansion of functional annotation in the equine genome and be used as a reference for studies of complex traits in horse. A well-annotated reference functional atlas will also help advance equine genetics in the pan-genome and precision medicine era.
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Affiliation(s)
- Sichong Peng
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA; (S.P.); (R.R.B.); (N.B.K.)
| | - Jessica L. Petersen
- Department of Animal Science, University of Nebraska, Lincoln, NE 68583-0908, USA; (J.L.P.); (A.M.B.)
| | - Rebecca R. Bellone
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA; (S.P.); (R.R.B.); (N.B.K.)
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Ted Kalbfleisch
- Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY 40503, USA;
| | - N. B. Kingsley
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA; (S.P.); (R.R.B.); (N.B.K.)
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Alexa M. Barber
- Department of Animal Science, University of Nebraska, Lincoln, NE 68583-0908, USA; (J.L.P.); (A.M.B.)
| | - Eleonora Cappelletti
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (E.C.); (E.G.)
| | - Elena Giulotto
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (E.C.); (E.G.)
| | - Carrie J. Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA; (S.P.); (R.R.B.); (N.B.K.)
- Correspondence:
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30
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DeBose-Scarlett EM, Sullivan BA. Genomic and Epigenetic Foundations of Neocentromere Formation. Annu Rev Genet 2021; 55:331-348. [PMID: 34496611 DOI: 10.1146/annurev-genet-071719-020924] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Centromeres are essential to genome inheritance, serving as the site of kinetochore assembly and coordinating chromosome segregation during cell division. Abnormal centromere function is associated with birth defects, infertility, and cancer. Normally, centromeres are assembled and maintained at the same chromosomal location. However, ectopic centromeres form spontaneously at new genomic locations and contribute to genome instability and developmental defects as well as to acquired and congenital human disease. Studies in model organisms have suggested that certain regions of the genome, including pericentromeres, heterochromatin, and regions of open chromatin or active transcription, support neocentromere activation. However, there is no universal mechanism that explains neocentromere formation. This review focuses on recent technological and intellectual advances in neocentromere research and proposes future areas of study. Understanding neocentromere biology will provide a better perspective on chromosome and genome organization and functional context for information generated from the Human Genome Project, ENCODE, and other large genomic consortia. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Evon M DeBose-Scarlett
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina 27710, USA;
| | - Beth A Sullivan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina 27710, USA;
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31
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Dong Q, Yang J, Gao J, Li F. Recent insights into mechanisms preventing ectopic centromere formation. Open Biol 2021; 11:210189. [PMID: 34493071 PMCID: PMC8424319 DOI: 10.1098/rsob.210189] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The centromere is a specialized chromosomal structure essential for chromosome segregation. Centromere dysfunction leads to chromosome segregation errors and genome instability. In most eukaryotes, centromere identity is specified epigenetically by CENP-A, a centromere-specific histone H3 variant. CENP-A replaces histone H3 in centromeres, and nucleates the assembly of the kinetochore complex. Mislocalization of CENP-A to non-centromeric regions causes ectopic assembly of CENP-A chromatin, which has a devastating impact on chromosome segregation and has been linked to a variety of human cancers. How non-centromeric regions are protected from CENP-A misincorporation in normal cells is largely unexplored. Here, we review the most recent advances on the mechanisms underlying the prevention of ectopic centromere formation, and discuss the implications in human disease.
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Affiliation(s)
- Qianhua Dong
- Department of Biology, New York University, New York, NY 10003-6688, USA
| | - Jinpu Yang
- Department of Biology, New York University, New York, NY 10003-6688, USA
| | - Jinxin Gao
- Department of Biology, New York University, New York, NY 10003-6688, USA
| | - Fei Li
- Department of Biology, New York University, New York, NY 10003-6688, USA
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32
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Liu X, Wang H, Zhao G. Centromere Protein A Goes Far Beyond the Centromere in Cancers. Mol Cancer Res 2021; 20:3-10. [PMID: 34465586 DOI: 10.1158/1541-7786.mcr-21-0311] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/05/2021] [Accepted: 08/26/2021] [Indexed: 11/16/2022]
Abstract
Centromere dysfunctions leading to numerical chromosome alterations are believed to be closely related to human cancers. As a centromere-specific protein, centromere protein A (CENP-A) replaces the histone H3 in centromeres and is therefore considered a key factor of centromere identity. Researches have shown that CENP-A is overexpressed in many types of human cancers. However, the behavior and function of CENP-A in tumorigenesis have not yet been systematically summarized. In this article, we describe the pleiotropic roles of CENP-A in human cells. Moreover, we provide a comprehensive review of the current knowledge on the relationship between aberrant expression and ectopic localization of CENP-A and tumorigenesis, and the mechanism of the ectopic deposition of CENP-A in cancers. Furthermore, we note that some oncogenic viruses can modulate the expression and localization of this centromere protein along with its chaperone. At last, we also discuss the therapeutic potential of targeting CENP-A for cancer therapy.
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Affiliation(s)
- Xiaolan Liu
- Affiliated Wuhan Mental Health Center, Tongji Medical College of Huazhong University of Science & Technology, Wuhan, Hubei, China. .,Research Center for Psychological and Health Sciences, China University of Geosciences, Wuhan, China
| | - Haiping Wang
- School of Medicine, Jianghan University, Wuhan, Hubei, China
| | - Guojun Zhao
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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33
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Ryu HY, Hochstrasser M. Histone sumoylation and chromatin dynamics. Nucleic Acids Res 2021; 49:6043-6052. [PMID: 33885816 PMCID: PMC8216275 DOI: 10.1093/nar/gkab280] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/28/2021] [Accepted: 04/08/2021] [Indexed: 12/17/2022] Open
Abstract
Chromatin structure and gene expression are dynamically controlled by post-translational modifications (PTMs) on histone proteins, including ubiquitylation, methylation, acetylation and small ubiquitin-like modifier (SUMO) conjugation. It was initially thought that histone sumoylation exclusively suppressed gene transcription, but recent advances in proteomics and genomics have uncovered its diverse functions in cotranscriptional processes, including chromatin remodeling, transcript elongation, and blocking cryptic initiation. Histone sumoylation is integral to complex signaling codes that prime additional histone PTMs as well as modifications of the RNA polymerase II carboxy-terminal domain (RNAPII-CTD) during transcription. In addition, sumoylation of histone variants is critical for the DNA double-strand break (DSB) response and for chromosome segregation during mitosis. This review describes recent findings on histone sumoylation and its coordination with other histone and RNAPII-CTD modifications in the regulation of chromatin dynamics.
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Affiliation(s)
- Hong-Yeoul Ryu
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, College of National Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
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Rakshit T, Melters DP, Dimitriadis EK, Dalal Y. Mechanical properties of nucleoprotein complexes determined by nanoindentation spectroscopy. Nucleus 2021; 11:264-282. [PMID: 32954931 PMCID: PMC7529419 DOI: 10.1080/19491034.2020.1816053] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The interplay between transcription factors, chromatin remodelers, 3-D organization, and mechanical properties of the chromatin fiber controls genome function in eukaryotes. Besides the canonical histones which fold the bulk of the chromatin into nucleosomes, histone variants create distinctive chromatin domains that are thought to regulate transcription, replication, DNA damage repair, and faithful chromosome segregation. Whether histone variants translate distinctive biochemical or biophysical properties to their associated chromatin structures, and whether these properties impact chromatin dynamics as the genome undergoes a multitude of transactions, is an important question in biology. Here, we describe single-molecule nanoindentation tools that we developed specifically to determine the mechanical properties of histone variant nucleosomes and their complexes. These methods join an array of cutting-edge new methods that further our quantitative understanding of the response of chromatin to intrinsic and extrinsic forces which act upon it during biological transactions in the nucleus.
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Affiliation(s)
- Tatini Rakshit
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH , Bethesda, MD, USA.,Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences , Salt Lake, India
| | - Daniël P Melters
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH , Bethesda, MD, USA
| | - Emilios K Dimitriadis
- Trans-NIH Shared Resource on Biomedical Engineering and Physical Science, National Cancer Institute, NIH , Bethesda, MD, USA
| | - Yamini Dalal
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH , Bethesda, MD, USA
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35
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Reduce, Retain, Recycle: Mechanisms for Promoting Histone Protein Degradation versus Stability and Retention. Mol Cell Biol 2021; 41:e0000721. [PMID: 33753462 DOI: 10.1128/mcb.00007-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The eukaryotic genome is packaged into chromatin. The nucleosome, the basic unit of chromatin, is composed of DNA coiled around a histone octamer. Histones are among the longest-lived protein species in mammalian cells due to their thermodynamic stability and their associations with DNA and histone chaperones. Histone metabolism plays an integral role in homeostasis. While histones are largely stable, the degradation of histone proteins is necessary under specific conditions. Here, we review the physiological and cellular contexts that promote histone degradation. We describe specific known mechanisms that drive histone proteolysis. Finally, we discuss the importance of histone degradation and regulation of histone supply for organismal and cellular fitness.
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36
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Shrestha RL, Rossi A, Wangsa D, Hogan AK, Zaldana KS, Suva E, Chung YJ, Sanders CL, Difilippantonio S, Karpova TS, Karim B, Foltz DR, Fachinetti D, Aplan PD, Ried T, Basrai MA. CENP-A overexpression promotes aneuploidy with karyotypic heterogeneity. J Cell Biol 2021; 220:211820. [PMID: 33620383 PMCID: PMC7905998 DOI: 10.1083/jcb.202007195] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 12/15/2020] [Accepted: 01/26/2021] [Indexed: 02/07/2023] Open
Abstract
Chromosomal instability (CIN) is a hallmark of many cancers. Restricting the localization of centromeric histone H3 variant CENP-A to centromeres prevents CIN. CENP-A overexpression (OE) and mislocalization have been observed in cancers and correlate with poor prognosis; however, the molecular consequences of CENP-A OE on CIN and aneuploidy have not been defined. Here, we show that CENP-A OE leads to its mislocalization and CIN with lagging chromosomes and micronuclei in pseudodiploid DLD1 cells and xenograft mouse model. CIN is due to reduced localization of proteins to the kinetochore, resulting in defects in kinetochore integrity and unstable kinetochore–microtubule attachments. CENP-A OE contributes to reduced expression of cell adhesion genes and higher invasion of DLD1 cells. We show that CENP-A OE contributes to aneuploidy with karyotypic heterogeneity in human cells and xenograft mouse model. In summary, our results provide a molecular link between CENP-A OE and aneuploidy, and suggest that karyotypic heterogeneity may contribute to the aggressive phenotype of CENP-A–overexpressing cancers.
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Affiliation(s)
- Roshan L Shrestha
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Austin Rossi
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Darawalee Wangsa
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Ann K Hogan
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL
| | - Kimberly S Zaldana
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Evelyn Suva
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Yang Jo Chung
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Chelsea L Sanders
- Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD
| | - Simone Difilippantonio
- Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD
| | - Tatiana S Karpova
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Baktiar Karim
- Laboratory Animal Sciences Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD
| | - Daniel R Foltz
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL
| | - Daniele Fachinetti
- Institut Curie, PSL Research University, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 144, Paris, France
| | - Peter D Aplan
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Munira A Basrai
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
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Abstract
Cancer is a complex disease characterized by loss of cellular homeostasis through genetic and epigenetic alterations. Emerging evidence highlights a role for histone variants and their dedicated chaperones in cancer initiation and progression. Histone variants are involved in processes as diverse as maintenance of genome integrity, nuclear architecture and cell identity. On a molecular level, histone variants add a layer of complexity to the dynamic regulation of transcription, DNA replication and repair, and mitotic chromosome segregation. Because these functions are critical to ensure normal proliferation and maintenance of cellular fate, cancer cells are defined by their capacity to subvert them. Hijacking histone variants and their chaperones is emerging as a common means to disrupt homeostasis across a wide range of cancers, particularly solid tumours. Here we discuss histone variants and histone chaperones as tumour-promoting or tumour-suppressive players in the pathogenesis of cancer.
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Affiliation(s)
| | - Dan Filipescu
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
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38
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Jeffery D, Gatto A, Podsypanina K, Renaud-Pageot C, Ponce Landete R, Bonneville L, Dumont M, Fachinetti D, Almouzni G. CENP-A overexpression promotes distinct fates in human cells, depending on p53 status. Commun Biol 2021; 4:417. [PMID: 33772115 PMCID: PMC7997993 DOI: 10.1038/s42003-021-01941-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 02/25/2021] [Indexed: 12/13/2022] Open
Abstract
Tumour evolution is driven by both genetic and epigenetic changes. CENP-A, the centromeric histone H3 variant, is an epigenetic mark that directly perturbs genetic stability and chromatin when overexpressed. Although CENP-A overexpression is a common feature of many cancers, how this impacts cell fate and response to therapy remains unclear. Here, we established a tunable system of inducible and reversible CENP-A overexpression combined with a switch in p53 status in human cell lines. Through clonogenic survival assays, single-cell RNA-sequencing and cell trajectory analysis, we uncover the tumour suppressor p53 as a key determinant of how CENP-A impacts cell state, cell identity and therapeutic response. If p53 is functional, CENP-A overexpression promotes senescence and radiosensitivity. Surprisingly, when we inactivate p53, CENP-A overexpression instead promotes epithelial-mesenchymal transition, an essential process in mammalian development but also a precursor for tumour cell invasion and metastasis. Thus, we uncover an unanticipated function of CENP-A overexpression to promote cell fate reprogramming, with important implications for development and tumour evolution.
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Grants
- Ligue Contre le Cancer
- Agence Nationale de la Recherche (French National Research Agency)
- Université de Recherche Paris Sciences et Lettres (PSL Research University)
- Centre National de la Recherche Scientifique (National Center for Scientific Research)
- Institut Curie
- AG, CRP, DJ, KP, LB, RPL and GA were supported by la Ligue Nationale contre le Cancer (Equipe labellisée Ligue), Labex DEEP (ANR-11-LABX-0044_DEEP, ANR-10-IDEX-0001-02), PSL, ERC-2015-ADG-694694 ChromADICT and ANR-16-CE12-0024 CHIFT. Funding for RPL provided by Horizon 2020 Marie Skłodowska-Curie Actions Initial Training Network “EpiSyStem” (grant number 765966). Individual funding was also provided to DJ from la Fondation ARC pour la recherche sur le cancer (“Aides individuelles” 3 years, post-doc), and to AG from the Horizon 2020 Framework Programme for Research and Innovation (H2020 Marie Skłodowska-Curie Actions grant agreement 798106 “REPLICHROM4D”). DF receives salary support from the Centre Nationale de Recherche Scientifique (CNRS). MD receives salary support from the City of Paris via Emergence(s) 2018 of DF.
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Affiliation(s)
- Daniel Jeffery
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, Equipe Labellisée Ligue contre le Cancer, Paris, France
| | - Alberto Gatto
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, Equipe Labellisée Ligue contre le Cancer, Paris, France
| | - Katrina Podsypanina
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, Equipe Labellisée Ligue contre le Cancer, Paris, France
| | - Charlène Renaud-Pageot
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, Equipe Labellisée Ligue contre le Cancer, Paris, France
| | - Rebeca Ponce Landete
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, Equipe Labellisée Ligue contre le Cancer, Paris, France
| | - Lorraine Bonneville
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, Equipe Labellisée Ligue contre le Cancer, Paris, France
| | - Marie Dumont
- Institut Curie, PSL Research University, Centre de Recherche, Sorbonne Université, Cell Biology and Cancer Unit, Paris, France
| | - Daniele Fachinetti
- Institut Curie, PSL Research University, Centre de Recherche, Sorbonne Université, Cell Biology and Cancer Unit, Paris, France
| | - Geneviève Almouzni
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, Equipe Labellisée Ligue contre le Cancer, Paris, France.
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39
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Hao X, Qiu Y, Cao L, Yang X, Zhou D, Liu J, Shi Z, Zhao S, Zhang J. Over-Expression of Centromere Protein U Participates in the Malignant Neoplastic Progression of Breast Cancer. Front Oncol 2021; 11:615427. [PMID: 33833984 PMCID: PMC8021899 DOI: 10.3389/fonc.2021.615427] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 01/27/2021] [Indexed: 01/02/2023] Open
Abstract
The expression of Centromere Protein U (CENP-U) is closely related to tumor malignancy. Till now, the role of CENP-U in the malignant progression of breast cancer remains unclear. In this study, we found that CENP-U protein was highly expressed in the primary invasive breast cancer tissues compared to the paired adjacent histologically normal tissues and ductal carcinoma in situ (DCIS) tissues. After CENP-U was knocked down, the proliferation and colony-forming abilities of breast cancer cells were significantly suppressed, whereas the portion of apoptotic cells was increased. Meanwhile, the PI3K/AKT/NF-κB pathway was significantly inhibited. In vivo studies showed that, the inhibition of CENP-U repressed the tumor growth in orthotopic breast cancer models. Therefore, our study demonstrated that the CENP-U might act as an oncogene and promote breast cancer progression via activation of the PI3K/AKT/NF-κB pathway, which suggests a promising direction for targeting therapy in breast cancer.
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Affiliation(s)
- Xiaomeng Hao
- Third Department of Breast Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Yufan Qiu
- Third Department of Breast Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Lixia Cao
- Third Department of Breast Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Xiaonan Yang
- Third Department of Breast Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Dongdong Zhou
- Third Department of Breast Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Jingjing Liu
- Third Department of Breast Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Zhendong Shi
- Third Department of Breast Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Shaorong Zhao
- Third Department of Breast Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
| | - Jin Zhang
- Third Department of Breast Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, China
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40
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Zhang S, Xie Y, Tian T, Yang Q, Zhou Y, Qiu J, Xu L, Wen N, Lv Q, Du Z. High expression levels of centromere protein A plus upregulation of the phosphatidylinositol 3-kinase/Akt/mammalian target of rapamycin signaling pathway affect chemotherapy response and prognosis in patients with breast cancer. Oncol Lett 2021; 21:410. [PMID: 33841571 PMCID: PMC8020387 DOI: 10.3892/ol.2021.12671] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 02/16/2021] [Indexed: 02/05/2023] Open
Abstract
Centromere proteins (CENPs) are involved in mitosis, and CENP gene expression levels are associated with chemotherapy responses in patients with breast cancer. The present study aimed to examine the roles and underlying mechanisms of the effects of CENP genes on chemotherapy responses and breast cancer prognosis. Using data obtained from the Gene Expression Omnibus (GEO) database, correlation and Cox multivariate regression analyses were used to determine the CENP genes associated with chemotherapy responses and survival in patients with breast cancer. Weighted gene co-expression network and correlation analyses were used to determine the gene modules co-expressed with the identified genes and the differential expression of gene modules associated with the pathological complete response (PCR) and residual disease (RD) subgroups. CENPA, CENPE, CENPF, CENPI, CENPJ and CENPN were associated with a high nuclear grade and low estrogen and progesterone receptor expression levels. In addition, CENPA, CENPB, CENPC and CENPO were independent factors affecting the distant relapse-free survival (DRFS) rates in patients with breast cancer. Patients with high expression levels of CENPA or CENPO exhibited poor prognoses, whereas those with high expression levels of CENPB or CENPC presented with favorable prognoses. For validation between databases, the Cancer Genome Atlas (TCGA) database analysis also revealed that CENPA, CENPB and CENPO exerted similar effects on overall survival. However, according to the multivariate analyses, only CENPA was an independent risk factor associated with DRFS in GEO database. In addition, in the RD subgroup, patients with higher CENPA expression levels had a worse prognosis compared with those with lower CENPA expression levels. Among patients with high expression levels of CENPA, the PI3K/Akt/mTOR pathway was more likely to be activated in the RD compared with the PCR subgroup. The same trend was observed in TCGA data. These results suggested that high CENPA expression levels plus upregulation of the PI3K/Akt/mTOR signaling pathway may affect DRFS in patients with breast cancer.
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Affiliation(s)
- Songbo Zhang
- Department of Breast Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Yanyan Xie
- Department of Breast Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Ting Tian
- Department of Breast Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Qianru Yang
- Department of Breast Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Yuting Zhou
- Department of Breast Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Juanjuan Qiu
- Department of Breast Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Li Xu
- Department of Breast Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Nan Wen
- Department of Breast Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Qing Lv
- Department of Breast Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Zhenggui Du
- Department of Breast Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
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41
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Eisenstatt JR, Ohkuni K, Au WC, Preston O, Gliford L, Suva E, Costanzo M, Boone C, Basrai MA. Reduced gene dosage of histone H4 prevents CENP-A mislocalization and chromosomal instability in Saccharomyces cerevisiae. Genetics 2021; 218:6159615. [PMID: 33751052 DOI: 10.1093/genetics/iyab033] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 02/20/2021] [Indexed: 12/14/2022] Open
Abstract
Mislocalization of the centromeric histone H3 variant (Cse4 in budding yeast, CID in flies, CENP-A in humans) to noncentromeric regions contributes to chromosomal instability (CIN) in yeast, fly, and human cells. Overexpression and mislocalization of CENP-A have been observed in cancers, however, the mechanisms that facilitate the mislocalization of overexpressed CENP-A have not been fully explored. Defects in proteolysis of overexpressed Cse4 (GALCSE4) lead to its mislocalization and synthetic dosage lethality (SDL) in mutants for E3 ubiquitin ligases (Psh1, Slx5, SCFMet30, and SCFCdc4), Doa1, Hir2, and Cdc7. In contrast, defects in sumoylation of overexpressed cse4K215/216/A/R prevent its mislocalization and do not cause SDL in a psh1Δ strain. Here, we used a genome-wide screen to identify factors that facilitate the mislocalization of overexpressed Cse4 by characterizing suppressors of the psh1Δ GALCSE4 SDL. Deletions of histone H4 alleles (HHF1 or HHF2), which were among the most prominent suppressors, also suppress slx5Δ, cdc4-1, doa1Δ, hir2Δ, and cdc7-4 GALCSE4 SDL. Reduced dosage of H4 leads to defects in sumoylation and reduced mislocalization of overexpressed Cse4, which contributes to suppression of CIN when Cse4 is overexpressed. We determined that the hhf1-20, cse4-102, and cse4-111 mutants, which are defective in the Cse4-H4 interaction, also exhibit reduced sumoylation of Cse4 and do not display psh1Δ GALCSE4 SDL. In summary, we have identified genes that contribute to the mislocalization of overexpressed Cse4 and defined a role for the gene dosage of H4 in facilitating Cse4 sumoylation and mislocalization to noncentromeric regions, leading to CIN when Cse4 is overexpressed.
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Affiliation(s)
- Jessica R Eisenstatt
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20894, USA
| | - Kentaro Ohkuni
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20894, USA
| | - Wei-Chun Au
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20894, USA
| | - Olivia Preston
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20894, USA
| | - Loran Gliford
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20894, USA
| | - Evelyn Suva
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20894, USA
| | - Michael Costanzo
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Charles Boone
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 3E1, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Munira A Basrai
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20894, USA
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42
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Ray-Gallet D, Almouzni G. The Histone H3 Family and Its Deposition Pathways. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1283:17-42. [PMID: 33155135 DOI: 10.1007/978-981-15-8104-5_2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Within the cell nucleus, the organization of the eukaryotic DNA into chromatin uses histones as components of its building block, the nucleosome. This chromatin organization contributes to the regulation of all DNA template-based reactions impacting genome function, stability, and plasticity. Histones and their variants endow chromatin with unique properties and show a distinct distribution into the genome that is regulated by dedicated deposition machineries. The histone variants have important roles during early development, cell differentiation, and chromosome segregation. Recent progress has also shed light on how mutations and transcriptional deregulation of these variants participate in tumorigenesis. In this chapter we introduce the organization of the genome in chromatin with a focus on the basic unit, the nucleosome, which contains histones as the major protein component. Then we review our current knowledge on the histone H3 family and its variants-in particular H3.3 and CenH3CENP-A-focusing on their deposition pathways and their dedicated histone chaperones that are key players in histone dynamics.
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Affiliation(s)
- Dominique Ray-Gallet
- Institut Curie, PSL Research University, CNRS UMR3664, Paris, France.,Institut Curie, Sorbonne Université, CNRS UMR3664, Paris, France
| | - Geneviève Almouzni
- Institut Curie, PSL Research University, CNRS UMR3664, Paris, France. .,Institut Curie, Sorbonne Université, CNRS UMR3664, Paris, France.
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43
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Melters DP, Dalal Y. Nano-Surveillance: Tracking Individual Molecules in a Sea of Chromatin. J Mol Biol 2020; 433:166720. [PMID: 33221335 PMCID: PMC8770095 DOI: 10.1016/j.jmb.2020.11.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/06/2020] [Accepted: 11/16/2020] [Indexed: 01/12/2023]
Abstract
Chromatin is the epigenomic platform for diverse nuclear processes such as DNA repair, replication, transcription, telomere, and centromere function. In cancer cells, mutations in key processes result in DNA amplification, chromosome translocations, and chromothripsis, severely distorting the natural chromatin state. In normal and diseased states, dozens of chromatin effectors alter the physical integrity and dynamics of chromatin at the level of both single nucleosomes and arrays of nucleosomes folded into 3-dimensional shapes. Integrating these length scales, from the 10 nm sized nucleosome to mitotic chromosomes, whilst jostling within the crowded environment of the cell, cannot yet be achieved by a single technology. In this review, we discuss tools that have proven powerful in the investigation of nucleosome and chromatin fiber dynamics. We also provide a deeper focus into atomic force microscopy (AFM) applications that can bridge diverse length and time scales. Using time course AFM, we observe that chromatin condensation by H1.5 is dynamic, whereas using nano-indentation force spectroscopy we observe that both histone variants and nucleosome binding partners alter material properties of individual nucleosomes. Finally, we demonstrate how high-speed AFM can visualize plasmid DNA dynamics, intermittent nucleosome-nucleosome contacts, and changes in nucleosome phasing along a contiguous chromatin fiber. Altogether, the development of innovative technologies holds the promise of revealing the secret lives of nucleosomes, potentially bridging the gaps in our understanding of how chromatin works within living cells and tissues.
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Affiliation(s)
- Daniël P Melters
- National Cancer Institute, Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, Bethesda, MD, United States.
| | - Yamini Dalal
- National Cancer Institute, Center for Cancer Research, Laboratory of Receptor Biology and Gene Expression, Bethesda, MD, United States.
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Ferrand J, Rondinelli B, Polo SE. Histone Variants: Guardians of Genome Integrity. Cells 2020; 9:E2424. [PMID: 33167489 PMCID: PMC7694513 DOI: 10.3390/cells9112424] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/30/2020] [Accepted: 11/03/2020] [Indexed: 12/12/2022] Open
Abstract
Chromatin integrity is key for cell homeostasis and for preventing pathological development. Alterations in core chromatin components, histone proteins, recently came into the spotlight through the discovery of their driving role in cancer. Building on these findings, in this review, we discuss how histone variants and their associated chaperones safeguard genome stability and protect against tumorigenesis. Accumulating evidence supports the contribution of histone variants and their chaperones to the maintenance of chromosomal integrity and to various steps of the DNA damage response, including damaged chromatin dynamics, DNA damage repair, and damage-dependent transcription regulation. We present our current knowledge on these topics and review recent advances in deciphering how alterations in histone variant sequence, expression, and deposition into chromatin fuel oncogenic transformation by impacting cell proliferation and cell fate transitions. We also highlight open questions and upcoming challenges in this rapidly growing field.
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Affiliation(s)
| | | | - Sophie E. Polo
- Epigenetics & Cell Fate Centre, UMR7216 CNRS, Université de Paris, 75013 Paris, France; (J.F.); (B.R.)
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Mullen DJ, Yan C, Kang DS, Zhou B, Borok Z, Marconett CN, Farnham PJ, Offringa IA, Rhie SK. TENET 2.0: Identification of key transcriptional regulators and enhancers in lung adenocarcinoma. PLoS Genet 2020; 16:e1009023. [PMID: 32925947 PMCID: PMC7515200 DOI: 10.1371/journal.pgen.1009023] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 09/24/2020] [Accepted: 08/02/2020] [Indexed: 01/09/2023] Open
Abstract
Lung cancer is the leading cause of cancer-related death and lung adenocarcinoma is its most common subtype. Although genetic alterations have been identified as drivers in subsets of lung adenocarcinoma, they do not fully explain tumor development. Epigenetic alterations have been implicated in the pathogenesis of tumors. To identify epigenetic alterations driving lung adenocarcinoma, we used an improved version of the Tracing Enhancer Networks using Epigenetic Traits method (TENET 2.0) in primary normal lung and lung adenocarcinoma cells. We found over 32,000 enhancers that appear differentially activated between normal lung and lung adenocarcinoma. Among the identified transcriptional regulators inactivated in lung adenocarcinoma vs. normal lung, NKX2-1 was linked to a large number of silenced enhancers. Among the activated transcriptional regulators identified, CENPA, FOXM1, and MYBL2 were linked to numerous cancer-specific enhancers. High expression of CENPA, FOXM1, and MYBL2 is particularly observed in a subgroup of lung adenocarcinomas and is associated with poor patient survival. Notably, CENPA, FOXM1, and MYBL2 are also key regulators of cancer-specific enhancers in breast adenocarcinoma of the basal subtype, but they are associated with distinct sets of activated enhancers. We identified individual lung adenocarcinoma enhancers linked to CENPA, FOXM1, or MYBL2 that were associated with poor patient survival. Knockdown experiments of FOXM1 and MYBL2 suggest that these factors regulate genes involved in controlling cell cycle progression and cell division. For example, we found that expression of TK1, a potential target gene of a MYBL2-linked enhancer, is associated with poor patient survival. Identification and characterization of key transcriptional regulators and associated enhancers in lung adenocarcinoma provides important insights into the deregulation of lung adenocarcinoma epigenomes, highlighting novel potential targets for clinical intervention.
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Affiliation(s)
- Daniel J. Mullen
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, CA, United States of America
- Department of Surgery, Keck School of Medicine, University of Southern California, CA, United States of America
| | - Chunli Yan
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, CA, United States of America
- Department of Surgery, Keck School of Medicine, University of Southern California, CA, United States of America
| | - Diane S. Kang
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, CA, United States of America
- Department of Surgery, Keck School of Medicine, University of Southern California, CA, United States of America
| | - Beiyun Zhou
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, CA, United States of America
| | - Zea Borok
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, CA, United States of America
- Hastings Center for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, CA, United States of America
| | - Crystal N. Marconett
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, CA, United States of America
- Department of Surgery, Keck School of Medicine, University of Southern California, CA, United States of America
| | - Peggy J. Farnham
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, CA, United States of America
| | - Ite A. Offringa
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, CA, United States of America
- Department of Surgery, Keck School of Medicine, University of Southern California, CA, United States of America
| | - Suhn Kyong Rhie
- Department of Biochemistry and Molecular Medicine and the Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, CA, United States of America
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Arunkumar G, Melters DP. Centromeric Transcription: A Conserved Swiss-Army Knife. Genes (Basel) 2020; 11:E911. [PMID: 32784923 PMCID: PMC7463856 DOI: 10.3390/genes11080911] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/05/2020] [Accepted: 08/07/2020] [Indexed: 12/11/2022] Open
Abstract
In most species, the centromere is comprised of repetitive DNA sequences, which rapidly evolve. Paradoxically, centromeres fulfill an essential function during mitosis, as they are the chromosomal sites wherein, through the kinetochore, the mitotic spindles bind. It is now generally accepted that centromeres are transcribed, and that such transcription is associated with a broad range of functions. More than a decade of work on this topic has shown that centromeric transcripts are found across the eukaryotic tree and associate with heterochromatin formation, chromatin structure, kinetochore structure, centromeric protein loading, and inner centromere signaling. In this review, we discuss the conservation of small and long non-coding centromeric RNAs, their associations with various centromeric functions, and their potential roles in disease.
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Affiliation(s)
| | - Daniël P. Melters
- Chromatin Structure and Epigenetic Mechanisms, Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA;
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Wong CYY, Lee BCH, Yuen KWY. Epigenetic regulation of centromere function. Cell Mol Life Sci 2020; 77:2899-2917. [PMID: 32008088 PMCID: PMC11105045 DOI: 10.1007/s00018-020-03460-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 12/23/2019] [Accepted: 01/10/2020] [Indexed: 12/20/2022]
Abstract
The centromere is a specialized region on the chromosome that directs equal chromosome segregation. Centromeres are usually not defined by DNA sequences alone. How centromere formation and function are determined by epigenetics is still not fully understood. Active centromeres are often marked by the presence of centromeric-specific histone H3 variant, centromere protein A (CENP-A). How CENP-A is assembled into the centromeric chromatin during the cell cycle and propagated to the next cell cycle or the next generation to maintain the centromere function has been intensively investigated. In this review, we summarize current understanding of how post-translational modifications of CENP-A and other centromere proteins, centromeric and pericentric histone modifications, non-coding transcription and transcripts contribute to centromere function, and discuss their intricate relationships and potential feedback mechanisms.
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Affiliation(s)
- Charmaine Yan Yu Wong
- School of Biological Sciences, The University of Hong Kong, Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong, China
| | - Bernard Chi Hang Lee
- School of Biological Sciences, The University of Hong Kong, Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong, China
| | - Karen Wing Yee Yuen
- School of Biological Sciences, The University of Hong Kong, Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong, China.
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Mahlke MA, Nechemia-Arbely Y. Guarding the Genome: CENP-A-Chromatin in Health and Cancer. Genes (Basel) 2020; 11:genes11070810. [PMID: 32708729 PMCID: PMC7397030 DOI: 10.3390/genes11070810] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/10/2020] [Accepted: 07/15/2020] [Indexed: 02/07/2023] Open
Abstract
Faithful chromosome segregation is essential for the maintenance of genomic integrity and requires functional centromeres. Centromeres are epigenetically defined by the histone H3 variant, centromere protein A (CENP-A). Here we highlight current knowledge regarding CENP-A-containing chromatin structure, specification of centromere identity, regulation of CENP-A deposition and possible contribution to cancer formation and/or progression. CENP-A overexpression is common among many cancers and predicts poor prognosis. Overexpression of CENP-A increases rates of CENP-A deposition ectopically at sites of high histone turnover, occluding CCCTC-binding factor (CTCF) binding. Ectopic CENP-A deposition leads to mitotic defects, centromere dysfunction and chromosomal instability (CIN), a hallmark of cancer. CENP-A overexpression is often accompanied by overexpression of its chaperone Holliday Junction Recognition Protein (HJURP), leading to epigenetic addiction in which increased levels of HJURP and CENP-A become necessary to support rapidly dividing p53 deficient cancer cells. Alterations in CENP-A posttranslational modifications are also linked to chromosome segregation errors and CIN. Collectively, CENP-A is pivotal to genomic stability through centromere maintenance, perturbation of which can lead to tumorigenesis.
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Affiliation(s)
- Megan A. Mahlke
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA;
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Yael Nechemia-Arbely
- UPMC Hillman Cancer Center, Pittsburgh, PA 15213, USA;
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Correspondence: ; Tel.: +1-412-623-3228; Fax: +1-412-623-7828
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Dbf4-Dependent Kinase (DDK)-Mediated Proteolysis of CENP-A Prevents Mislocalization of CENP-A in Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2020; 10:2057-2068. [PMID: 32295767 PMCID: PMC7263675 DOI: 10.1534/g3.120.401131] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The evolutionarily conserved centromeric histone H3 variant (Cse4 in budding yeast, CENP-A in humans) is essential for faithful chromosome segregation. Mislocalization of CENP-A to non-centromeric chromatin contributes to chromosomal instability (CIN) in yeast, fly, and human cells and CENP-A is highly expressed and mislocalized in cancers. Defining mechanisms that prevent mislocalization of CENP-A is an area of active investigation. Ubiquitin-mediated proteolysis of overexpressed Cse4 (GALCSE4) by E3 ubiquitin ligases such as Psh1 prevents mislocalization of Cse4, and psh1 Δ strains display synthetic dosage lethality (SDL) with GALCSE4 We previously performed a genome-wide screen and identified five alleles of CDC7 and DBF4 that encode the Dbf4-dependent kinase (DDK) complex, which regulates DNA replication initiation, among the top twelve hits that displayed SDL with GALCSE4 We determined that cdc7 -7 strains exhibit defects in ubiquitin-mediated proteolysis of Cse4 and show mislocalization of Cse4 Mutation of MCM5 (mcm5 -bob1) bypasses the requirement of Cdc7 for replication initiation and rescues replication defects in a cdc7 -7 strain. We determined that mcm5 -bob1 does not rescue the SDL and defects in proteolysis of GALCSE4 in a cdc7 -7 strain, suggesting a DNA replication-independent role for Cdc7 in Cse4 proteolysis. The SDL phenotype, defects in ubiquitin-mediated proteolysis, and the mislocalization pattern of Cse4 in a cdc7 -7 psh1 Δ strain were similar to that of cdc7 -7 and psh1 Δ strains, suggesting that Cdc7 regulates Cse4 in a pathway that overlaps with Psh1 Our results define a DNA replication initiation-independent role of DDK as a regulator of Psh1-mediated proteolysis of Cse4 to prevent mislocalization of Cse4.
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Wong CYY, Ling YH, Mak JKH, Zhu J, Yuen KWY. "Lessons from the extremes: Epigenetic and genetic regulation in point monocentromere and holocentromere establishment on artificial chromosomes". Exp Cell Res 2020; 390:111974. [PMID: 32222413 DOI: 10.1016/j.yexcr.2020.111974] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/16/2020] [Accepted: 03/18/2020] [Indexed: 02/08/2023]
Abstract
The formation of de novo centromeres on artificial chromosomes in humans (HACs) and fission yeast (SpYACs) has provided much insights to the epigenetic and genetic control on regional centromere establishment and maintenance. Similarly, the use of artificial chromosomes in point centromeric budding yeast Saccharomyces cerevisiae (ScYACs) and holocentric Caenorhabditis elegans (WACs) has revealed epigenetic regulation in the originally thought purely genetically-determined point centromeres and some centromeric DNA sequence features in holocentromeres, respectively. These relatively extreme and less characterized centromere organizations, on the endogenous chromosomes and artificial chromosomes, will be discussed and compared to the more well-studied regional centromere systems. This review will highlight some of the common epigenetic and genetic features in different centromere architectures, including the presence of the centromeric histone H3 variant, CENP-A or CenH3, centromeric and pericentric transcription, AT-richness and repetitiveness of centromeric DNA sequences.
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Affiliation(s)
- Charmaine Yan Yu Wong
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Yick Hin Ling
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Jason Ka Ho Mak
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Jing Zhu
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Karen Wing Yee Yuen
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong.
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