1
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Choudhury R, Venkateswaran Venkatasubramani A, Hua J, Borsò M, Franconi C, Kinkley S, Forné I, Imhof A. The role of RNA in the maintenance of chromatin domains as revealed by antibody-mediated proximity labelling coupled to mass spectrometry. eLife 2024; 13:e95718. [PMID: 38717135 PMCID: PMC11147508 DOI: 10.7554/elife.95718] [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: 12/29/2023] [Accepted: 04/26/2024] [Indexed: 06/04/2024] Open
Abstract
Eukaryotic chromatin is organized into functional domains, that are characterized by distinct proteomic compositions and specific nuclear positions. In contrast to cellular organelles surrounded by lipid membranes, the composition of distinct chromatin domains is rather ill described and highly dynamic. To gain molecular insight into these domains and explore their composition, we developed an antibody-based proximity biotinylation method targeting the RNA and proteins constituents. The method that we termed antibody-mediated proximity labelling coupled to mass spectrometry (AMPL-MS) does not require the expression of fusion proteins and therefore constitutes a versatile and very sensitive method to characterize the composition of chromatin domains based on specific signature proteins or histone modifications. To demonstrate the utility of our approach we used AMPL-MS to characterize the molecular features of the chromocenter as well as the chromosome territory containing the hyperactive X chromosome in Drosophila. This analysis identified a number of known RNA-binding proteins in proximity of the hyperactive X and the centromere, supporting the accuracy of our method. In addition, it enabled us to characterize the role of RNA in the formation of these nuclear bodies. Furthermore, our method identified a new set of RNA molecules associated with the Drosophila centromere. Characterization of these novel molecules suggested the formation of R-loops in centromeres, which we validated using a novel probe for R-loops in Drosophila. Taken together, AMPL-MS improves the selectivity and specificity of proximity ligation allowing for novel discoveries of weak protein-RNA interactions in biologically diverse domains.
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Affiliation(s)
- Rupam Choudhury
- Department of Molecular Biology, Biomedical Center Munich, Ludwig-Maximilians UniversityPlanegg-MartinsriedGermany
| | - Anuroop Venkateswaran Venkatasubramani
- Department of Molecular Biology, Biomedical Center Munich, Ludwig-Maximilians UniversityPlanegg-MartinsriedGermany
- Graduate School of Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität MünchenMunichGermany
| | - Jie Hua
- Department of Molecular Biology, Biomedical Center Munich, Ludwig-Maximilians UniversityPlanegg-MartinsriedGermany
| | - Marco Borsò
- Protein Analysis Unit, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians, University (LMU) MunichPlanegg-MartinsriedGermany
| | - Celeste Franconi
- Chromatin Structure and Function group, Department of Computational Molecular Biology, Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Sarah Kinkley
- Chromatin Structure and Function group, Department of Computational Molecular Biology, Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Ignasi Forné
- Protein Analysis Unit, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians, University (LMU) MunichPlanegg-MartinsriedGermany
| | - Axel Imhof
- Department of Molecular Biology, Biomedical Center Munich, Ludwig-Maximilians UniversityPlanegg-MartinsriedGermany
- Protein Analysis Unit, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians, University (LMU) MunichPlanegg-MartinsriedGermany
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2
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Liu Y, Liu S, Jing R, Li C, Guo Y, Cai Z, Xi P, Dai P, Jia L, Zhu H, Zhang X. Identification of ASF1A and HJURP by global H3-H4 histone chaperone analysis as a prognostic two-gene model in hepatocellular carcinoma. Sci Rep 2024; 14:7666. [PMID: 38561384 PMCID: PMC10984954 DOI: 10.1038/s41598-024-58368-1] [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: 11/20/2023] [Accepted: 03/28/2024] [Indexed: 04/04/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is a malignancy with poor prognosis. Abnormal expression of H3-H4 histone chaperones has been identified in many cancers and holds promise as a biomarker for diagnosis and prognosis. However, systemic analysis of H3-H4 histone chaperones in HCC is still lacking. Here, we investigated the expression of 19 known H3-H4 histone chaperones in HCC. Integrated analysis of multiple public databases indicated that these chaperones are highly expressed in HCC tumor tissues, which was further verified by immunohistochemistry (IHC) staining in offline samples. Additionally, survival analysis suggested that HCC patients with upregulated H3-H4 histone chaperones have poor prognosis. Using LASSO and Cox regression, we constructed a two-gene model (ASF1A, HJURP) that accurately predicts prognosis in ICGC-LIRI and GEO HCC data, which was further validated in HCC tissue microarrays with follow-up information. GSEA revealed that HCCs in the high-risk group were associated with enhanced cell cycle progression and DNA replication. Intriguingly, HCCs in the high-risk group exhibited increased immune infiltration and sensitivity to immune checkpoint therapy (ICT). In summary, H3-H4 histone chaperones play a critical role in HCC progression, and the two-gene (ASF1A, HJURP) risk model is effective for predicting survival outcomes and sensitivity to immunotherapy for HCC patients.
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Affiliation(s)
- Yongkang Liu
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, 710069, Shaanxi, China
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, 710032, Shaanxi, China
| | - Shihui Liu
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Rui Jing
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, 710069, Shaanxi, China
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, 710032, Shaanxi, China
| | - Congcong Li
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Yongqi Guo
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Zhiye Cai
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Pei Xi
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Penggao Dai
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Lintao Jia
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, 710032, Shaanxi, China
| | - Hongli Zhu
- National Engineering Research Center for Miniaturized Detection Systems, College of Life Science, Northwest University, Xi'an, 710069, Shaanxi, China.
| | - Xiang Zhang
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, 710032, Shaanxi, China.
- The Ministry of Education Key Lab of Hazard Assessment and Control in Special Operational Environment, Fourth Military Medical University, Xi'an, 710032, Shaanxi, China.
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3
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Yamada M, Keller RR, Gutierrez RL, Cameron D, Suzuki H, Sanghrajka R, Vaynshteyn J, Gerwin J, Maura F, Hooper W, Shah M, Robine N, Demarest P, Bayin NS, Zapater LJ, Reed C, Hébert S, Masilionis I, Chaligne R, Socci ND, Taylor MD, Kleinman CL, Joyner AL, Raju GP, Kentsis A. Childhood cancer mutagenesis caused by transposase-derived PGBD5. SCIENCE ADVANCES 2024; 10:eadn4649. [PMID: 38517960 PMCID: PMC10959420 DOI: 10.1126/sciadv.adn4649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/16/2024] [Indexed: 03/24/2024]
Abstract
Genomic rearrangements are a hallmark of most childhood tumors, including medulloblastoma, one of the most common brain tumors in children, but their causes remain largely unknown. Here, we show that PiggyBac transposable element derived 5 (Pgbd5) promotes tumor development in multiple developmentally accurate mouse models of Sonic Hedgehog (SHH) medulloblastoma. Most Pgbd5-deficient mice do not develop tumors, while maintaining normal cerebellar development. Ectopic activation of SHH signaling is sufficient to enforce cerebellar granule cell progenitor-like cell states, which exhibit Pgbd5-dependent expression of distinct DNA repair and neurodevelopmental factors. Mouse medulloblastomas expressing Pgbd5 have increased numbers of somatic structural DNA rearrangements, some of which carry PGBD5-specific sequences at their breakpoints. Similar sequence breakpoints recurrently affect somatic DNA rearrangements of known tumor suppressors and oncogenes in medulloblastomas in 329 children. This identifies PGBD5 as a medulloblastoma mutator and provides a genetic mechanism for the generation of oncogenic DNA rearrangements in childhood cancer.
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Affiliation(s)
- Makiko Yamada
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
| | - Ross R. Keller
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
| | | | - Daniel Cameron
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
| | - Hiromichi Suzuki
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Reeti Sanghrajka
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Jake Vaynshteyn
- Departments of Neurology and Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeffrey Gerwin
- Departments of Neurology and Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Francesco Maura
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - William Hooper
- Computational Biology, New York Genome Center, New York, NY, USA
| | - Minita Shah
- Computational Biology, New York Genome Center, New York, NY, USA
| | - Nicolas Robine
- Computational Biology, New York Genome Center, New York, NY, USA
| | - Phillip Demarest
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
| | - N. Sumru Bayin
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
- Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge University, Cambridge, UK
| | - Luz Jubierre Zapater
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
| | - Casie Reed
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
| | - Steven Hébert
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Ignas Masilionis
- Single-Cell Analytics Innovation Lab, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ronan Chaligne
- Single-Cell Analytics Innovation Lab, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicholas D. Socci
- Bioinformatics Core, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael D. Taylor
- Department of Pediatrics—Hematology/Oncology and Neurosurgery, Baylor College of Medicine, Houston, TX, USA
- Hematology-Oncology Section, Texas Children’s Cancer Center, Houston, TX, USA
- The Arthur and Sonia Labatt Brain Tumour Research Centre and the Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Claudia L. Kleinman
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Alexandra L. Joyner
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
- Biochemistry, Cell and Molecular Biology Program and Neuroscience Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - G. Praveen Raju
- Departments of Neurology and Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alex Kentsis
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
- Departments of Pediatrics, Pharmacology, and Physiology & Biophysics, Weill Medical College of Cornell University, New York, NY, USA
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4
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Graham E, Esashi F. DNA strand breaks at centromeres: Friend or foe? Semin Cell Dev Biol 2024; 156:141-151. [PMID: 37872040 DOI: 10.1016/j.semcdb.2023.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 09/22/2023] [Accepted: 10/11/2023] [Indexed: 10/25/2023]
Abstract
Centromeres are large structural regions in the genomic DNA, which are essential for accurately transmitting a complete set of chromosomes to daughter cells during cell division. In humans, centromeres consist of highly repetitive α-satellite DNA sequences and unique epigenetic components, forming large proteinaceous structures required for chromosome segregation. Despite their biological importance, there is a growing body of evidence for centromere breakage across the cell cycle, including periods of quiescence. In this review, we provide an up-to-date examination of the distinct centromere environments at different stages of the cell cycle, highlighting their plausible contribution to centromere breakage. Additionally, we explore the implications of these breaks on centromere function, both in terms of negative consequences and potential positive effects.
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Affiliation(s)
- Emily Graham
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Fumiko Esashi
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
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5
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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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6
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Folco H, Xiao H, Wheeler D, Feng H, Bai Y, Grewal SS. The cysteine-rich domain in CENP-A chaperone Scm3HJURP ensures centromere targeting and kinetochore integrity. Nucleic Acids Res 2024; 52:1688-1701. [PMID: 38084929 PMCID: PMC10899784 DOI: 10.1093/nar/gkad1182] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 11/20/2023] [Accepted: 11/28/2023] [Indexed: 02/29/2024] Open
Abstract
Centromeric chromatin plays a crucial role in kinetochore assembly and chromosome segregation. Centromeres are specified through the loading of the histone H3 variant CENP-A by the conserved chaperone Scm3/HJURP. The N-terminus of Scm3/HJURP interacts with CENP-A, while the C-terminus facilitates centromere localization by interacting with the Mis18 holocomplex via a small domain, called the Mis16-binding domain (Mis16-BD) in fission yeast. Fungal Scm3 proteins contain an additional conserved cysteine-rich domain (CYS) of unknown function. Here, we find that CYS binds zinc in vitro and is essential for the localization and function of fission yeast Scm3. Disrupting CYS by deletion or introduction of point mutations within its zinc-binding motif prevents Scm3 centromere localization and compromises kinetochore integrity. Interestingly, CYS alone can localize to the centromere, albeit weakly, but its targeting is greatly enhanced when combined with Mis16-BD. Expressing a truncated protein containing both Mis16-BD and CYS, but lacking the CENP-A binding domain, causes toxicity and is accompanied by considerable chromosome missegregation and kinetochore loss. These effects can be mitigated by mutating the CYS zinc-binding motif. Collectively, our findings establish the essential role of the cysteine-rich domain in fungal Scm3 proteins and provide valuable insights into the mechanism of Scm3 centromere targeting.
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Affiliation(s)
- H Diego Folco
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hua Xiao
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Wheeler
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hanqiao Feng
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yawen Bai
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shiv I S Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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7
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Xu R, Pan Z, Nakagawa T. Gross Chromosomal Rearrangement at Centromeres. Biomolecules 2023; 14:28. [PMID: 38254628 PMCID: PMC10813616 DOI: 10.3390/biom14010028] [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: 11/28/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024] Open
Abstract
Centromeres play essential roles in the faithful segregation of chromosomes. CENP-A, the centromere-specific histone H3 variant, and heterochromatin characterized by di- or tri-methylation of histone H3 9th lysine (H3K9) are the hallmarks of centromere chromatin. Contrary to the epigenetic marks, DNA sequences underlying the centromere region of chromosomes are not well conserved through evolution. However, centromeres consist of repetitive sequences in many eukaryotes, including animals, plants, and a subset of fungi, including fission yeast. Advances in long-read sequencing techniques have uncovered the complete sequence of human centromeres containing more than thousands of alpha satellite repeats and other types of repetitive sequences. Not only tandem but also inverted repeats are present at a centromere. DNA recombination between centromere repeats can result in gross chromosomal rearrangement (GCR), such as translocation and isochromosome formation. CENP-A chromatin and heterochromatin suppress the centromeric GCR. The key player of homologous recombination, Rad51, safeguards centromere integrity through conservative noncrossover recombination between centromere repeats. In contrast to Rad51-dependent recombination, Rad52-mediated single-strand annealing (SSA) and microhomology-mediated end-joining (MMEJ) lead to centromeric GCR. This review summarizes recent findings on the role of centromere and recombination proteins in maintaining centromere integrity and discusses how GCR occurs at centromeres.
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Affiliation(s)
- Ran Xu
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, Osaka, Japan
- Forefront Research Center, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, Osaka, Japan
| | - Ziyi Pan
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, Osaka, Japan
- Forefront Research Center, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, Osaka, Japan
| | - Takuro Nakagawa
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, Osaka, Japan
- Forefront Research Center, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, Osaka, Japan
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8
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Scelfo A, Fachinetti D. Centromere: A Trojan horse for genome stability. DNA Repair (Amst) 2023; 130:103569. [PMID: 37708591 DOI: 10.1016/j.dnarep.2023.103569] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/22/2023] [Accepted: 09/05/2023] [Indexed: 09/16/2023]
Abstract
Centromeres play a key role in the maintenance of genome stability to prevent carcinogenesis and diseases. They are specialized chromosome loci essential to ensure faithful transmission of genomic information across cell generations by mediating the interaction with spindle microtubules. Nonetheless, while fulfilling these essential roles, their distinct repetitive composition and susceptibility to mechanical stresses during cell division render them susceptible to breakage events. In this review, we delve into the present understanding of the underlying causes of centromere fragility, from the mechanisms governing its DNA replication and repair, to the pathways acting to counteract potential challenges. We propose that the centromere represents a "Trojan horse" exerting vital functions that, at the same time, potentially threatens whole genome stability.
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Affiliation(s)
- Andrea Scelfo
- Institut Curie, CNRS, UMR 144, Sorbonne University, 26 rue d'Ulm, 75005 Paris, France.
| | - Daniele Fachinetti
- Institut Curie, CNRS, UMR 144, Sorbonne University, 26 rue d'Ulm, 75005 Paris, France.
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9
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Zhou J, Chen D, Zhang S, Wang C, Zhang L. Identification of two molecular subtypes and a novel prognostic model of lung adenocarcinoma based on a cuproptosis-associated gene signature. Front Genet 2023; 13:1039983. [PMID: 36712848 PMCID: PMC9877306 DOI: 10.3389/fgene.2022.1039983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 12/28/2022] [Indexed: 01/15/2023] Open
Abstract
Lung adenocarcinoma is the most common subtype of lung cancer clinically, with high mortality and poor prognosis. Cuproptosis present a newly discovered mode of cell death characterized by aggregation of fatty acylated proteins, depletion of iron-sulfur clusterin, triggering of HSP70, and induction of intracellular toxic oxidative stress. However, the impact of cuproptosis on lung adenocarcinoma development, prognosis, and treatment has not been elucidated. By systematically analyzing the genetic alterations of 10 cuproptosis-related genes in lung adenocarcinoma, we found that CDKN2A, DLAT, LIAS, PDHA1, FDX1, GLS, and MTF1 were differentially expressed between lung cancer tissues and adjacent tissues. Based on the expression levels of 10 cuproptosis-related genes, we classified lung adenocarcinoma patients into two molecular subtypes using the Consensus clustering method, of which subtype 2 had a worse prognosis. Differential expression genes associated with prognosis between the two subtypes were obtained by differential analysis and survival analysis, and cox lasso regression was applied to construct a cuproptosis-related prognostic model. Its survival predicting ability was validated in three extrinsic validation cohorts. The results of multivariate cox analysis indicated that cuproptosis risk score was an independent prognostic predictor, and the mixed model formed by cupproptosis prognostic model combined with stage had more robust prognostic prediction accuracy. We found the differences in cell cycle, mitosis, and p53 signaling pathways between high- and low-risk groups according to GO and KEGG enrichment analysis. The results of immune microenvironment analysis showed that the enrichment score of activated dendritic cells, mast cells, and type 2 interferon response were down-regulated in the high-risk group, while the fraction of neutrophils and M0 macrophages were upregulated in the high-risk group. Compared with the high-risk group, subjects in the low-risk group had higher Immunophenoscore and may be more sensitive to immunotherapy. We identified seven chemotherapy agents may improve the curative effect in LUAD samples with higher risk score. Overall, we discovered that cuproptosis is closely related to the occurrence, prognosis, and treatment of lung adenocarcinoma. The cuproptosis prognostic model is a potential prognostic predictor and may provide new strategies for precision therapy in lung adenocarcinoma.
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Affiliation(s)
- Jinlin Zhou
- Department of Respiratory Medicine, Bazhong Central Hospital, Bazhong, Sichuan, China
| | - Dehe Chen
- Department of Respiratory Medicine, Bazhong Central Hospital, Bazhong, Sichuan, China
| | - Shiguo Zhang
- Department of Respiratory Medicine, Bazhong Central Hospital, Bazhong, Sichuan, China
| | - Chunmei Wang
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Li Zhang
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, China,*Correspondence: Li Zhang,
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10
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Li L, Yuan Q, Chu YM, Jiang HY, Zhao JH, Su Q, Huo DQ, Zhang XF. Advances in holliday junction recognition protein (HJURP): Structure, molecular functions, and roles in cancer. Front Cell Dev Biol 2023; 11:1106638. [PMID: 37025176 PMCID: PMC10070699 DOI: 10.3389/fcell.2023.1106638] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 03/13/2023] [Indexed: 04/08/2023] Open
Abstract
Oncogenes are increasingly recognized as important factors in the development and progression of cancer. Holliday Junction Recognition Protein (HJURP) is a highly specialized mitogenic protein that is a chaperone protein of histone H3. The HJURP gene is located on chromosome 2q37.1 and is involved in nucleosome composition in the mitotic region, forming a three-dimensional crystal structure with Centromere Protein A (CENP-A) and the histone 4 complex. HJURP is involved in the recruitment and assembly of centromere and kinetochore and plays a key role in stabilizing the chromosome structure of tumor cells, and its dysfunction may contribute to tumorigenesis. In the available studies HJURP is upregulated in a variety of cancer tissues and cancer cell lines and is involved in tumor proliferation, invasion, metastasis and immune response. In an in vivo model, overexpression of HJURP in most cancer cell lines promotes cell proliferation and invasiveness, reduces susceptibility to apoptosis, and promotes tumor growth. In addition, upregulation of HJURP was associated with poorer prognosis in a variety of cancers. These properties suggest that HJURP may be a possible target for the treatment of certain cancers. Various studies targeting HJURP as a prognostic and therapeutic target for cancer are gradually attracting interest and attention. This paper reviews the functional and molecular mechanisms of HJURP in a variety of tumor types with the aim of providing new targets for future cancer therapy.
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Affiliation(s)
- Lin Li
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing, China
- Department of Pharmacy, The Second Clinical Medical College of North Sichuan Medical College, Nanchong, China
| | - Qiang Yuan
- Department of Pharmacy, The Second Clinical Medical College of North Sichuan Medical College, Nanchong, China
- School of Pharmacy, North Sichuan Medical College, Nanchong, China
| | - Yue-Ming Chu
- Department of Pharmacy, The Second Clinical Medical College of North Sichuan Medical College, Nanchong, China
- School of Pharmacy, North Sichuan Medical College, Nanchong, China
| | - Hang-Yu Jiang
- Department of Pharmacy, The Second Clinical Medical College of North Sichuan Medical College, Nanchong, China
- School of Pharmacy, North Sichuan Medical College, Nanchong, China
| | - Ju-Hua Zhao
- Department of Pharmacy, The Second Clinical Medical College of North Sichuan Medical College, Nanchong, China
| | - Qiang Su
- Institute of Tissue Engineering and Stem Cells, The Second Clinical Medical College of North Sichuan Medical College, Nanchong, China
- Nanchong Key Laboratory of Individualized Drug Therapy, Nanchong, China
| | - Dan-Qun Huo
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing, China
- *Correspondence: Dan-Qun Huo, ; Xiao-Fen Zhang,
| | - Xiao-Fen Zhang
- Department of Pharmacy, The Second Clinical Medical College of North Sichuan Medical College, Nanchong, China
- *Correspondence: Dan-Qun Huo, ; Xiao-Fen Zhang,
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11
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McQuaid K, Pipier A, Cardin C, Monchaud D. Interactions of small molecules with DNA junctions. Nucleic Acids Res 2022; 50:12636-12656. [PMID: 36382400 PMCID: PMC9825177 DOI: 10.1093/nar/gkac1043] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/13/2022] [Accepted: 10/23/2022] [Indexed: 11/17/2022] Open
Abstract
The four natural DNA bases (A, T, G and C) associate in base pairs (A=T and G≡C), allowing the attached DNA strands to assemble into the canonical double helix of DNA (or duplex-DNA, also known as B-DNA). The intrinsic supramolecular properties of nucleobases make other associations possible (such as base triplets or quartets), which thus translates into a diversity of DNA structures beyond B-DNA. To date, the alphabet of DNA structures is ripe with approximately 20 letters (from A- to Z-DNA); however, only a few of them are being considered as key players in cell biology and, by extension, valuable targets for chemical biology intervention. In the present review, we summarise what is known about alternative DNA structures (what are they? When, where and how do they fold?) and proceed to discuss further about those considered nowadays as valuable therapeutic targets. We discuss in more detail the molecular tools (ligands) that have been recently developed to target these structures, particularly the three- and four-way DNA junctions, in order to intervene in the biological processes where they are involved. This new and stimulating chemical biology playground allows for devising innovative strategies to fight against genetic diseases.
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Affiliation(s)
- Kane T McQuaid
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - Angélique Pipier
- Institut de Chimie Moléculaire de l’Université de Bourgogne (ICMUB), CNRS UMR 6302, UBFC Dijon, 21078 Dijon, France
| | - Christine J Cardin
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - David Monchaud
- Institut de Chimie Moléculaire de l’Université de Bourgogne (ICMUB), CNRS UMR 6302, UBFC Dijon, 21078 Dijon, France
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12
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HJURP inhibits proliferation of ovarian cancer cells by regulating CENP-A/CENP-N. Bull Cancer 2022; 109:1007-1016. [DOI: 10.1016/j.bulcan.2021.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/08/2021] [Accepted: 12/13/2021] [Indexed: 11/19/2022]
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13
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Ghimire ML, Gibbs DR, Mahmoud R, Dhakal S, Reiner JE. Nanopore Analysis as a Tool for Studying Rapid Holliday Junction Dynamics and Analyte Binding. Anal Chem 2022; 94:10027-10034. [PMID: 35786863 DOI: 10.1021/acs.analchem.2c00342] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Holliday junctions (HJs) are an important class of nucleic acid structure utilized in DNA break repair processes. As such, these structures have great importance as therapeutic targets and for understanding the onset and development of various diseases. Single-molecule fluorescence resonance energy transfer (smFRET) has been used to study HJ structure-fluctuation kinetics, but given the rapid time scales associated with these kinetics (approximately sub-milliseconds) and the limited bandwidth of smFRET, these studies typically require one to slow down the structure fluctuations using divalent ions (e.g., Mg2+). This modification limits the ability to understand and model the underlying kinetics associated with HJ fluctuations. We address this here by utilizing nanopore sensing in a gating configuration to monitor DNA structure fluctuations without divalent ions. A nanopore analysis shows that HJ fluctuations occur on the order of 0.1-10 ms and that the HJ remains locked in a single conformation with short-lived transitions to a second conformation. It is not clear what role the nanopore plays in affecting these kinetics, but the time scales observed indicate that HJs are capable of undergoing rapid transitions that are not detectable with lower bandwidth measurement techniques. In addition to monitoring rapid HJ fluctuations, we also report on the use of nanopore sensing to develop a highly selective sensor capable of clear and rapid detection of short oligo DNA strands that bind to various HJ targets.
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Affiliation(s)
- Madhav L Ghimire
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Dalton R Gibbs
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Roaa Mahmoud
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Joseph E Reiner
- Department of Physics, Virginia Commonwealth University, Richmond, Virginia 23284, United States
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14
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Senaratne AP, Cortes-Silva N, Drinnenberg IA. Evolution of holocentric chromosomes: Drivers, diversity, and deterrents. Semin Cell Dev Biol 2022; 127:90-99. [PMID: 35031207 DOI: 10.1016/j.semcdb.2022.01.003] [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: 08/27/2021] [Revised: 12/14/2021] [Accepted: 01/05/2022] [Indexed: 02/06/2023]
Abstract
Centromeres are specialized chromosomal regions that recruit kinetochore proteins and mediate spindle microtubule attachment to ensure faithful chromosome segregation during mitosis and meiosis. Centromeres can be restricted to one region of the chromosome. Named "monocentromere", this type represents the most commonly found centromere organization across eukaryotes. Alternatively, centromeres can also be assembled at sites chromosome-wide. This second type is called "holocentromere". Despite their early description over 100 years ago, research on holocentromeres has lagged behind that of monocentromeres. Nevertheless, the application of next generation sequencing approaches and advanced microscopic technologies enabled recent advances understanding the molecular organization and regulation of holocentromeres in different organisms. Here we review the current state of research on holocentromeres focusing on evolutionary considerations. First, we provide a brief historical perspective on the discovery of holocentric chromosomes. We then discuss models/drivers that have been proposed over the years to explain the evolutionary transition from mono- to holocentric chromosomes. We continue to review the description of holocentric chromosomes in diverse eukaryotic groups and then focus our discussion on a specific and recently characterized type of holocentromere organization in insects that functions independently of the otherwise essential centromeric marker protein CenH3, thus providing novel insights into holocentromere evolution in insects. Finally, we propose reasons to explain why the holocentric trait is not more frequent across eukaryotes despite putative selective advantages.
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Affiliation(s)
| | - Nuria Cortes-Silva
- Wellcome Trust/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Ines A Drinnenberg
- Institut Curie, PSL Research University, CNRS, UMR3664, F-75005 Paris, France; Sorbonne Université, Institut Curie, CNRS, UMR3664, F-75005 Paris, France.
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15
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Haig D. Paradox lost: Concerted evolution and centromeric instability: Centromeres are hospitable habitats for repeats that evolve adaptations for proliferation within the nucleus sometimes at organismal cost.: Centromeres are hospitable habitats for repeats that evolve adaptations for proliferation within the nucleus sometimes at organismal cost. Bioessays 2022; 44:e2200023. [PMID: 35748194 DOI: 10.1002/bies.202200023] [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: 01/28/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 11/11/2022]
Abstract
Homologous centromeres compete for segregation to the secondary oocyte nucleus at female meiosis I. Centromeric repeats also compete with each other to populate centromeres in mitotic cells of the germline and have become adapted to use the recombinational machinery present at centromeres to promote their own propagation. Repeats are not needed at centromeres, rather centromeres appear to be hospitable habitats for the colonization and proliferation of repeats. This is probably an indirect consequence of two distinctive features of centromeric DNA. Centromeres are subject to breakage by the mechanical forces exerted by microtubules and meiotic crossing-over is suppressed. Centromeric proteins acting in trans are under selection to mitigate the costs of centromeric repeats acting in cis. Collateral costs of mitotic competition at centromeres may help to explain the high rates of aneuploidy observed in early human embryos.
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Affiliation(s)
- David Haig
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
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16
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Zhou L, Chen Z, Liu C. Identification and verification of the role of crucial genes through which methionine restriction inhibits the progression of colon cancer cells. Oncol Lett 2022; 24:274. [PMID: 35782898 PMCID: PMC9247659 DOI: 10.3892/ol.2022.13394] [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: 02/12/2022] [Accepted: 05/25/2022] [Indexed: 11/05/2022] Open
Abstract
Studies have shown that methionine restriction (MR) can inhibit tumor progression, but its mechanism in colon cancer is unknown. Through DESeq2 and Edge analysis of the GSE72131 and GSE103602 datasets, 649 co-upregulated and 532 co-downregulated genes affected by MR were identified, respectively. Enrichment analysis showed that these genes were closely associated with tumor progression. Combined with the differentially expressed genes of colon cancer in The Cancer Genome Atlas database, MR affected 330 dysregulated genes in colon cancer. On this basis, a transcriptional regulatory and competing endogenous RNA network was established and F transcription factor 1 and microRNA 17-92a-1 Cluster Host Gene were identified as a key transcription factor and long non-coding RNA, respectively. In addition, four genes (FA Complementation Group I, Holliday Junction Recognition Protein, Karyopherin Subunit Alpha 2 and Kinesin Family Member 15) were identified by analyzing the relationship between dysregulated genes and overall survival. Finally, western blotting, reverse transcription-quantitative PCR, Transwell and other in vitro experiments verified that MR inhibits HCT116 colon cancer cell proliferation, metastasis and invasion, induces apoptosis and downregulates 6 hub genes. Collectively, the present study identified potential targets for MR to inhibit colon cancer progression and contributed to the clinical application of MR.
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Affiliation(s)
- Liqiang Zhou
- Department of General Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Zhiqing Chen
- Jiangxi Provincial Key Laboratory of Molecular Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Chuan Liu
- Jiangxi Provincial Key Laboratory of Molecular Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, P.R. China
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17
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Chen L, Zeng C, Yan L, Liao W, Zhen C, Yao J. Prognostic value of Holliday junction‑recognizing protein and its correlation with immune infiltrates in lung adenocarcinoma. Oncol Lett 2022; 24:232. [PMID: 35720487 DOI: 10.3892/ol.2022.13353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/19/2021] [Indexed: 12/24/2022] Open
Affiliation(s)
- Long Chen
- Department of Laboratory Medicine and Medical Research Center, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan, Guangdong 528308, P.R. China
| | - Chong Zeng
- Department of Laboratory Medicine and Medical Research Center, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan, Guangdong 528308, P.R. China
| | - Limei Yan
- Department of Laboratory Medicine and Medical Research Center, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan, Guangdong 528308, P.R. China
| | - Wanyu Liao
- Department of Pathology, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan, Guangdong 528308, P.R. China
| | - Chen Zhen
- Department of Laboratory Medicine and Medical Research Center, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan, Guangdong 528308, P.R. China
| | - Jie Yao
- Department of Laboratory Medicine and Medical Research Center, Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde), Foshan, Guangdong 528308, P.R. China
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18
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Patchigolla VS, Mellone BG. Enrichment of Non-B-Form DNA at D. melanogaster Centromeres. Genome Biol Evol 2022; 14:evac054. [PMID: 35441684 PMCID: PMC9070824 DOI: 10.1093/gbe/evac054] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2022] [Indexed: 11/17/2022] Open
Abstract
Centromeres are essential chromosomal regions that mediate the accurate inheritance of genetic information during eukaryotic cell division. Despite their conserved function, centromeres do not contain conserved DNA sequences and are instead epigenetically marked by the presence of the centromere-specific histone H3 variant centromeric protein A. The functional contribution of centromeric DNA sequences to centromere identity remains elusive. Previous work found that dyad symmetries with a propensity to adopt noncanonical secondary DNA structures are enriched at the centromeres of several species. These findings lead to the proposal that noncanonical DNA structures may contribute to centromere specification. Here, we analyze the predicted secondary structures of the recently identified centromere DNA sequences of Drosophila melanogaster. Although dyad symmetries are only enriched on the Y centromere, we find that other types of noncanonical DNA structures, including melted DNA and G-quadruplexes, are common features of all D. melanogaster centromeres. Our work is consistent with previous models suggesting that noncanonical DNA secondary structures may be conserved features of centromeres with possible implications for centromere specification.
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Affiliation(s)
| | - Barbara G. Mellone
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
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19
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Al-Soodani AT, Wu X, Kelp NC, Brown AJ, Roberts SA, Her C. hMSH5 Regulates NHEJ and Averts Excessive Nucleotide Alterations at Repair Joints. Genes (Basel) 2022; 13:genes13040673. [PMID: 35456479 PMCID: PMC9026759 DOI: 10.3390/genes13040673] [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: 03/11/2022] [Revised: 04/04/2022] [Accepted: 04/08/2022] [Indexed: 02/05/2023] Open
Abstract
Inappropriate repair of DNA double-strand breaks (DSBs) leads to genomic instability, cell death, or malignant transformation. Cells minimize these detrimental effects by selectively activating suitable DSB repair pathways in accordance with their underlying cellular context. Here, we report that hMSH5 down-regulates NHEJ and restricts the extent of DSB end processing before rejoining, thereby reducing “excessive” deletions and insertions at repair joints. RNAi-mediated knockdown of hMSH5 led to large nucleotide deletions and longer insertions at the repair joints, while at the same time reducing the average length of microhomology (MH) at repair joints. Conversely, hMSH5 overexpression reduced end-joining activity and increased RPA foci formation (i.e., more stable ssDNA at DSB ends). Furthermore, silencing of hMSH5 delayed 53BP1 chromatin spreading, leading to increased end resection at DSB ends.
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20
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Abstract
Centromeres, the chromosomal loci where spindle fibers attach during cell division to segregate chromosomes, are typically found within satellite arrays in plants and animals. Satellite arrays have been difficult to analyze because they comprise megabases of tandem head-to-tail highly repeated DNA sequences. Much evidence suggests that centromeres are epigenetically defined by the location of nucleosomes containing the centromere-specific histone H3 variant cenH3, independently of the DNA sequences where they are located; however, the reason that cenH3 nucleosomes are generally found on rapidly evolving satellite arrays has remained unclear. Recently, long-read sequencing technology has clarified the structures of satellite arrays and sparked rethinking of how they evolve, and new experiments and analyses have helped bring both understanding and further speculation about the role these highly repeated sequences play in centromere identification.
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Affiliation(s)
- Paul B Talbert
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | - Steven Henikoff
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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21
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Chardon F, Japaridze A, Witt H, Velikovsky L, Chakraborty C, Wilhelm T, Dumont M, Yang W, Kikuti C, Gangnard S, Mace AS, Wuite G, Dekker C, Fachinetti D. CENP-B-mediated DNA loops regulate activity and stability of human centromeres. Mol Cell 2022; 82:1751-1767.e8. [PMID: 35320753 DOI: 10.1016/j.molcel.2022.02.032] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 12/25/2022]
Abstract
Chromosome inheritance depends on centromeres, epigenetically specified regions of chromosomes. While conventional human centromeres are known to be built of long tandem DNA repeats, much of their architecture remains unknown. Using single-molecule techniques such as AFM, nanopores, and optical tweezers, we find that human centromeric DNA exhibits complex DNA folds such as local hairpins. Upon binding to a specific sequence within centromeric regions, the DNA-binding protein CENP-B compacts centromeres by forming pronounced DNA loops between the repeats, which favor inter-chromosomal centromere compaction and clustering. This DNA-loop-mediated organization of centromeric chromatin participates in maintaining centromere position and integrity upon microtubule pulling during mitosis. Our findings emphasize the importance of DNA topology in centromeric regulation and stability.
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Affiliation(s)
- Florian Chardon
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Aleksandre Japaridze
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Hannes Witt
- Department of Physics and Astronomy, LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, the Netherlands
| | - Leonid Velikovsky
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Camellia Chakraborty
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Therese Wilhelm
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Marie Dumont
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Wayne Yang
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Carlos Kikuti
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Stephane Gangnard
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Anne-Sophie Mace
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France
| | - Gijs Wuite
- Department of Physics and Astronomy, LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, the Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Daniele Fachinetti
- Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, 75005 Paris, France.
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22
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Li J, Wang C, Cheng R, Su H, Wang L, Ji L, Ji H. KLF11 promotes the progression of glioma via regulating HJURP. Cell Biol Int 2022; 46:1144-1155. [PMID: 35293659 DOI: 10.1002/cbin.11795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 03/05/2022] [Accepted: 03/13/2022] [Indexed: 11/09/2022]
Abstract
Understanding the molecular mechanism of glioma is very important for the diagnosis and treatment of glioma. Recently, a new study illustrated that KLF11 could be a potential prognostic and diagnostic biomarker in glioma, but the critical role is not illustrated. In this paper, we found that KLF11 was highly expressed in glioma cancer tissues and cells, and KLF11 high expression of glioblastoma (GBM) and Lower-grade glioma (LGG) were correlated with poorer overall survival and disease-free survival percentages. KLF11 knockdown inhibited glioma cell proliferation and migration, while KLF11 overexpression enhanced cell proliferation and migration. In vivo, knockdown of KLF11 reduced the tumor size of glioma. With regard to the molecular regulatory mechanism, we clarified that the Holliday Junction Recognition Protein (HJURP) was positively regulated by KLF11. Meanwhile, we demonstrated that HJURP knockdown also inhibited glioma carcinoma progression. Overexpression of HJURP rescued the suppressed proliferation and migration function of glioma cells with depletion of KLF11. Therefore, our study demonstrated the function of KLF11 in glioma and showed KLF11 and HJURP could be prognostic and diagnostic markers in glioma, which provides a new insight of glioma therapy. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jian Li
- The Fifth Clinical Medical College of Shanxi Medical University, Taiyuan, 030012, Shanxi Province, China.,Department of neurosurgery, Chanzhi City People's hospital, Chanzhi, 046099, Shanxi Province, China
| | - Chunhong Wang
- The Fifth Clinical Medical College of Shanxi Medical University, Taiyuan, 030012, Shanxi Province, China.,Department of neurosurgery, Shanxi Provincial People's hospital, Taiyuan, 030012, Shanxi, China
| | - Rui Cheng
- The Fifth Clinical Medical College of Shanxi Medical University, Taiyuan, 030012, Shanxi Province, China.,Department of neurosurgery, Shanxi Provincial People's hospital, Taiyuan, 030012, Shanxi, China
| | - Haiyang Su
- The Fifth Clinical Medical College of Shanxi Medical University, Taiyuan, 030012, Shanxi Province, China.,Department of neurosurgery, Shanxi Provincial People's hospital, Taiyuan, 030012, Shanxi, China
| | - Lijun Wang
- The Fifth Clinical Medical College of Shanxi Medical University, Taiyuan, 030012, Shanxi Province, China.,Department of neurosurgery, Shanxi Provincial People's hospital, Taiyuan, 030012, Shanxi, China
| | - Lei Ji
- The Fifth Clinical Medical College of Shanxi Medical University, Taiyuan, 030012, Shanxi Province, China.,Department of neurosurgery, Shanxi Provincial People's hospital, Taiyuan, 030012, Shanxi, China
| | - Hongming Ji
- The Fifth Clinical Medical College of Shanxi Medical University, Taiyuan, 030012, Shanxi Province, China.,Department of neurosurgery, Shanxi Provincial People's hospital, Taiyuan, 030012, Shanxi, China
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23
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Su R, Huang H, Gao X, Zhou Y, Yin S, Xie H, Zhou L, Zheng S. A pan-cancer analysis of the oncogenic role of Holliday junction recognition protein in human tumors. Open Med (Wars) 2022; 17:317-328. [PMID: 35274047 PMCID: PMC8854909 DOI: 10.1515/med-2022-0423] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 11/30/2021] [Accepted: 12/14/2021] [Indexed: 01/16/2023] Open
Abstract
Abstract
Although cell-based or animal-based research evidence support the association of Holliday junction recognition protein (HJURP) with cancers, no pan-cancer investigation has been reported. The datasets of Gene Expression Omnibus database along with The Cancer Genome Atlas project were used to evaluate the expression of HJURP in various types of tumors. HJURP is overexpressed in a considerable number of cancers, and some changes in DNA methylation and genetic alterations are discovered in some types of tumors, such as kidney-related and adrenal gland-related tumors. Based on PrognoScan and gene expression profiling interactive analysis (GEPIA), the elevated expression of HJURP worsened the survival time of individuals with cancer. The biological general repository for interaction datasets (BioGRID) and The database for annotation, visualization and integrated discovery (DAVID) were used to establish the functional molecular network. It revealed that the cell cycle and p53 signaling pathway are the key molecular mechanisms that HJURP promotes carcinogenesis. The nomograms between HJURP and clinical pathological factors based on the Cox proportional hazards model showed a good prognostic performance in kidney carcinoma, hepatocellular carcinoma, and lung adenocarcinoma. Our first pan-cancer study provides a relatively profound insights into the oncogenic roles of HJURP across different tumors.
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Affiliation(s)
- Rong Su
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine , Hangzhou 310003 , China
- NHC Key Laboratory of Combined Multi-organ Transplantation , Hangzhou 310003 , China
- Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment for Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences , Hangzhou 310003 , China
- Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Zhejiang Province , Hangzhou 310003 , China
| | - Hechen Huang
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine , Hangzhou 310003 , China
- NHC Key Laboratory of Combined Multi-organ Transplantation , Hangzhou 310003 , China
- Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment for Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences , Hangzhou 310003 , China
- Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Zhejiang Province , Hangzhou 310003 , China
| | - Xingxing Gao
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine , Hangzhou 310003 , China
- NHC Key Laboratory of Combined Multi-organ Transplantation , Hangzhou 310003 , China
- Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment for Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences , Hangzhou 310003 , China
- Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Zhejiang Province , Hangzhou 310003 , China
| | - Yuan Zhou
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine , Hangzhou 310003 , China
- NHC Key Laboratory of Combined Multi-organ Transplantation , Hangzhou 310003 , China
- Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment for Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences , Hangzhou 310003 , China
- Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Zhejiang Province , Hangzhou 310003 , China
| | - Shengyong Yin
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine , Hangzhou 310003 , China
- NHC Key Laboratory of Combined Multi-organ Transplantation , Hangzhou 310003 , China
- Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment for Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences , Hangzhou 310003 , China
- Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Zhejiang Province , Hangzhou 310003 , China
| | - Haiyang Xie
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine , Hangzhou 310003 , China
- NHC Key Laboratory of Combined Multi-organ Transplantation , Hangzhou 310003 , China
- Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment for Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences , Hangzhou 310003 , China
- Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Zhejiang Province , Hangzhou 310003 , China
| | - Lin Zhou
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine , Hangzhou 310003 , China
- NHC Key Laboratory of Combined Multi-organ Transplantation , Hangzhou 310003 , China
- Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment for Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences , Hangzhou 310003 , China
- Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Zhejiang Province , Hangzhou 310003 , China
| | - Shusen Zheng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine , #79 Qingchun Road , Hangzhou 310003 , China
- NHC Key Laboratory of Combined Multi-organ Transplantation , Hangzhou 310003 , China
- Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment for Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Sciences , Hangzhou 310003 , China
- Key Laboratory of Organ Transplantation, Research Center for Diagnosis and Treatment of Hepatobiliary Diseases, Zhejiang Province , Hangzhou 310003 , China
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24
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Phillips EO, Gunjan A. Histone Variants: The Unsung Guardians of the Genome. DNA Repair (Amst) 2022; 112:103301. [DOI: 10.1016/j.dnarep.2022.103301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 02/01/2022] [Accepted: 02/12/2022] [Indexed: 12/15/2022]
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25
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Jia Y, Zhou J, Tan TK, Chung TH, Chen Y, Chooi JY, Sanda T, Fullwood MJ, Xiong S, Toh SH, Balan K, Wong RW, Lim JS, Zhang E, Cai Z, Shen P, Chng WJ. Super Enhancer-Mediated Upregulation of HJURP Promotes Growth and Survival of t(4;14)-Positive Multiple Myeloma. Cancer Res 2022; 82:406-418. [PMID: 34893510 PMCID: PMC9397631 DOI: 10.1158/0008-5472.can-21-0921] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 10/05/2021] [Accepted: 11/30/2021] [Indexed: 01/07/2023]
Abstract
Multiple myeloma is an incurable malignancy with marked clinical and genetic heterogeneity. The cytogenetic abnormality t(4;14) (p16.3;q32.3) confers aggressive behavior in multiple myeloma. Recently, essential oncogenic drivers in a wide range of cancers have been shown to be controlled by super-enhancers (SE). We used chromatin immunoprecipitation sequencing of the active enhancer marker histone H3 lysine 27 acetylation (H3K27ac) to profile unique SEs in t(4;14)-translocated multiple myeloma. The histone chaperone HJURP was aberrantly overexpressed in t(4;14)-positive multiple myeloma due to transcriptional activation by a distal SE induced by the histone lysine methyltransferase NSD2. Silencing of HJURP with short hairpin RNA or CRISPR interference of SE function impaired cell viability and led to apoptosis. Conversely, HJURP overexpression promoted cell proliferation and abrogated apoptosis. Mechanistically, the NSD2/BRD4 complex positively coregulated HJURP transcription by binding the promoter and active elements of its SE. In summary, this study introduces SE profiling as an efficient approach to identify new targets and understand molecular pathogenesis in specific subtypes of cancer. Moreover, HJURP could be a valuable therapeutic target in patients with t(4;14)-positive myeloma. SIGNIFICANCE: A super-enhancer screen in t(4;14) multiple myeloma serves to identify genes that promote growth and survival of myeloma cells, which may be evaluated in future studies as therapeutic targets.
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Affiliation(s)
- Yunlu Jia
- Cancer Science Institute of Singapore, National University of Singapore, Centre for Translational Medicine, Singapore, Republic of Singapore.,Department of Medical Oncology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jianbiao Zhou
- Cancer Science Institute of Singapore, National University of Singapore, Centre for Translational Medicine, Singapore, Republic of Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Tze King Tan
- Cancer Science Institute of Singapore, National University of Singapore, Centre for Translational Medicine, Singapore, Republic of Singapore
| | - Tae-Hoon Chung
- Cancer Science Institute of Singapore, National University of Singapore, Centre for Translational Medicine, Singapore, Republic of Singapore
| | - Yongxia Chen
- Department of Surgical Oncology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jing-Yuan Chooi
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Takaomi Sanda
- Cancer Science Institute of Singapore, National University of Singapore, Centre for Translational Medicine, Singapore, Republic of Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Melissa J. Fullwood
- Cancer Science Institute of Singapore, National University of Singapore, Centre for Translational Medicine, Singapore, Republic of Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore
| | - Sinan Xiong
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Sabrina H.M. Toh
- Cancer Science Institute of Singapore, National University of Singapore, Centre for Translational Medicine, Singapore, Republic of Singapore
| | - Kalpnaa Balan
- Cancer Science Institute of Singapore, National University of Singapore, Centre for Translational Medicine, Singapore, Republic of Singapore
| | - Regina W.J. Wong
- Cancer Science Institute of Singapore, National University of Singapore, Centre for Translational Medicine, Singapore, Republic of Singapore
| | - Julia S.L. Lim
- Cancer Science Institute of Singapore, National University of Singapore, Centre for Translational Medicine, Singapore, Republic of Singapore
| | - Enfan Zhang
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhen Cai
- Bone Marrow Transplantation Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Peng Shen
- Department of Medical Oncology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wee Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, Centre for Translational Medicine, Singapore, Republic of Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore.,Department of Hematology-Oncology, National University Cancer Institute of Singapore (NCIS), The National University Health System (NUHS), Singapore, Republic of Singapore.,Corresponding Author: Wee Joo Chng, Department of Haematology-Oncology, National University Cancer Institute of Singapore (NCIS), The National University Health System (NUHS), 1E, Kent Ridge Road, Singapore 119228. Phone: 656-772-4613; Fax: 656-777-5545; E-mail:
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26
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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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27
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Lin W, Wang X, Wang Z, Shao F, Yang Y, Cao Z, Feng X, Gao Y, He J. Comprehensive Analysis Uncovers Prognostic and Immunogenic Characteristics of Cellular Senescence for Lung Adenocarcinoma. Front Cell Dev Biol 2021; 9:780461. [PMID: 34869385 PMCID: PMC8636167 DOI: 10.3389/fcell.2021.780461] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 10/27/2021] [Indexed: 01/10/2023] Open
Abstract
Cellular senescence plays a crucial role in tumorigenesis, development and immune modulation in cancers. However, to date, a robust and reliable cellular senescence-related signature and its value in clinical outcomes and immunotherapy response remain unexplored in lung adenocarcinoma (LUAD) patients. Through exploring the expression profiles of 278 cellular senescence-related genes in 936 LUAD patients, a cellular senescence-related signature (SRS) was constructed and validated as an independent prognostic predictor for LUAD patients. Notably, patients with high SRS scores exhibited upregulation of senescence-associated secretory phenotype (SASP) and an immunosuppressive phenotype. Further analysis showed that SRS combined with immune checkpoint expression or TMB served as a good predictor for patients’ clinical outcomes, and patients with low SRS scores might benefit from immunotherapy. Collectively, our findings demonstrated that SRS involved in the regulation of the tumor immune microenvironment through SASP was a robust biomarker for the immunotherapeutic response and prognosis in LUAD.
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Affiliation(s)
- Weihao Lin
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xin Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhen Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fei Shao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yannan Yang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zheng Cao
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaoli Feng
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yibo Gao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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28
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Ghaderi-Zefrehi H, Rezaei M, Sadeghi F, Heiat M. Genetic polymorphisms in DNA repair genes and hepatocellular carcinoma risk. DNA Repair (Amst) 2021; 107:103196. [PMID: 34416543 DOI: 10.1016/j.dnarep.2021.103196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 05/23/2021] [Accepted: 07/26/2021] [Indexed: 01/27/2023]
Abstract
Hepatocellular carcinoma (HCC) is one of the most frequent types of tumors worldwide. Its occurrence and development have been related to various risk factors, such as chronic infection with hepatitis B or C viruses and alcohol addiction. DNA repair systems play a critical role in maintaining the integrity of the genome. Defects in these systems have been related to increased susceptibility to various types of cancer. Multiple genetic polymorphisms in genes of DNA repair systems have been reported that may affect DNA repair capacity (DRC) and modulate risk to cancer. Several studies have been conducted to assess the role of polymorphisms of DNA repair genes on the HCC risk. Identifying these polymorphisms and their association with HCC risk may help to improve prevention and treatment strategies. In this study, we review investigations that evaluated the association between genetic polymorphisms of DNA repair genes and risk of HCC.
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Affiliation(s)
- Hossein Ghaderi-Zefrehi
- Department of Clinical Biochemistry, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran; Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Maryam Rezaei
- Department of Clinical Biochemistry, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Farzin Sadeghi
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Mohammad Heiat
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases, Baqiyatallah University of Medical Sciences, Tehran, Iran.
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29
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Caron P, Pobega E, Polo SE. DNA Double-Strand Break Repair: All Roads Lead to HeterochROMAtin Marks. Front Genet 2021; 12:730696. [PMID: 34539757 PMCID: PMC8440905 DOI: 10.3389/fgene.2021.730696] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/06/2021] [Indexed: 12/21/2022] Open
Abstract
In response to DNA double-strand breaks (DSBs), chromatin modifications orchestrate DNA repair pathways thus safeguarding genome integrity. Recent studies have uncovered a key role for heterochromatin marks and associated factors in shaping DSB repair within the nucleus. In this review, we present our current knowledge of the interplay between heterochromatin marks and DSB repair. We discuss the impact of heterochromatin features, either pre-existing in heterochromatin domains or de novo established in euchromatin, on DSB repair pathway choice. We emphasize how heterochromatin decompaction and mobility further support DSB repair, focusing on recent mechanistic insights into these processes. Finally, we speculate about potential molecular players involved in the maintenance or the erasure of heterochromatin marks following DSB repair, and their implications for restoring epigenome function and integrity.
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Affiliation(s)
- Pierre Caron
- Epigenetics and Cell Fate Centre, CNRS, University of Paris, Paris, France
| | - Enrico Pobega
- Epigenetics and Cell Fate Centre, CNRS, University of Paris, Paris, France
| | - Sophie E Polo
- Epigenetics and Cell Fate Centre, CNRS, University of Paris, Paris, France
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30
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VE-822, a novel DNA Holliday junction stabilizer, inhibits homologous recombination repair and triggers DNA damage response in osteogenic sarcomas. Biochem Pharmacol 2021; 193:114767. [PMID: 34537248 DOI: 10.1016/j.bcp.2021.114767] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 12/20/2022]
Abstract
Homologous recombination repair (HRR) is crucial for genomic stability of cancer cells and is an attractive target in cancer therapy. Holliday junction (HJ) is a four-way DNA intermediate that performs an essential role in homology-directed repair. However, few studies about regulatory mechanisms of HJs have been reported. In this study, to better understand the biological effects of HJs, VE-822 was identified as an effective DNA HJ stabilizer to promote the assembly of HJs both in vitro and in cells. This compound could inhibit the HRR level, activate DNA-PKCS to trigger DNA damage response (DDR) and induce telomeric DNA damage via stabilizing DNA HJs. Furthermore, VE-822 was demonstrated to sensitize the osteosarcoma cells to doxorubicin (Dox) by enhancing DNA damage and cellular apoptosis. This work thus reports one novel HJ stabilizer, and provide a potential anticancer strategy through the modulation of DNA HJs.
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31
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HJURP is a prognostic biomarker for clear cell renal cell carcinoma and is linked to immune infiltration. Int Immunopharmacol 2021; 99:107899. [PMID: 34217993 DOI: 10.1016/j.intimp.2021.107899] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 01/11/2023]
Abstract
BACKGROUND Clear cell renal cell carcinoma (ccRCC) is the most prevalent and highly malignant pathological type of kidney cancer. Finding more precise biomarkers is critical for enhancing the prognosis of patients with ccRCC. Multiple studies have suggested that Holliday junction recognition protein (HJURP) promotes tumor progression and predicts poor prognosis in a variety of cancers. However, the role of HJURP in ccRCC remains unclear. METHODS The ccRCC dataset was obtained from The Cancer Genome Atlas (TCGA), and the relationship between HJURP expression and ccRCC clinical features was investigated using R software. The effect of HJURP expression on survival was assessed using survival probabilities and Cox regression. Gene set enrichment analysis (GSEA) was used to identify HJURP-related signaling pathways in ccRCC. Finally, Tumor IMmune Estimation Resource (TIMER) and Gene Expression Profiling Interactive Analysis (GEPIA)were used to analyzethe correlation between HJURP expression and immunocyte infiltrates in ccRCC. RESULTS HJURP expression was upregulated in ccRCC. Increased HJURP expression was associated with poor pathological features and correlated with poor prognosis in patients with ccRCC. Cox regression further found that HJURP expression was a high-risk factor for ccRCC patients. GSEA revealed that HJURP was closely linked to multiple immune-related signaling pathways. In ccRCC, HJURP expression was closely correlated with infiltration of various immune cells and expression of a wide range of immunocyte gene markers. CONCLUSION HJURP is a potential independent prognostic marker in ccRCC that plays an essential role in the tumor microenvironment by regulating immunocyte infiltration.
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32
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Li Y, Yi Q, Liao X, Han C, Zheng L, Li H, Yu Q, Yan X, Chen X, Zhu H, Zhao B, Lin Q, Liang L, Wang L, Qin F, Xie W, Li Y, Huang W. Hypomethylation-driven overexpression of HJURP promotes progression of hepatocellular carcinoma and is associated with poor prognosis. Biochem Biophys Res Commun 2021; 566:67-74. [PMID: 34119827 DOI: 10.1016/j.bbrc.2021.05.102] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 05/31/2021] [Indexed: 12/18/2022]
Abstract
Our previous studies have initially identified HJURP, which encodes a Holliday junction recognizing protein, as a hepatocellular carcinoma (HCC) susceptibility gene. In this report, we showed that the HJURP is highly expressed in HCC tissues compared to adjacent normal tissues. Overexpression of HJURP in HCC tissues is mainly due to the hypomethylation of HJURP promoter region. Clinically, high expression of HJURP is significantly associated with poor overall survival and disease-free survival of patients with HCC, as well as in multiple other types of cancer. Gain- and loss-of functional studies demonstrated that HJURP promotes HCC cell proliferation, clone formation, migration and invasion. Additionally, HJURP enhances HCC tumorigenesis via reducing G0/G1 arrest and apoptosis. Mechanistically, by gene set enrichment analysis (GSEA) analysis, HJURP was identified as a modulator involved in CENPA-mediated centromere maintenance. Our results provide evidence of HJURP as an important oncogene that promotes HCC progression, and the HJURP pathway may be a potential target for the treatment of HCC.
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Affiliation(s)
- Ye Li
- Medical Oncology Department, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Qing Yi
- Graduate School of Guangxi Medical University, Nanning, Guangxi, China
| | - Xiaoli Liao
- Department of First Chemotherapy, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
| | - Chenglong Han
- Department of Oncology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Li Zheng
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin, China
| | - Hui Li
- Department of Oncology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Qian Yu
- Medical Oncology Department, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Xuexin Yan
- Medical Oncology Department, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Xinyu Chen
- Medical Oncology Department, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Huawei Zhu
- Department of Oncology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Bi Zhao
- Department of Oncology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Qiulu Lin
- Department of Oncology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Li Liang
- Department of Oncology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Li Wang
- Department of Oncology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Fanghui Qin
- Department of Fifth Chemotherapy, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
| | - Weimin Xie
- Department of Fifth Chemotherapy, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China.
| | - Yongqiang Li
- Department of First Chemotherapy, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China.
| | - Wenfeng Huang
- Department of Oncology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China.
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Lai W, Zhu W, Xiao C, Li X, Wang Y, Han Y, Zheng J, Li Y, Li M, Wen X. HJURP promotes proliferation in prostate cancer cells through increasing CDKN1A degradation via the GSK3β/JNK signaling pathway. Cell Death Dis 2021; 12:583. [PMID: 34099634 PMCID: PMC8184824 DOI: 10.1038/s41419-021-03870-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 05/04/2021] [Accepted: 05/07/2021] [Indexed: 12/22/2022]
Abstract
Genes with cross-cancer aberrations are most likely to be functional genes or potential therapeutic targets. Here, we found a total of 137 genes were ectopically expressed in eight cancer types, of which Holliday junction recognition protein (HJURP ) was significantly upregulated in prostate cancer (PCa). Moreover, patients with higher HJURP mRNA and protein levels had poorer outcomes, and the protein levels served as an independent prognosis factor for the overall survival of PCa patients. Functionally, ectopic HJURP expression promoted PCa cells proliferation in vitro and in vivo. Mechanistically, HJURP increased the ubiquitination of cyclin-dependent kinase inhibitor 1 (CDKN1A) via the GSK3β/JNK signaling pathway and decreased its stability. This study investigated the role of HJURP in PCa proliferation and may provide a novel prognostic and therapeutic target for PCa.
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Affiliation(s)
- Wenjie Lai
- Department of Urology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Weian Zhu
- Department of Urology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Chutian Xiao
- Department of Urology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiaojuan Li
- Department of Health Care, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Yu Wang
- Department of Urology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yuefu Han
- Department of Urology, Yue Bei People’s Hospital, Shaoguan, China
| | - Jiayu Zheng
- Department of Urology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yingqiu Li
- State Key Laboratory of Biocontrol, Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Mingqiang Li
- Laboratory of Biomaterials and Translational Medicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xingqiao Wen
- Department of Urology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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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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Sreekumar L, Kumari K, Guin K, Bakshi A, Varshney N, Thimmappa BC, Narlikar L, Padinhateeri R, Siddharthan R, Sanyal K. Orc4 spatiotemporally stabilizes centromeric chromatin. Genome Res 2021; 31:607-621. [PMID: 33514624 PMCID: PMC8015856 DOI: 10.1101/gr.265900.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 01/27/2021] [Indexed: 11/24/2022]
Abstract
The establishment of centromeric chromatin and its propagation by the centromere-specific histone CENPA is mediated by epigenetic mechanisms in most eukaryotes. DNA replication origins, origin binding proteins, and replication timing of centromere DNA are important determinants of centromere function. The epigenetically regulated regional centromeres in the budding yeast Candida albicans have unique DNA sequences that replicate earliest in every chromosome and are clustered throughout the cell cycle. In this study, the genome-wide occupancy of the replication initiation protein Orc4 reveals its abundance at all centromeres in C. albicans Orc4 is associated with four different DNA sequence motifs, one of which coincides with tRNA genes (tDNA) that replicate early and cluster together in space. Hi-C combined with genome-wide replication timing analyses identify that early replicating Orc4-bound regions interact with themselves stronger than with late replicating Orc4-bound regions. We simulate a polymer model of chromosomes of C. albicans and propose that the early replicating and highly enriched Orc4-bound sites preferentially localize around the clustered kinetochores. We also observe that Orc4 is constitutively localized to centromeres, and both Orc4 and the helicase Mcm2 are essential for cell viability and CENPA stability in C. albicans Finally, we show that new molecules of CENPA are recruited to centromeres during late anaphase/telophase, which coincides with the stage at which the CENPA-specific chaperone Scm3 localizes to the kinetochore. We propose that the spatiotemporal localization of Orc4 within the nucleus, in collaboration with Mcm2 and Scm3, maintains centromeric chromatin stability and CENPA recruitment in C. albicans.
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Affiliation(s)
- Lakshmi Sreekumar
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Kiran Kumari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
- IITB-Monash Research Academy, Mumbai 400076, India
- Department of Chemical Engineering, Monash University, Melbourne 3800, Australia
| | - Krishnendu Guin
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Asif Bakshi
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Neha Varshney
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Bhagya C Thimmappa
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Leelavati Narlikar
- Department of Chemical Engineering, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Ranjith Padinhateeri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Rahul Siddharthan
- The Institute of Mathematical Sciences/HBNI, Taramani, Chennai 600113, India
| | - Kaustuv Sanyal
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
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Nagpal H, Fierz B. The Elusive Structure of Centro-Chromatin: Molecular Order or Dynamic Heterogenetity? J Mol Biol 2021; 433:166676. [PMID: 33065112 DOI: 10.1016/j.jmb.2020.10.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/07/2020] [Accepted: 10/08/2020] [Indexed: 01/09/2023]
Abstract
The centromere is an essential chromatin domain required for kinetochore recruitment and chromosome segregation in eukaryotes. To perform this role, centro-chromatin adopts a unique structure that provides access to kinetochore proteins and maintains stability under tension during mitosis. This is achieved by the presence of nucleosomes containing the H3 variant CENP-A, which also acts as the epigenetic mark defining the centromere. In this review, we discuss the role of CENP-A on the structure and dynamics of centromeric chromatin. We further discuss the impact of the CENP-A binding proteins CENP-C, CENP-N, and CENP-B on modulating centro-chromatin structure. Based on these findings we provide an overview of the higher order structure of the centromere.
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Affiliation(s)
- Harsh Nagpal
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Beat Fierz
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
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Gomes TF, Lima AM, Marques APP, da Silva LC. Effects of fluoride emission on the morphoanatomy of three plant species endemics to Brazil using passive biomonitoring. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:10.1007/s11356-021-13017-2. [PMID: 33638070 DOI: 10.1007/s11356-021-13017-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 02/15/2021] [Indexed: 06/12/2023]
Abstract
Fluoride is the most phytotoxic atmospheric pollutant. The objective of this study was to evaluate the effects of fluoride emissions by an aluminum smelter on three plant species endemics to Brazil, located at Parque Estadual do Itacolomi (PEI). The monitored species were Byrsonima variabilis (Malpighiaceae), Myrceugenia alpigena (Myrtaceae), and Eremanthus erythropappus (Asteraceae), which were monitored during 9 months using passive biomonitoring at five different locations with different distances from the smelter. The monitored species did not show macroscopic phytotoxicity damage to fluoride; however, they did show microscopic damage. The species closer to the smelter presented more severe anatomic damages, such as rupture of cell walls, protoplast retraction, and trichome alterations. Damaged stomatal ledges, flaking epicuticular wax, and damages to trichomes were observed. M. alpigena showed a higher accumulation of fluoride than the other species at all monitored sites. The test for cell death with Evans Blue was positive for the three studied species. Through biomonitoring in the PEI, we concluded that the emissions from the aluminum smelter affect the native vegetation and that due to the greater accumulation of fluoride and the diversity of microscopic damage in M. alpigena, the use of this species in the monitoring of environments polluted by fluoride is enhanced.
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Affiliation(s)
- Thamires Fernanda Gomes
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Av. P.H. Rolfs, s/n, Campus Universitário, Vicosa, MG, 36570-900, Brazil
| | - Ademir Martins Lima
- Departamento de Agronomia, Universidade Federal de Viçosa, Av. P.H. Rolfs, s/n, Campus Universitário, Vicosa, MG, 36570-900, Brazil
| | - Ana Paula Pires Marques
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Av. P.H. Rolfs, s/n, Campus Universitário, Vicosa, MG, 36570-900, Brazil
| | - Luzimar Campos da Silva
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Av. P.H. Rolfs, s/n, Campus Universitário, Vicosa, MG, 36570-900, Brazil.
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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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Takeuchi S, Kagabu M, Shoji T, Nitta Y, Sugiyama T, Sato J, Nakamura Y. Anti-cancer immunotherapy using cancer-derived multiple epitope-peptides cocktail vaccination clinical studies in patients with refractory/persistent disease of uterine cervical cancer and ovarian cancer [phase 2]. Oncoimmunology 2020; 9:1838189. [PMID: 33235818 PMCID: PMC7671072 DOI: 10.1080/2162402x.2020.1838189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/08/2020] [Accepted: 10/08/2020] [Indexed: 01/04/2023] Open
Abstract
We had conducted phase 1/2 studies of cancer vaccination therapy using neo-tumor antigens in patients with refractory/persistent cervical cancer (CC) and ovarian cancer (OC) to assess the feasibility and efficacy. Enrollees must be refractory/persistent disease for usual treatments with Human Leukocyte Antigen-A*0201 or A*2402. The targets were epitope peptides obtained from driver genes in surviving pathways as follows: for CC A*0201, peptides from Up Regulating Lung Cancer 10 gene (URLC10) and Hypoxia-inducible gene 2 (HIG-2) and for OC A*0201, HIG2, VEGFR (vascular epithelial growth factor receptor) 1 and 2 were used. For CC A*2402, Forkhead Box M1 (FOXM1), Maternal Embryonic Leucine zipper Kinase (MELK), and Holliday Junction Recognition Protein (HJURP) were used. For OC A*2402, cocktails of peptides from FOXM1, MELK, HJURP, VEGFR1, and VEGFR2 were used. Subcutaneous administration was performed with adjuvant weekly. The toxicity profiles and tumor-response were analyzed in eight-week interval. Sixty-six patients were accrued, and 64 were evaluable for adverse events (AEs), and 35 for response. AEs of G2/3 dermatologic reaction (DR) of injection site had been identified in 15.6% and no other severe AEs were detected. Response rate in OC and CC were 22.9% and 20%, respectively. Median overall survival showed longer in performance status (PS) 0 (versus PS1/2), in CRP negative (versus positive) and in DR positive (versus negative) such as 8.7 m versus 1.2 m (p < .001), 8.8 m versus 3.0 m (p < .05) and 10.2 m versus 1.2 m (p < .001), respectively. In conclusion, our vaccination therapy was feasible and effective in this cohort of patients.
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Affiliation(s)
- Satoshi Takeuchi
- Department of Obstetrics and Gynecology, Iwate Medical University School of Medicine, Yahaba town, Japan
- Division of Gynecologic Oncology, Department of Gynecology, Women Health Care, Kobe Tokushukai Hospital Women’s Cancer Center, Gynecologic Oncology, Kobe, Japan
| | - Masahiro Kagabu
- Department of Obstetrics and Gynecology, Iwate Medical University School of Medicine, Yahaba town, Japan
| | - Tadahiro Shoji
- Department of Obstetrics and Gynecology, Iwate Medical University School of Medicine, Yahaba town, Japan
| | - Yukari Nitta
- Department of Obstetrics and Gynecology, Iwate Medical University School of Medicine, Yahaba town, Japan
| | - Toru Sugiyama
- Department of Obstetrics and Gynecology, Iwate Medical University School of Medicine, Yahaba town, Japan
- Gynecology, St. Mary’s Hospital, Kurume, Japan
| | - Junya Sato
- Department of Obstetrics and Gynecology, Iwate Medical University School of Medicine, Yahaba town, Japan
- Department of Pharmacy, Shizuoka Cancer Center, Tokyo, Japan
| | - Yusuke Nakamura
- Department of Cancer, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Cancer precision Medicine, Cancer Institute Hospital of JFCR (Japanese Foundation for Cancer Research), Tokyo, Japan
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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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41
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Kang DH, Woo J, Kim H, Kim SY, Ji S, Jaygal G, Ahn TS, Kim HJ, Kwak HJ, Kim CJ, Baek MJ, Jeong D. Prognostic Relevance of HJURP Expression in Patients with Surgically Resected Colorectal Cancer. Int J Mol Sci 2020; 21:ijms21217928. [PMID: 33114545 PMCID: PMC7662712 DOI: 10.3390/ijms21217928] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/03/2020] [Accepted: 10/09/2020] [Indexed: 12/12/2022] Open
Abstract
HJURP is a key factor for CENP-A deposition and maintenance in centromeres. The role of mis-regulation of histone chaperones in cancer initiation and progression has been studied. However, its role in colorectal cancer is still unclear. In this study, we aimed to evaluate the expression of HJURP in 162 colorectal cancer tissue. To investigate the function of HJURP in the colorectal cancer cell, we suppressed HJURP expression by siRNA and confirmed proliferation, migration, invasion, and anchorage independent of colony forming ability. The association between HJURP expression levels and clinicopathological factors was evaluated in 162 CRC tissues using immunohistochemistry. The overall survival rate in patients of HJURP high expression was higher than those in HJURP low expression in CRC. Suppressing HJURP expression decreased cellular proliferation, invasion, and migration in four CRC cell lines: HT29, HCT116, SW480, SW620 in vitro study. Our findings revealed that the knockdown of HJURP suppressed the proliferation, migration, invasion, and tumorigenicity in CRC cells. Due to its strong association with CRC, HJURP could be a potential prognostic biomarker and a novel target for drug discovery.
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Affiliation(s)
- Dong Hyun Kang
- Department of Surgery, College of Medicine, Soonchunhyang University, 31 Soonchunhyang 6 gil, Dongnam-gu, Cheonan, Chungcheongnam-do 31151, Korea; (D.H.K.); (T.S.A.); (M.-J.B.)
| | - Jongsoo Woo
- Soonchunhyang Medical Science Research Institute, College of Medicine, Soonchunhyang University 31 Soonchunhyang 6 gil, Dongnam-gu, Cheonan, Chungcheongnam-do 330-722, Korea; (J.W.); (H.K.); (S.Y.K.); (S.J.); (G.J.)
| | - Hyeongjoo Kim
- Soonchunhyang Medical Science Research Institute, College of Medicine, Soonchunhyang University 31 Soonchunhyang 6 gil, Dongnam-gu, Cheonan, Chungcheongnam-do 330-722, Korea; (J.W.); (H.K.); (S.Y.K.); (S.J.); (G.J.)
| | - Soo Youn Kim
- Soonchunhyang Medical Science Research Institute, College of Medicine, Soonchunhyang University 31 Soonchunhyang 6 gil, Dongnam-gu, Cheonan, Chungcheongnam-do 330-722, Korea; (J.W.); (H.K.); (S.Y.K.); (S.J.); (G.J.)
| | - Sanghee Ji
- Soonchunhyang Medical Science Research Institute, College of Medicine, Soonchunhyang University 31 Soonchunhyang 6 gil, Dongnam-gu, Cheonan, Chungcheongnam-do 330-722, Korea; (J.W.); (H.K.); (S.Y.K.); (S.J.); (G.J.)
| | - Gunn Jaygal
- Soonchunhyang Medical Science Research Institute, College of Medicine, Soonchunhyang University 31 Soonchunhyang 6 gil, Dongnam-gu, Cheonan, Chungcheongnam-do 330-722, Korea; (J.W.); (H.K.); (S.Y.K.); (S.J.); (G.J.)
| | - Tae Sung Ahn
- Department of Surgery, College of Medicine, Soonchunhyang University, 31 Soonchunhyang 6 gil, Dongnam-gu, Cheonan, Chungcheongnam-do 31151, Korea; (D.H.K.); (T.S.A.); (M.-J.B.)
| | - Han Jo Kim
- Department of Oncology, College of Medicine, Soonchunhyang University, 31 Soonchunhyang 6 gil, Dongnam-gu, Cheonan, Chungcheongnam-do 31151, Korea;
| | - Hyoung Jong Kwak
- Research Institute of Clinical Medicine, Woori Madi Medical Center, 111 Baekjedae-ro, Wansan-gu, Jeonju, Jeollabuk-do 55082, Korea; (H.J.K.); (C.-J.K.)
| | - Chang-Jin Kim
- Research Institute of Clinical Medicine, Woori Madi Medical Center, 111 Baekjedae-ro, Wansan-gu, Jeonju, Jeollabuk-do 55082, Korea; (H.J.K.); (C.-J.K.)
| | - Moo-Jun Baek
- Department of Surgery, College of Medicine, Soonchunhyang University, 31 Soonchunhyang 6 gil, Dongnam-gu, Cheonan, Chungcheongnam-do 31151, Korea; (D.H.K.); (T.S.A.); (M.-J.B.)
| | - Dongjun Jeong
- Department of Pathology, College of Medicine, Soonchunhyang University, 31 Soonchunhyang 6 gil, Dongnam-gu, Cheonan, Chungcheongnam-do 31151, Korea
- Correspondence: ; Tel.: +82-41-413-5049; Fax: +92-41-570-2546
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Hofstatter PG, Ribeiro GM, Porfírio‐Sousa AL, Lahr DJG. The Sexual Ancestor of all Eukaryotes: A Defense of the “Meiosis Toolkit”. Bioessays 2020; 42:e2000037. [DOI: 10.1002/bies.202000037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/08/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Paulo G. Hofstatter
- Universidade de São Paulo Instituto de Biociencias, Rua do Matão, travessa 14, A101. São Paulo, CEP.: 05508‐090, Brazil
| | - Giulia M. Ribeiro
- Universidade de São Paulo Instituto de Biociencias, Rua do Matão, travessa 14, A101. São Paulo, CEP.: 05508‐090, Brazil
| | - Alfredo L. Porfírio‐Sousa
- Universidade de São Paulo Instituto de Biociencias, Rua do Matão, travessa 14, A101. São Paulo, CEP.: 05508‐090, Brazil
| | - Daniel J. G. Lahr
- Universidade de São Paulo Instituto de Biociencias, Rua do Matão, travessa 14, A101. São Paulo, CEP.: 05508‐090, Brazil
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Nakamura M, Takano A, Thang PM, Tsevegjav B, Zhu M, Yokose T, Yamashita T, Miyagi Y, Daigo Y. Characterization of KIF20A as a prognostic biomarker and therapeutic target for different subtypes of breast cancer. Int J Oncol 2020; 57:277-288. [PMID: 32467984 DOI: 10.3892/ijo.2020.5060] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 03/06/2020] [Indexed: 11/05/2022] Open
Abstract
The aim of the present study was to identify novel prognostic biomarkers and therapeutic targets for breast cancer; thus, genes that are frequently overexpressed in several types of breast cancer were screened. Kinesin family member 20A (KIF20A) was identified as a candidate molecule during this process. Immunohistochemical staining performed using tissue microarrays from 257 samples of different breast cancer subtypes revealed that KIF20A was expressed in 195 (75.9%) of these samples, whereas it was seldom expressed in normal breast tissue. KIF20A protein was expressed in all types of breast cancer observed. However, it was more frequently expressed in human epidermal growth factor receptor 2 (HER2)‑positive and triple‑negative breast cancer than in the luminal type. Moreover, KIF20A expression was significantly associated with the poor prognosis of patients with breast cancer. A multivariate analysis indicated that KIF20A expression was an independent prognostic factor for patients with breast cancer. The suppression of endogenous KIF20A expression using small interfering ribonucleic acids or via treatment with paprotrain, a selective inhibitor of KIF20A, significantly inhibited breast cancer cell growth through cell cycle arrest at the G2/M phase and subsequent mitotic cell death. These results suggest that KIF20A is a candidate prognostic biomarker and therapeutic target for different types of breast cancer.
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Affiliation(s)
- Masako Nakamura
- Department of Medical Oncology and Cancer Center, Shiga University of Medical Science, Otsu, Shiga 520‑2192, Japan
| | - Atsushi Takano
- Department of Medical Oncology and Cancer Center, Shiga University of Medical Science, Otsu, Shiga 520‑2192, Japan
| | - Phung Manh Thang
- Department of Medical Oncology and Cancer Center, Shiga University of Medical Science, Otsu, Shiga 520‑2192, Japan
| | - Bayarbat Tsevegjav
- Department of Medical Oncology and Cancer Center, Shiga University of Medical Science, Otsu, Shiga 520‑2192, Japan
| | - Ming Zhu
- Department of Medical Oncology and Cancer Center, Shiga University of Medical Science, Otsu, Shiga 520‑2192, Japan
| | - Tomoyuki Yokose
- Department of Pathology, Kanagawa Cancer Center, Yokohama, Kanagawa 241‑8515, Japan
| | - Toshinari Yamashita
- Department of Breast and Endocrine Surgery, Kanagawa Cancer Center, Yokohama, Kanagawa 241‑8515, Japan
| | - Yohei Miyagi
- Molecular Pathology and Genetics Division, Kanagawa Cancer Center Research Institute, Yokohama, Kanagawa 241‑8515, Japan
| | - Yataro Daigo
- Department of Medical Oncology and Cancer Center, Shiga University of Medical Science, Otsu, Shiga 520‑2192, Japan
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Wen Y, Chen J, Li J, Arif W, Kalsotra A, Irudayaraj J. Effect of PFOA on DNA Methylation and Alternative Splicing in Mouse Liver. Toxicol Lett 2020; 329:38-46. [PMID: 32320774 DOI: 10.1016/j.toxlet.2020.04.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 03/13/2020] [Accepted: 04/16/2020] [Indexed: 02/07/2023]
Abstract
Perfluorooctanoic acid (PFOA) is a persistent organic pollutant prevalent in the environment and implicated in damage to the liver leading to a fatty liver phenotype called hepatocellular steatosis. Our goal is to provide a basis for PFOA-induced hepatocellular steatosis in relation to epigenetic alterations and mRNA splicing. Young adult female mice exposed to different concentrations of PFOA showed an increase in liver weight with decreased global DNA methylation (5-mC). At higher concentrations, the expression of DNA methyltransferase 3A (Dnmt3a) was significantly reduced and the expression of tet methycytosine dioxygenase 1 (Tet1) was significantly increased. There was no significant change in the other Dnmts and Tets. PFOA exposure significantly increased the expression of cell cycle regulators and anti-apoptotic genes. The expression of multiple genes involved in mTOR (mammalian target of rapamycin) signaling pathway were altered significantly with reduction in Pten (phosphatase and tensin homolog, primary inhibitor of mTOR pathway) expression. Multiple splicing factors whose protein but not mRNA levels affected by PFOA exposure were identified. The changes in protein abundance of the splicing factors was also reflected in altered splicing pattern of their target genes, which provided new insights on the previously unexplored mechanisms of PFOA-mediated hepatotoxicity and pathogenesis.
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Affiliation(s)
- Yi Wen
- Department of Bioengineering. University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Biomedical Research Center in Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, IL 61801, USA; Cancer Center at Illinois (CCIL), University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jackie Chen
- Department of Biochemistry, School of Molecular and Cell Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Junya Li
- Department of Biochemistry, School of Molecular and Cell Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Waqar Arif
- Department of Biochemistry, School of Molecular and Cell Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Auinash Kalsotra
- Department of Biochemistry, School of Molecular and Cell Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Cancer Center at Illinois (CCIL), University of Illinois at Urbana-Champaign, Urbana, IL, USA; Carl R. Woese Institute of Genomic Biology, University of Illinois, Urbana-Champaign, Illinois, USA
| | - Joseph Irudayaraj
- Department of Bioengineering. University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Biomedical Research Center in Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, IL 61801, USA; Micro and Nanotechnology Laboratory. University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA; Cancer Center at Illinois (CCIL), University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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Medina‐Pritchard B, Lazou V, Zou J, Byron O, Abad MA, Rappsilber J, Heun P, Jeyaprakash AA. Structural basis for centromere maintenance by Drosophila CENP-A chaperone CAL1. EMBO J 2020; 39:e103234. [PMID: 32134144 PMCID: PMC7110144 DOI: 10.15252/embj.2019103234] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 01/25/2020] [Accepted: 02/11/2020] [Indexed: 01/08/2023] Open
Abstract
Centromeres are microtubule attachment sites on chromosomes defined by the enrichment of histone variant CENP-A-containing nucleosomes. To preserve centromere identity, CENP-A must be escorted to centromeres by a CENP-A-specific chaperone for deposition. Despite this essential requirement, many eukaryotes differ in the composition of players involved in centromere maintenance, highlighting the plasticity of this process. In humans, CENP-A recognition and centromere targeting are achieved by HJURP and the Mis18 complex, respectively. Using X-ray crystallography, we here show how Drosophila CAL1, an evolutionarily distinct CENP-A histone chaperone, binds both CENP-A and the centromere receptor CENP-C without the requirement for the Mis18 complex. While an N-terminal CAL1 fragment wraps around CENP-A/H4 through multiple physical contacts, a C-terminal CAL1 fragment directly binds a CENP-C cupin domain dimer. Although divergent at the primary structure level, CAL1 thus binds CENP-A/H4 using evolutionarily conserved and adaptive structural principles. The CAL1 binding site on CENP-C is strategically positioned near the cupin dimerisation interface, restricting binding to just one CAL1 molecule per CENP-C dimer. Overall, by demonstrating how CAL1 binds CENP-A/H4 and CENP-C, we provide key insights into the minimalistic principles underlying centromere maintenance.
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Affiliation(s)
| | - Vasiliki Lazou
- Wellcome Centre for Cell BiologyUniversity of EdinburghEdinburghUK
| | - Juan Zou
- Wellcome Centre for Cell BiologyUniversity of EdinburghEdinburghUK
| | - Olwyn Byron
- School of Life SciencesUniversity of GlasgowGlasgowUK
| | - Maria A Abad
- Wellcome Centre for Cell BiologyUniversity of EdinburghEdinburghUK
| | - Juri Rappsilber
- Wellcome Centre for Cell BiologyUniversity of EdinburghEdinburghUK,Institute of BiotechnologyTechnische Universität BerlinBerlinGermany
| | - Patrick Heun
- Wellcome Centre for Cell BiologyUniversity of EdinburghEdinburghUK
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Nandy D, Rajam SM, Dutta D. A three layered histone epigenetics in breast cancer metastasis. Cell Biosci 2020; 10:52. [PMID: 32257110 PMCID: PMC7106732 DOI: 10.1186/s13578-020-00415-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 03/26/2020] [Indexed: 12/13/2022] Open
Abstract
Thanks to the advancement in science and technology and a significant number of cancer research programs being carried out throughout the world, the prevention, prognosis and treatment of breast cancer are improving with a positive and steady pace. However, a stern thoughtful attention is required for the metastatic breast cancer cases—the deadliest of all types of breast cancer, with a character of relapse even when treated. In an effort to explore the less travelled avenues, we summarize here studies underlying the aspects of histone epigenetics in breast cancer metastasis. Authoritative reviews on breast cancer epigenetics are already available; however, there is an urgent need to focus on the epigenetics involved in metastatic character of this cancer. Here we put forward a comprehensive review on how different layers of histone epigenetics comprising of histone chaperones, histone variants and histone modifications interplay to create breast cancer metastasis landscape. Finally, we propose a hypothesis of integrating histone-epigenetic factors as biomarkers that encompass different breast cancer subtypes and hence could be exploited as a target of larger population.
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Affiliation(s)
- Debparna Nandy
- Regenerative Biology Program, Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Poojappura, Thiruvananthapuram, Kerala 695014 India
| | - Sruthy Manuraj Rajam
- Regenerative Biology Program, Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Poojappura, Thiruvananthapuram, Kerala 695014 India
| | - Debasree Dutta
- Regenerative Biology Program, Rajiv Gandhi Centre for Biotechnology, Thycaud PO, Poojappura, Thiruvananthapuram, Kerala 695014 India
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47
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Hori T, Fukagawa T. Artificial generation of centromeres and kinetochores to understand their structure and function. Exp Cell Res 2020; 389:111898. [PMID: 32035949 DOI: 10.1016/j.yexcr.2020.111898] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/18/2020] [Accepted: 02/05/2020] [Indexed: 01/19/2023]
Abstract
The centromere is an essential genomic region that provides the surface to form the kinetochore, which binds to the spindle microtubes to mediate chromosome segregation during mitosis and meiosis. Centromeres of most organisms possess highly repetitive sequences, making it difficult to study these loci. However, an unusual centromere called a "neocentromere," which does not contain repetitive sequences, was discovered in a patient and can be generated experimentally. Recent advances in genome biology techniques allow us to analyze centromeric chromatin using neocentromeres. In addition to neocentromeres, artificial kinetochores have been generated on non-centromeric loci, using protein tethering systems. These are powerful tools to understand the mechanism of the centromere specification and kinetochore assembly. In this review, we introduce recent studies utilizing the neocentromeres and artificial kinetochores and discuss current problems in centromere biology.
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Affiliation(s)
- Tetsuya Hori
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan.
| | - Tatsuo Fukagawa
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, 565-0871, Japan.
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48
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Talbert PB, Henikoff S. What makes a centromere? Exp Cell Res 2020; 389:111895. [PMID: 32035948 DOI: 10.1016/j.yexcr.2020.111895] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 01/18/2020] [Accepted: 02/05/2020] [Indexed: 12/26/2022]
Abstract
Centromeres are the eukaryotic chromosomal sites at which the kinetochore forms and attaches to spindle microtubules to orchestrate chromosomal segregation in mitosis and meiosis. Although centromeres are essential for cell division, their sequences are not conserved and evolve rapidly. Centromeres vary dramatically in size and organization. Here we categorize their diversity and explore the evolutionary forces shaping them. Nearly all centromeres favor AT-rich DNA that is gene-free and transcribed at a very low level. Repair of frequent centromere-proximal breaks probably contributes to their rapid sequence evolution. Point centromeres are only ~125 bp and are specified by common protein-binding motifs, whereas short regional centromeres are 1-5 kb, typically have unique sequences, and may have pericentromeric repeats adapted to facilitate centromere clustering. Transposon-rich centromeres are often ~100-300 kb and are favored by RNAi machinery that silences transposons, by suppression of meiotic crossovers at centromeres, and by the ability of some transposons to target centromeres. Megabase-length satellite centromeres arise in plants and animals with asymmetric female meiosis that creates centromere competition, and favors satellite monomers one or two nucleosomes in length that position and stabilize centromeric nucleosomes. Holocentromeres encompass the length of a chromosome and may differ dramatically between mitosis and meiosis. We propose a model in which low level transcription of centromeres facilitates the formation of non-B DNA that specifies centromeres and promotes loading of centromeric nucleosomes.
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Affiliation(s)
- Paul B Talbert
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
| | - Steven Henikoff
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA.
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Sousa JFD, Serafim RB, Freitas LMD, Fontana CR, Valente V. DNA repair genes in astrocytoma tumorigenesis, progression and therapy resistance. Genet Mol Biol 2019; 43:e20190066. [PMID: 31930277 PMCID: PMC7198033 DOI: 10.1590/1678-4685-gmb-2019-0066] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 07/21/2019] [Indexed: 12/26/2022] Open
Abstract
Glioblastoma (GBM) is the most common and malignant type of primary brain tumor,
showing rapid development and resistance to therapies. On average, patients
survive 14.6 months after diagnosis and less than 5% survive five years or more.
Several pieces of evidence have suggested that the DNA damage signaling and
repair activities are directly correlated with GBM phenotype and exhibit
opposite functions in cancer establishment and progression. The functions of
these pathways appear to present a dual role in tumorigenesis and cancer
progression. Activation and/or overexpression of ATRX, ATM and RAD51 genes were
extensively characterized as barriers for GBM initiation, but paradoxically the
exacerbated activity of these genes was further associated with cancer
progression to more aggressive stages. Excessive amounts of other DNA repair
proteins, namely HJURP, EXO1, NEIL3, BRCA2, and BRIP, have also been connected
to proliferative competence, resistance and poor prognosis. This scenario
suggests that these networks help tumor cells to manage replicative stress and
treatment-induced damage, diminishing genome instability and conferring therapy
resistance. Finally, in this review we address promising new drugs and
therapeutic approaches with potential to improve patient survival. However,
despite all technological advances, the prognosis is still dismal and further
research is needed to dissect such complex mechanisms.
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Affiliation(s)
- Juliana Ferreira de Sousa
- Radiation Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, U.S.A
| | - Rodolfo Bortolozo Serafim
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Laura Marise de Freitas
- Universidade de São Paulo, Instituto de Química, Departamento de Bioquímica, São Paulo, SP, Brazil
| | - Carla Raquel Fontana
- Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP), Faculdade de Ciências Farmacêuticas, Departamento de Análises Clínicas, Araraquara, SP, Brazil
| | - Valeria Valente
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.,Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP), Faculdade de Ciências Farmacêuticas, Departamento de Análises Clínicas, Araraquara, SP, Brazil.,Centro de Terapia Celular (CEPID-FAPESP), Ribeirão Preto, SP, Brazil
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50
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Chen YF, Liang YX, Yang JA, Yuan DZ, Li J, Zheng SS, Wan YP, Wang B, Han ZD, Zhong WD. Upregulation of Holliday junction recognition protein predicts poor prognosis and biochemical recurrence in patients with prostate cancer. Oncol Lett 2019; 18:6697-6703. [PMID: 31814851 PMCID: PMC6888104 DOI: 10.3892/ol.2019.11061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 09/26/2019] [Indexed: 12/16/2022] Open
Abstract
Abnormal expression of Holliday junction recognition protein (HJURP) in several types of tumor cells plays a vital role in the formation and progression of tumors. Few studies have investigated the role of HJURP in prostate cancer (PCa). The aim of this study was to analyze the expression levels of HJURP in PCa and to establish the association with clinicopathological data. Reverse transcription quantitative polymerase chain reaction and immunohistochemical analysis were used to detect the expression levels of HJURP in benign and PCa prostate tissues. The Taylor dataset was statistically analyzed to determine if HJURP expression levels were associated with PCa clinicopathological data. HJURP was overexpressed in PCa tissues compared with benign prostate tissues. Statistical analysis of the Taylor dataset indicated that upregulation of HJURP was significantly associated with positive prostate-specific antigen (PSA) levels (P=0.004), high Gleason score (P=0.005), advanced pathological stage (P=0.007), metastasis (P<0.001) and PSA failure (P<0.001). Higher HJURP mRNA expression levels were significantly associated with shorter biochemical recurrence (BCR)-free survival (P<0.001). To the best of our knowledge, this study is the first report of HJURP upregulation in PCa tissues. Upregulation of HJURP may predict BCR-free survival and HJURP may be an oncogene that impacts the prognosis of patients with PCa.
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Affiliation(s)
- Yan-Fei Chen
- Department of Urology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, Guangdong 510095, P.R. China
| | - Yu-Xiang Liang
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, P.R. China
| | - Jian-An Yang
- Department of Urology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, Guangdong 510095, P.R. China
| | - Dao-Zhang Yuan
- Department of Urology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, Guangdong 510095, P.R. China
| | - Jing Li
- Department of Urology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, Guangdong 510095, P.R. China
| | - Shun-Sheng Zheng
- Department of Urology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, Guangdong 510095, P.R. China
| | - Yue-Ping Wan
- Department of Urology, Huadu District People's Hospital, Southern Medical University, Guangzhou, Guangdong 510180, P.R. China
| | - Bin Wang
- Department of Urology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, Guangdong 510095, P.R. China
| | - Zhao-Dong Han
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, P.R. China
| | - Wei-De Zhong
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510180, P.R. China.,Department of Urology, The Second Affiliated Hospital, South China University of Technology, Guangzhou, Guangdong 510180, P.R. China
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