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Xiao X, Zhang Z, Luo R, Peng R, Sun Y, Wang J, Chen X. Identification of potential oncogenes in triple-negative breast cancer based on bioinformatics analyses. Oncol Lett 2021; 21:363. [PMID: 33747220 PMCID: PMC7967975 DOI: 10.3892/ol.2021.12624] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 02/02/2021] [Indexed: 12/28/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is a subtype with high rates of metastasis, poor prognosis and limited therapeutic options. The present study aimed to identify the potential pivotal genes for prognosis and treatment in TNBC. A total of two microarray expression datasets, GSE38959 and GSE65212, were downloaded from the Gene Expression Omnibus database, and RNA-sequencing data of breast cancer from The Cancer Genome Atlas database were analyzed to screen out differentially expressed genes (DEGs) between TNBC tissues and normal tissues. The intersection of DEGs was submitted to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses. A protein-protein interaction (PPI) network was constructed and visualized using Cytoscape software. Furthermore, module, centrality and survival analyses were performed to identify the potential hub genes. Reverse transcription-quantitative (RT-q)PCR analysis was performed to detect the expression levels of key genes in TNBC samples, and 377 DEGs were identified. Functional analysis revealed that the DEGs were significantly involved in cell cycle process, nuclear division and the p53 signaling pathway. A PPI network was constructed with these DEGs, and 66 core genes with high centrality features in module 1 were selected. Relapse-free survival analysis confirmed that high expression levels of five genes [cyclin B1 (CCNB1), GINS complex subunit 2, non-SMC condensin I complex subunit G (NCAPG), minichromosome maintenance 4 (MCM4) and ribonucleotide reductase regulatory subunit M2 (RRM2)] were significantly associated with poor prognosis in TNBC. RT-qPCR analysis demonstrated that CCNB1, NCAPG, MCM4 and RRM2 were significantly upregulated in 25 TNBC tissues compared with adjacent normal breast tissues. Furthermore, gene set enrichment analysis revealed that CCNB1, NCAPG, MCM4 and RRM2 were closely associated with tumor proliferation. Taken together, these results suggest that CCNB1, NCAPG, MCM4 and RRM2 are associated with tumorigenesis and TNBC progression, and thus may act as promising prognostic biomarkers and therapeutic targets for TNBC.
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Affiliation(s)
- Xiao Xiao
- Department of Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400010, P.R. China
| | - Zheng Zhang
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Ruihan Luo
- Department of Bioinformatics, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Rui Peng
- Department of Bioinformatics, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Yan Sun
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Jia Wang
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing 400016, P.R. China
| | - Xin Chen
- Department of Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400010, P.R. China
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Liang Z, Zhang Y, Chen Q, Hao J, Wang H, Li Y, Yan Y. Analysis of MCM Proteins' Role as a Potential Target of Statins in Patients with Acute Type A Aortic Dissection through Bioinformatics. Genes (Basel) 2021; 12:genes12030387. [PMID: 33803192 PMCID: PMC7998850 DOI: 10.3390/genes12030387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 02/27/2021] [Accepted: 03/02/2021] [Indexed: 11/18/2022] Open
Abstract
Acute aortic dissection is one of the most severe vascular diseases. The molecular mechanisms of aortic expansion and dissection are unclear. Clinical studies have found that statins play a protective role in aortic dissection development and therapy; however, the mechanism of statins’ effects on the aorta is unknown. The Gene Expression Omnibus (GEO) dataset GSE52093, GSE2450and GSE8686 were analyzed, and genes expressed differentially between aortic dissection samples and normal samples were determined using the Networkanalyst and iDEP tools. Weight gene correlation network analysis (WGCNA), functional annotation, pathway enrichment analysis, and the analysis of the regional variations of genomic features were then performed. We found that the minichromosome maintenance proteins (MCMs), a family of proteins targeted by statins, were upregulated in dissected aortic wall tissues and play a central role in cell-cycle and mitosis regulation in aortic dissection patients. Our results indicate a potential molecular target and mechanism for statins’ effects in patients with acute type A aortic dissection.
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Calaf GM, Bleak TC, Roy D. Signs of carcinogenicity induced by parathion, malathion, and estrogen in human breast epithelial cells (Review). Oncol Rep 2021; 45:24. [PMID: 33649804 PMCID: PMC7905528 DOI: 10.3892/or.2021.7975] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 01/29/2021] [Indexed: 02/07/2023] Open
Abstract
Cancer development is a multistep process that may be induced by a variety of compounds. Environmental substances, such as pesticides, have been associated with different human diseases. Organophosphorus pesticides (OPs) are among the most commonly used insecticides. Despite the fact that organophosphorus has been associated with an increased risk of cancer, particularly hormone-mediated cancer, few prospective studies have examined the use of individual insecticides. Reported results have demonstrated that OPs and estrogen induce a cascade of events indicative of the transformation of human breast epithelial cells. In vitro studies analyzing an immortalized non-tumorigenic human breast epithelial cell line may provide us with an approach to analyzing cell transformation under the effects of OPs in the presence of estrogen. The results suggested hormone-mediated effects of these insecticides on the risk of cancer among women. It can be concluded that, through experimental models, the initiation of cancer can be studied by analyzing the steps that transform normal breast cells to malignant ones through certain substances, such as pesticides and estrogen. Such substances cause genomic instability, and therefore tumor formation in the animal, and signs of carcinogenesis in vitro. Cancer initiation has been associated with an increase in genomic instability, indicated by the inactivation of tumor-suppressor genes and activation of oncogenes in the presence of malathion, parathion, and estrogen. In the present study, a comprehensive summary of the impact of OPs in human and rat breast cancer, specifically their effects on the cell cycle, signaling pathways linked to epidermal growth factor, drug metabolism, and genomic instability in an MCF-10F estrogen receptor-negative breast cell line is provided.
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Affiliation(s)
- Gloria M Calaf
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica 1000000, Chile
| | - Tammy C Bleak
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica 1000000, Chile
| | - Debasish Roy
- Department of Natural Sciences, Hostos Community College of The City University of New York, Bronx, NY 10451, USA
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Wolfs JRE, Hermans TJN, Koldewijn EL, van de Kerkhof D. Novel urinary biomarkers ADXBLADDER and bladder EpiCheck for diagnostics of bladder cancer: A review. Urol Oncol 2021; 39:161-170. [DOI: 10.1016/j.urolonc.2020.11.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/02/2020] [Accepted: 11/09/2020] [Indexed: 10/22/2022]
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He Y, Yin X, Dong J, Yang Q, Wu Y, Gong Z. Transcriptome Analysis of Caco-2 Cells upon the Exposure of Mycotoxin Deoxynivalenol and Its Acetylated Derivatives. Toxins (Basel) 2021; 13:167. [PMID: 33671637 PMCID: PMC7927021 DOI: 10.3390/toxins13020167] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/16/2021] [Accepted: 02/19/2021] [Indexed: 11/17/2022] Open
Abstract
Deoxynivalenol (DON), 3-acetyldeoxynivalenol (3-ADON) and 15-acetyldeoxynivalenol (15-ADON) are type B trichothecenes; one of the major pollutants in food and feed products. Although the toxicity of DON has been well documented, information on the toxicity of its acetylated derivative remains incomplete. To acquire more detailed insight into 3-ADON and 15-ADON, Caco-2 cells under 0.5 µM DON, 3-ADON and 15-ADON treatment for 24 h were subjected to RNA-seq analysis. In the present study, 2656, 3132 and 2425 differentially expressed genes (DEGs) were selected, respectively, and were enriched utilizing the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Gene Ontology (GO) database. The upregulation of ataxia-telangiectasia mutated kinase (ATM), WEE1 homolog 2 (WEE2) and downregulation of proliferating cell nuclear antigen (PCNA), minichromosome maintenance (MCMs), cyclin dependent kinase (CDKs), and E2Fs indicate that the three toxins induced DNA damage, inhibition of DNA replication and cell cycle arrest in Caco-2 cells. Additionally, the upregulation of sestrin (SENEs) and NEIL1 implied that the reason for DNA damage may be attributable to oxidative stress. Our study provides insight into the toxic mechanism of 3-ADON and 15-ADON.
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Affiliation(s)
- Yuyun He
- Key Laboratory for Deep Processing of Major Grain and Oil of Ministry of Education, Wuhan Polytechnic University, Wuhan 430023, China; (Y.H.); (X.Y.); (J.D.); (Q.Y.)
| | - Xiaoyao Yin
- Key Laboratory for Deep Processing of Major Grain and Oil of Ministry of Education, Wuhan Polytechnic University, Wuhan 430023, China; (Y.H.); (X.Y.); (J.D.); (Q.Y.)
| | - Jingjing Dong
- Key Laboratory for Deep Processing of Major Grain and Oil of Ministry of Education, Wuhan Polytechnic University, Wuhan 430023, China; (Y.H.); (X.Y.); (J.D.); (Q.Y.)
| | - Qing Yang
- Key Laboratory for Deep Processing of Major Grain and Oil of Ministry of Education, Wuhan Polytechnic University, Wuhan 430023, China; (Y.H.); (X.Y.); (J.D.); (Q.Y.)
| | - Yongning Wu
- China National Center for Food Safety Risk Assessment, NHC Key Laboratory of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of Chinese Academy of Medical Science, Beijing 100000, China;
| | - Zhiyong Gong
- Key Laboratory for Deep Processing of Major Grain and Oil of Ministry of Education, Wuhan Polytechnic University, Wuhan 430023, China; (Y.H.); (X.Y.); (J.D.); (Q.Y.)
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Zeng T, Guan Y, Li YK, Wu Q, Tang XJ, Zeng X, Ling H, Zou J. The DNA replication regulator MCM6: An emerging cancer biomarker and target. Clin Chim Acta 2021; 517:92-98. [PMID: 33609557 DOI: 10.1016/j.cca.2021.02.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/01/2021] [Accepted: 02/05/2021] [Indexed: 01/07/2023]
Abstract
MCM6 is a significant DNA replication regulator that plays a crucial role in sustaining the cell cycle. In many cancer cells, MCM6 expression is enhanced. For example, persistently increased expression of MCM6 promotes the formation, development and progression of hepatocellular carcinoma (HCC). Up- and down-regulation studies have indicated that MCM6 regulates cell cycle, proliferation, metastasis, immune response and the maintenance of the DNA replication system. MCM6 can also regulate downstream signaling such as MEK/ERK thus promoting carcinogenesis. Accordingly, MCM6 may represent a sensitive and specific biomarker to predict adverse progression and poor outcome. Furthermore, inhibition of MCM6 may be an effective cancer treatment. The present review summarizes the latest results on the inactivating and activating functions of MCM6, underlining its function in carcinogenesis. Further studies of the carcinogenic functions of MCM6 may provide novel insight into cancer biology and shed light on new approaches for cancer diagnosis and treatment.
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Affiliation(s)
- Tian Zeng
- Hunan Province Key Laboratory of Tumor Cellular & Molecular Pathology, Cancer Research Institute, University of South China, Hengyang, Hunan 421001, PR China
| | - Yang Guan
- Jiangxi University of Traditional Chinese Medicine, Nanchang, Jiangxi 330000, PR China
| | - Yu-Kun Li
- Hunan Province Key Laboratory of Tumor Cellular & Molecular Pathology, Cancer Research Institute, University of South China, Hengyang, Hunan 421001, PR China
| | - Qing Wu
- Department of Digestive Medical, The Affiliated Nanhua Hospital, University of South China, Hengyang 421002, PR China
| | - Xiao-Jun Tang
- Department of Spinal Surgery, The Second Affiliated Hospital of University of South China, Hengyang, Hunan 421001, PR China
| | - Xin Zeng
- Department of Histology and Embryology, Chongqing Three Gorges Medical College, Wanzhou, Chongqing 404000, PR China
| | - Hui Ling
- Hunan Province Key Laboratory of Tumor Cellular & Molecular Pathology, Cancer Research Institute, University of South China, Hengyang, Hunan 421001, PR China.
| | - Juan Zou
- Hunan Province Key Laboratory of Tumor Cellular & Molecular Pathology, Cancer Research Institute, University of South China, Hengyang, Hunan 421001, PR China.
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Guo R, Li J, Chen C, Xiao M, Liao M, Hu Y, Liu Y, Li D, Zou J, Sun D, Torre V, Zhang Q, Chai R, Tang M. Biomimetic 3D bacterial cellulose-graphene foam hybrid scaffold regulates neural stem cell proliferation and differentiation. Colloids Surf B Biointerfaces 2021; 200:111590. [PMID: 33529926 DOI: 10.1016/j.colsurfb.2021.111590] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/29/2020] [Accepted: 01/22/2021] [Indexed: 01/09/2023]
Abstract
Neural stem cell (NSC)-based therapy is a promising candidate for treating neurodegenerative diseases and the preclinical researches call an urgent need for regulating the growth and differentiation of such cells. The recognition that three-dimensional culture has the potential to be a biologically significant system has stimulated an extraordinary impetus for scientific researches in tissue engineering and regenerative medicine. Here, A novel scaffold for culturing NSCs, three-dimensional bacterial cellulose-graphene foam (3D-BC/G), which was prepared via in situ bacterial cellulose interfacial polymerization on the skeleton surface of porous graphene foam has been reported. 3D-BC/G not only supports NSC growth and adhesion, but also maintains NSC stemness and enhances their proliferative capacity. Further phenotypic analysis indicated that 3D-BC/G induces NSCs to selectively differentiate into neurons, forming a neural network in a short amount of time. The scaffold has good biocompatibility with primary cortical neurons enhancing the neuronal network activities. To explore the underlying mechanisms, RNA-Seq analysis to identify genes and signaling pathways was performed and it suggests that 3D-BC/G offers a more promising three-dimensional conductive substrate for NSC research and neural tissue engineering, and the repertoire of gene expression serves as a basis for further studies to better understand NSC biology.
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Affiliation(s)
- Rongrong Guo
- School of Radiation Medicine and Protection and School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Medical College of Soochow University, Suzhou, Jiangsu, 215123, China; Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China; Key Laboratory for Developmental Genes and Human Disease, Ministry of Education, School of Life Sciences and Technology, Southeast University, Nanjing, 210096, China; Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China
| | - Jian Li
- Key Laboratory for Developmental Genes and Human Disease, Ministry of Education, School of Life Sciences and Technology, Southeast University, Nanjing, 210096, China
| | - Chuntao Chen
- Institute of Chemicobiology and Functional Materials, Key Laboratory for Soft Chemistry and Functional Materials of Ministry Education, School of Chemical Engineering, Nanjing University of Science and Technology, 200 Xiao Ling Wei Street, Nanjing, 210094, Jiangsu Province, China
| | - Miao Xiao
- Institute for Cardiovascular Science & Department of Cardiovascular Surgery of the First Affiliated Hospital, Medical College, Soochow University, Suzhou, 215000, China; International School for Advanced Studies (SISSA), via Bonomea 265, Trieste, 34136, Italy
| | - Menghui Liao
- Key Laboratory for Developmental Genes and Human Disease, Ministry of Education, School of Life Sciences and Technology, Southeast University, Nanjing, 210096, China; Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China
| | - Yangnan Hu
- Key Laboratory for Developmental Genes and Human Disease, Ministry of Education, School of Life Sciences and Technology, Southeast University, Nanjing, 210096, China; Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China
| | - Yun Liu
- Key Laboratory for Developmental Genes and Human Disease, Ministry of Education, School of Life Sciences and Technology, Southeast University, Nanjing, 210096, China; Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China
| | - Dan Li
- State Key Laboratory of Bioelectronics, School of Life Sciences and Technology, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, Southeast University, Nanjing, 210096, China; Key Laboratory for Developmental Genes and Human Disease, Ministry of Education, School of Life Sciences and Technology, Southeast University, Nanjing, 210096, China
| | - Jun Zou
- Department of Orthopaedic Surgery, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou, Jiangsu, 215006, China
| | - Dongping Sun
- Institute of Chemicobiology and Functional Materials, Key Laboratory for Soft Chemistry and Functional Materials of Ministry Education, School of Chemical Engineering, Nanjing University of Science and Technology, 200 Xiao Ling Wei Street, Nanjing, 210094, Jiangsu Province, China
| | - Vincent Torre
- International School for Advanced Studies (SISSA), via Bonomea 265, Trieste, 34136, Italy
| | - Qi Zhang
- School of Radiation Medicine and Protection and School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Medical College of Soochow University, Suzhou, Jiangsu, 215123, China.
| | - Renjie Chai
- Key Laboratory for Developmental Genes and Human Disease, Ministry of Education, School of Life Sciences and Technology, Southeast University, Nanjing, 210096, China; Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China; Institute for Stem Cell and Regeneration, Chinese Academy of Science, Beijing, China; Beijing Key Laboratory of Neural Regeneration and Repair, Capital Medical University, Beijing, 100069, China.
| | - Mingliang Tang
- Key Laboratory for Developmental Genes and Human Disease, Ministry of Education, School of Life Sciences and Technology, Southeast University, Nanjing, 210096, China; Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001, China; Institute for Cardiovascular Science & Department of Cardiovascular Surgery of the First Affiliated Hospital, Medical College, Soochow University, Suzhou, 215000, China.
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Comparative genomic analysis reveals evolutionary and structural attributes of MCM gene family in Arabidopsis thaliana and Oryza sativa. J Biotechnol 2020; 327:117-132. [PMID: 33373625 DOI: 10.1016/j.jbiotec.2020.12.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 11/16/2020] [Accepted: 12/17/2020] [Indexed: 11/20/2022]
Abstract
The mini-chromosome maintenance (MCM) family, a large and functionally diverse protein family belonging to the AAA+ superfamily, is essential for DNA replication in all eukaryotic organisms. The MCM 2-7 form a hetero-hexameric complex which serves as licensing factor necessary to ensure the proper genomic DNA replication during the S phase of cell cycle. MCM 8-10 are also associated with the DNA replication process though their roles are particularly unclear. In this study, we report an extensive in silico analysis of MCM gene family (MCM 2-10) in Arabidopsis and rice. Comparative analysis of genomic distribution across eukaryotes revealed conservation of core MCMs 2-7 while MCMs 8-10 are absent in some taxa. Domain architecture analysis underlined MCM 2-10 subfamily specific features. Phylogenetic analyses clustered MCMs into 9 clades as per their subfamily. Duplication events are prominent in plant MCM family, however no duplications are observed in Arabidopsis and rice MCMs. Synteny analysis among Arabidopsis thaliana, Oryza sativa, Glycine max and Zea mays MCMs demonstrated orthologous relationships and duplication events. Further, estimation of synonymous and non-synonymous substitution rates illustrated evolution of MCM family under strong constraints. Expression profiling using available microarray data and qRT-PCR revealed differential expression under various stress conditions, hinting at their potential use to develop stress resilient crops. Homology modeling of Arabidopsis and rice MCM 2-7 and detailed comparison with yeast MCMs identified conservation of eukaryotic specific insertions and extensions as compared to archeal MCMs. Protein-protein interaction analysis revealed an extensive network of putative interacting partners mainly involved in DNA replication and repair. The present study provides novel insights into the MCM family in Arabidopsis and rice and identifies unique features, thus opening new perspectives for further targeted analyses.
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Liu M, Jia S, Dong T, Zhao F, Xu T, Yang Q, Gong J, Fang M. Metabolomic and Transcriptomic Analysis of MCF-7 Cells Exposed to 23 Chemicals at Human-Relevant Levels: Estimation of Individual Chemical Contribution to Effects. ENVIRONMENTAL HEALTH PERSPECTIVES 2020; 128:127008. [PMID: 33325755 PMCID: PMC7741182 DOI: 10.1289/ehp6641] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 11/20/2020] [Accepted: 11/20/2020] [Indexed: 05/18/2023]
Abstract
BACKGROUND Humans are constantly being exposed to various xenobiotics at relatively low concentrations. To date, limited evidence is available to ascertain whether a complex xenobiotic mixture at human-relevant levels causes any health effect. Moreover, there is no effective method to pinpoint the contribution of each chemical toward such an effect. OBJECTIVES This study aims to understand the responses of cells to a mixture containing 23 xenobiotics at human-relevant levels and develop a feasible method to decipher the chemical(s) that contribute significantly to the observed effect. METHODS We characterized the metabolome and transcriptome of breast cancer cells (MCF-7) before and after exposure to the mixture at human-relevant levels; preexposure levels were derived from existing large-scale biomonitoring data. A high-throughput metabolomics-based "leave-one-out" method was proposed to understand the relative contribution of each component by comparing the metabolome with and without the particular chemical in the mixture. RESULTS The metabolomic analysis suggested that the mixture altered metabolites associated with cell proliferation and oxidative stress. For the transcriptomes, gene ontology terms and pathways including "cell cycle," "cell proliferation," and "cell division" were significantly altered after mixture exposure. The mixture altered genes associated with pathways such as "genotoxicity" and "nuclear factor erythroid 2-related factor 2 (Nrf2)." Through joint pathways analysis, metabolites and genes were observed to be well-aligned in pyrimidine and purine metabolisms. The leave-one-out results showed that many chemicals made their contributions to specific metabolic pathways. The overall metabolome pattern of the absence of 2,4-dihyroxybenzophenone (DHB) or bisphenol A (BPA) showed great resemblance to controls, suggesting their higher relative contribution to the observed effect. DISCUSSION The omics results showed that exposure to the mixture at human-relevant levels can induce significant in vitro cellular changes. Also, the leave one out method offers an effective approach for deconvoluting the effects of the mixture. https://doi.org/10.1289/EHP6641.
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Affiliation(s)
- Min Liu
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore
- Nanyang Environment & Water Research Institute, Nanyang Technological University, Singapore
| | - Shenglan Jia
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore
- Nanyang Environment & Water Research Institute, Nanyang Technological University, Singapore
| | - Ting Dong
- School of Environment, Jinan University, Guangdong, Guangzhou, P.R. China
| | - Fanrong Zhao
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore
- Nanyang Environment & Water Research Institute, Nanyang Technological University, Singapore
| | - Tengfei Xu
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore
- Nanyang Environment & Water Research Institute, Nanyang Technological University, Singapore
| | - Qin Yang
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore
- Nanyang Environment & Water Research Institute, Nanyang Technological University, Singapore
| | - Jicheng Gong
- College of Environmental Sciences and Engineering, Peking University, Beijing, P.R. China
| | - Mingliang Fang
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore
- Nanyang Environment & Water Research Institute, Nanyang Technological University, Singapore
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Niu Y, Shan L, Gao H, Zhang C, Qian Z, Wang Z, Xu X, Zhang X, Wang J, Ma L, Chen L, Yu Y. Huaier Suppresses the Hepatocellular Carcinoma Cell Cycle by Regulating Minichromosome Maintenance Proteins. Onco Targets Ther 2020; 13:12015-12025. [PMID: 33244243 PMCID: PMC7685376 DOI: 10.2147/ott.s279723] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/07/2020] [Indexed: 12/24/2022] Open
Abstract
Purpose Hepatocellular carcinoma (HCC) is a common malignant tumor with limited treatment. Our previous studies demonstrated that Huaier enhanced chemotherapy sensitivity and restrained HCC proliferation. This study aimed to identify differentially expressed proteins with Huaier treatment in HCC cells, providing molecular targets for future targeted therapy of HCC. Materials and Methods The effects of Huaier on the cell cycle were determined by flow cytometry and Western blot (WB). Xenograft models were used to verify the effects of Huaier on tumor growth. Then, proteomics was performed to identify the potential proteins regulated by Huaier. The enrichment analysis of GO and KEGG was performed for the differentially expressed proteins. Western blot (WB) and immunohistochemistry (IHC) were used to detect the levels of proteins after Huaier treatment. After that the correlation of differentially expressed proteins with pathological stages was analyzed via the GEPIA database. We also analyzed candidate expression after Huaier treatment in HCC cells by WB and qRT-PCR. Furthermore, siRNA was performed to verify the targeted regulation of Huaier on candidate proteins. Results First, the proteomics data showed that a total of 160 proteins were identified as differentially expressed proteins, among which six minichromosome maintenance (MCM) family members were enriched in the tumor-associated pathways after Huaier treatment. Moreover, MCM proteins were highly expressed in HCC and closely correlated with the survival of HCC patients. Finally, we confirmed that MCM proteins were targets of Huaier treatment in HCC cells. Conclusion Huaier treatment was closely associated with the activation and inhibition of cancer-related pathways, and the MCM family was identified as a potential target in the antitumor process of Huaier. This study is helpful in understanding the molecular alterations and clinical relevance of HCC after Huaier treatment, which is beneficial for finding new targets and designing effective chemotherapy regimens for the future treatment of HCC.
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Affiliation(s)
- Yongjie Niu
- Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200071, People's Republic of China
| | - Liang Shan
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, People's Republic of China
| | - Han Gao
- Encephalopathy Department, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200071, People's Republic of China
| | - Congcong Zhang
- Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200071, People's Republic of China
| | - Zijun Qian
- Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200071, People's Republic of China
| | - Zhixian Wang
- Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200071, People's Republic of China
| | - Xin Xu
- Institute for Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China
| | - Xiao Zhang
- Institute for Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China
| | - Jiayi Wang
- Institute for Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China
| | - Lifang Ma
- Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200071, People's Republic of China.,Institute for Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China
| | - Liyun Chen
- Institute of Science, Technology and Humanities of Shanghai University of Traditional Chinese Medicine, Shanghai 200071, People's Republic of China
| | - Yongchun Yu
- Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200071, People's Republic of China.,Institute for Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China
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Huang B, Lin M, Lu L, Chen W, Tan J, Zhao J, Cao Z, Zhu X, Lin J. Identification of mini-chromosome maintenance 8 as a potential prognostic marker and its effects on proliferation and apoptosis in gastric cancer. J Cell Mol Med 2020; 24:14415-14425. [PMID: 33155430 PMCID: PMC7753872 DOI: 10.1111/jcmm.16062] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 10/06/2020] [Accepted: 10/19/2020] [Indexed: 12/11/2022] Open
Abstract
Mini‐chromosome maintenance (MCM) proteins play important roles in initiating eukaryotic genome replication. The MCM family of proteins includes several members associated with the development and progression of certain cancers. We performed online data mining to assess the expression of MCMs in gastric cancer (GC) and the correlation between their expression and survival in patients with GC. Notably, MCM8 expression was undoubtedly up‐regulated in GC, and higher expression correlated with shorter overall survival (OS) and progression‐free survival (PFS) in patients with GC. However, the role of MCM8 in GC has not been previously explored. Our in vitro experiments revealed that MCM8 knockdown inhibited cell growth and metastasis. Moreover, MCM8 knockdown induced apoptosis. Mechanistically, the expression levels of Bax and cleaved caspase‐3 were increased, whereas Bcl‐2 expression decreased. Additionally, we demonstrated that MCM8 knockdown suppressed tumorigenesis in vivo. Overall, these results suggest that MCM8 plays a significant role in GC progression.
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Affiliation(s)
- Bin Huang
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Minghe Lin
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Lisha Lu
- Department of Oncology, Affiliated People's Hospital of Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Wujin Chen
- Department of Oncology, Affiliated People's Hospital of Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Jingzhuang Tan
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Jinyan Zhao
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Zhiyun Cao
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Xiaoqin Zhu
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Jiumao Lin
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China.,Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, Fuzhou, China
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62
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Mace EM, Paust S, Conte MI, Baxley RM, Schmit MM, Patil SL, Guilz NC, Mukherjee M, Pezzi AE, Chmielowiec J, Tatineni S, Chinn IK, Akdemir ZC, Jhangiani SN, Muzny DM, Stray-Pedersen A, Bradley RE, Moody M, Connor PP, Heaps AG, Steward C, Banerjee PP, Gibbs RA, Borowiak M, Lupski JR, Jolles S, Bielinsky AK, Orange JS. Human NK cell deficiency as a result of biallelic mutations in MCM10. J Clin Invest 2020; 130:5272-5286. [PMID: 32865517 PMCID: PMC7524476 DOI: 10.1172/jci134966] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 06/24/2020] [Indexed: 12/16/2022] Open
Abstract
Human natural killer cell deficiency (NKD) arises from inborn errors of immunity that lead to impaired NK cell development, function, or both. Through the understanding of the biological perturbations in individuals with NKD, requirements for the generation of terminally mature functional innate effector cells can be elucidated. Here, we report a cause of NKD resulting from compound heterozygous mutations in minichromosomal maintenance complex member 10 (MCM10) that impaired NK cell maturation in a child with fatal susceptibility to CMV. MCM10 has not been previously associated with monogenic disease and plays a critical role in the activation and function of the eukaryotic DNA replisome. Through evaluation of patient primary fibroblasts, modeling patient mutations in fibroblast cell lines, and MCM10 knockdown in human NK cell lines, we have shown that loss of MCM10 function leads to impaired cell cycle progression and induction of DNA damage-response pathways. By modeling MCM10 deficiency in primary NK cell precursors, including patient-derived induced pluripotent stem cells, we further demonstrated that MCM10 is required for NK cell terminal maturation and acquisition of immunological system function. Together, these data define MCM10 as an NKD gene and provide biological insight into the requirement for the DNA replisome in human NK cell maturation and function.
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Affiliation(s)
- Emily M. Mace
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
| | - Silke Paust
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, California, USA
| | - Matilde I. Conte
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
| | - Ryan M. Baxley
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Megan M. Schmit
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Sagar L. Patil
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
| | - Nicole C. Guilz
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
| | - Malini Mukherjee
- Center for Human Immunobiology, Texas Children’s Hospital, Houston, Texas, USA
- Department of Pediatrics
| | - Ashley E. Pezzi
- Center for Human Immunobiology, Texas Children’s Hospital, Houston, Texas, USA
- Department of Pediatrics
| | - Jolanta Chmielowiec
- Center for Cell and Gene Therapy, and
- Molecular and Cellular Biology Department, Baylor College of Medicine, Houston, Texas, USA
| | - Swetha Tatineni
- Department of Pediatrics
- Department of BioSciences, Rice University, Houston, Texas, USA
| | - Ivan K. Chinn
- Department of Pediatrics
- Department of Molecular and Human Genetics and
| | | | - Shalini N. Jhangiani
- Department of Molecular and Human Genetics and
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Donna M. Muzny
- Department of Molecular and Human Genetics and
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Asbjørg Stray-Pedersen
- Norwegian National Unit for Newborn Screening, Division of Pediatric and Adolescent Medicine, Oslo, Norway
| | - Rachel E. Bradley
- Immunodeficiency Centre for Wales, University Hospital of Wales, Cardiff, Wales
| | - Mo Moody
- Immunodeficiency Centre for Wales, University Hospital of Wales, Cardiff, Wales
| | - Philip P. Connor
- Immunodeficiency Centre for Wales, University Hospital of Wales, Cardiff, Wales
| | - Adrian G. Heaps
- Department of Virology and Immunology, North Cumbria University Hospitals, Carlisle, United Kingdom
| | - Colin Steward
- Department of Paediatric Haematology, Oncology and Bone Marrow Transplantation, Bristol Royal Hospital for Children, Bristol, United Kingdom
| | - Pinaki P. Banerjee
- Center for Human Immunobiology, Texas Children’s Hospital, Houston, Texas, USA
- Department of Pediatrics
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics and
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Malgorzata Borowiak
- Center for Cell and Gene Therapy, and
- Molecular and Cellular Biology Department, Baylor College of Medicine, Houston, Texas, USA
- Adam Mickiewicz University, Poznan, Poland
- McNair Medical Institute, Baylor College of Medicine, Houston, Texas, USA
| | - James R. Lupski
- Department of Pediatrics
- Department of Molecular and Human Genetics and
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Hospital, Houston, Texas, USA
| | - Stephen Jolles
- Immunodeficiency Centre for Wales, University Hospital of Wales, Cardiff, Wales
| | - Anja K. Bielinsky
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jordan S. Orange
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, New York, USA
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63
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Yuan Z, Li H. Molecular mechanisms of eukaryotic origin initiation, replication fork progression, and chromatin maintenance. Biochem J 2020; 477:3499-3525. [PMID: 32970141 PMCID: PMC7574821 DOI: 10.1042/bcj20200065] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/29/2020] [Accepted: 09/04/2020] [Indexed: 12/13/2022]
Abstract
Eukaryotic DNA replication is a highly dynamic and tightly regulated process. Replication involves several dozens of replication proteins, including the initiators ORC and Cdc6, replicative CMG helicase, DNA polymerase α-primase, leading-strand DNA polymerase ε, and lagging-strand DNA polymerase δ. These proteins work together in a spatially and temporally controlled manner to synthesize new DNA from the parental DNA templates. During DNA replication, epigenetic information imprinted on DNA and histone proteins is also copied to the daughter DNA to maintain the chromatin status. DNA methyltransferase 1 is primarily responsible for copying the parental DNA methylation pattern into the nascent DNA. Epigenetic information encoded in histones is transferred via a more complex and less well-understood process termed replication-couple nucleosome assembly. Here, we summarize the most recent structural and biochemical insights into DNA replication initiation, replication fork elongation, chromatin assembly and maintenance, and related regulatory mechanisms.
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Affiliation(s)
- Zuanning Yuan
- Structural Biology Program, Van Andel Institute, Grand Rapids, Michigan, U.S.A
| | - Huilin Li
- Structural Biology Program, Van Andel Institute, Grand Rapids, Michigan, U.S.A
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64
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Cao T, Yi SJ, Wang LX, Zhao JX, Xiao J, Xie N, Zeng Z, Han Q, Tang HO, Li YK, Zou J, Wu Q. Identification of the DNA Replication Regulator MCM Complex Expression and Prognostic Significance in Hepatic Carcinoma. BIOMED RESEARCH INTERNATIONAL 2020; 2020:3574261. [PMID: 32964028 PMCID: PMC7499325 DOI: 10.1155/2020/3574261] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 08/08/2020] [Accepted: 08/12/2020] [Indexed: 12/21/2022]
Abstract
BACKGROUND The microliposome maintenance (MCM) complex, MCM2-7, is revealed to be involved in multiple cellular processes and plays a key role in the development and progression of human cancers. However, the MCM complex remains poorly elaborated in hepatic carcinoma (HCC). METHODS In the study, we found the mRNA and protein level by bioinformatics. We also explored the prognostic value, genetic alteration, interaction network, and functional enrichment of MCM2-7. The MCM expression and correlation among these MCMs in HCC cell lines were identified by western blot. RESULTS MCM2-7 was significantly increased in HCC tissues compared to normal liver tissues. The high level of MCM2-7 had a positive correlation with poor prognosis. However, MCM2-7 alterations were not correlated with poor OS. MCMs were both increased in HCC cell lines compared to the normal hepatocyte cell line. Furthermore, the positive correlation was found among MCMs in HCC cell lines. CONCLUSIONS The MCM complex was increased in HCC tissues and cell lines and negatively correlated with prognosis, which might be important biomarkers for HCC.
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Affiliation(s)
- Ting Cao
- Department of Digestive Medical, The Affiliated Nanhua Hospital, University of South China, Hengyang 421002, China
| | - Shi-jie Yi
- Department of Gastrointestinal Surgery, The Affiliated Nanhua Hospital, University of South China, Hengyang 421002, China
| | - Li-xin Wang
- Center for Traditional Chinese Medicine and Immunology Research, School of Basic Medical Sciences, Shanghai University of Traditional Chinese Medicine, 1200 Cai Lun Rd., Shanghai 201203, China
| | - Juan-xia Zhao
- Department of Pathology, The Affiliated Nanhua Hospital, University of South China, Hengyang 421002, China
| | - Jiao Xiao
- Department of Endocrinology, The Affiliated Nanhua Hospital, University of South China, Hengyang 421002, China
| | - Ni Xie
- Department of Digestive Medical, The Affiliated Nanhua Hospital, University of South China, Hengyang 421002, China
| | - Zhi Zeng
- Department of Pathology, Xianning Central Hospital, The First Affiliated Hospital of Hubei University of Science and Technology, Xianning 437000, China
| | - Qi Han
- Department of Oncology, Xianning Central Hospital, The First Affiliated Hospital of Hubei University of Science and Technology, Xianning 437000, China
| | - Hai-ou Tang
- Jishou University College of Medicine, Jishou 416000, China
| | - Yu-kun Li
- Key Laboratory of Tumor Cellular and Molecular Pathology, College of Hunan Province, Cancer Research Institute, University of South China, Hengyang, Hunan 421001, China
| | - Juan Zou
- Key Laboratory of Tumor Cellular and Molecular Pathology, College of Hunan Province, Cancer Research Institute, University of South China, Hengyang, Hunan 421001, China
| | - Qing Wu
- Department of Digestive Medical, The Affiliated Nanhua Hospital, University of South China, Hengyang 421002, China
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65
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MCM family in gastrointestinal cancer and other malignancies: From functional characterization to clinical implication. Biochim Biophys Acta Rev Cancer 2020; 1874:188415. [PMID: 32822825 DOI: 10.1016/j.bbcan.2020.188415] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/15/2020] [Accepted: 08/15/2020] [Indexed: 02/07/2023]
Abstract
Despite the recent advances in cancer research and treatment, gastrointestinal (GI) cancers remain the most common deadly disease worldwide. The aberrant DNA replication serves as a major source of genomic instability and enhances cell proliferation that contributes to tumor initiation and progression. Minichromosome maintenance family (MCMs) is a well-recognized group of proteins responsible for DNA synthesis. Recent studies suggested that dysregulated MCMs lead to tumor initiation, progression, and chemoresistance via modulating cell cycle and DNA replication stress. Their underlying mechanisms in various cancer types have been gradually identified. Furthermore, multiple studies have investigated the association between MCMs expression and clinicopathological features of cancer patients, implying that MCMs might serve as prominent prognostic biomarkers for GI cancers. This review summarizes the current knowledge on the oncogenic role of MCM proteins and highlights their clinical implications in various malignancies, especially in GI cancers. Targeting MCMs might shed light on the potential for identifying novel therapeutic strategies.
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66
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Zhang J, Bellani MA, James RC, Pokharel D, Zhang Y, Reynolds JJ, McNee GS, Jackson AP, Stewart GS, Seidman MM. DONSON and FANCM associate with different replisomes distinguished by replication timing and chromatin domain. Nat Commun 2020; 11:3951. [PMID: 32769987 PMCID: PMC7414851 DOI: 10.1038/s41467-020-17449-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 06/30/2020] [Indexed: 12/11/2022] Open
Abstract
Duplication of mammalian genomes requires replisomes to overcome numerous impediments during passage through open (eu) and condensed (hetero) chromatin. Typically, studies of replication stress characterize mixed populations of challenged and unchallenged replication forks, averaged across S phase, and model a single species of “stressed” replisome. Here, in cells containing potent obstacles to replication, we find two different lesion proximal replisomes. One is bound by the DONSON protein and is more frequent in early S phase, in regions marked by euchromatin. The other interacts with the FANCM DNA translocase, is more prominent in late S phase, and favors heterochromatin. The two forms can also be detected in unstressed cells. ChIP-seq of DNA associated with DONSON or FANCM confirms the bias of the former towards regions that replicate early and the skew of the latter towards regions that replicate late. Eukaryotic replisomes are multiprotein complexes. Here the authors reveal two distinct stressed replisomes, associated with DONSON and FANCM, displaying a bias in replication timing and chromatin domain.
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Affiliation(s)
- Jing Zhang
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Marina A Bellani
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Ryan C James
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA
| | | | - Yongqing Zhang
- Gene Expression and Genomics Unit, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA
| | - John J Reynolds
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Gavin S McNee
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Andrew P Jackson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Grant S Stewart
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Michael M Seidman
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA.
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67
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Qian W, Li Z, Song W, Zhao T, Wang W, Peng J, Wei L, Xia Q, Cheng D. A novel transcriptional cascade is involved in Fzr-mediated endoreplication. Nucleic Acids Res 2020; 48:4214-4229. [PMID: 32182338 PMCID: PMC7192621 DOI: 10.1093/nar/gkaa158] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 02/29/2020] [Indexed: 01/08/2023] Open
Abstract
Endoreplication, known as endocycle, is a variant of the cell cycle that differs from mitosis and occurs in specific tissues of different organisms. Endoreplicating cells generally undergo multiple rounds of genome replication without chromosome segregation. Previous studies demonstrated that Drosophila fizzy-related protein (Fzr) and its mammalian homolog Cdh1 function as key regulators of endoreplication entrance by activating the anaphase-promoting complex/cyclosome to initiate the ubiquitination and subsequent degradation of cell cycle factors such as Cyclin B (CycB). However, the molecular mechanism underlying Fzr-mediated endoreplication is not completely understood. In this study, we demonstrated that the transcription factor Myc acts downstream of Fzr during endoreplication in Drosophila salivary gland. Mechanistically, Fzr interacts with chromatin-associated histone H2B to enhance H2B ubiquitination in the Myc promoter and promotes Myc transcription. In addition to negatively regulating CycB transcription, the Fzr-ubiquitinated H2B (H2Bub)-Myc signaling cascade also positively regulates the transcription of the MCM6 gene that is involved in DNA replication by directly binding to specific motifs within their promoters. We further found that the Fzr-H2Bub-Myc signaling cascade regulating endoreplication progression is conserved between insects and mammalian cells. Altogether, our work uncovers a novel transcriptional cascade that is involved in Fzr-mediated endoreplication.
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Affiliation(s)
- Wenliang Qian
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Sericultural Science, Chongqing engineering and technology research center for novel silk materials, Southwest University, Chongqing 400715, China
| | - Zheng Li
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Sericultural Science, Chongqing engineering and technology research center for novel silk materials, Southwest University, Chongqing 400715, China
| | - Wei Song
- Medical Research Institute, Wuhan University, Wuhan 430071, China.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Tujing Zhao
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Sericultural Science, Chongqing engineering and technology research center for novel silk materials, Southwest University, Chongqing 400715, China
| | - Weina Wang
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Sericultural Science, Chongqing engineering and technology research center for novel silk materials, Southwest University, Chongqing 400715, China
| | - Jian Peng
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Sericultural Science, Chongqing engineering and technology research center for novel silk materials, Southwest University, Chongqing 400715, China
| | - Ling Wei
- School of Life Science, Southwest University, Chongqing 400715, China
| | - Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Sericultural Science, Chongqing engineering and technology research center for novel silk materials, Southwest University, Chongqing 400715, China
| | - Daojun Cheng
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Chongqing 400715, China.,Chongqing Key Laboratory of Sericultural Science, Chongqing engineering and technology research center for novel silk materials, Southwest University, Chongqing 400715, China
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Pan L, Wang X, Yang L, Zhao L, Zhai L, Xu J, Yang Y, Mao Y, Cheng S, Xiao T, Tan M. Proteomic and Phosphoproteomic Maps of Lung Squamous Cell Carcinoma From Chinese Patients. Front Oncol 2020; 10:963. [PMID: 32612956 PMCID: PMC7308564 DOI: 10.3389/fonc.2020.00963] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 05/15/2020] [Indexed: 12/29/2022] Open
Abstract
Lung squamous cell carcinoma (LUSC) is one of the leading causes of tumor-driven deaths in the world. To date, studies on the tumor heterogeneity of LUSC at genomic level have only revealed limited therapeutic benefits. Therefore, system-wide research of LUSC at proteomic level may further improve precision medicine strategies on individual demands. To this end, we performed proteomic and phosphoproteomic study for LUSC samples of 25 Chinese patients. From our results, two subgroups (Cluster I and II) based on proteomic data were identified, which were associated with distinct molecular characteristics and clinicopathologic features. Combined with phosphoproteomic data, our result showed that spliceosome pathway was enriched in Cluster I, while focal adhesion pathway, immune-related pathways and Ras signaling pathway were enriched in Cluster II. In addition, we found that lymph node metastasis (LNM) was associated with our proteomic subgroups and cell cycle pathway was enriched in patients with LNM. Further analysis showed that MCM2, a DNA replication licensing factor involved in cell cycle pathway, was highly expressed in patients with poor prognosis, which was further proved by immunohistochemistry (IHC) analysis. In summary, our study provided a resource of the proteomic and phosphoproteomic features of LUSC in Chinese patients.
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Affiliation(s)
- Lulu Pan
- Chemical Proteomics Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Xijun Wang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Longhai 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.,Department of Cardiothoracic Surgery, Shenzhen University General Hospital/Shenzhen University Clinical Medical Academy, Shenzhen, China
| | - Lei Zhao
- Chemical Proteomics Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Linhui Zhai
- Chemical Proteomics Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Junyu Xu
- Chemical Proteomics Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yikun 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
| | - Yousheng Mao
- 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
| | - Shujun Cheng
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ting Xiao
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Minjia Tan
- Chemical Proteomics Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,School of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
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69
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Tessier-Cloutier B, Cochrane DR, Karnezis AN, Colborne S, Magrill J, Talhouk A, Zhang J, Leung S, Hughes CS, Piskorz A, Cheng AS, Greening K, du Bois A, Pfisterer J, Soslow RA, Kommoss S, Brenton JD, Morin GB, Gilks CB, Huntsman DG, Kommoss F. Proteomic analysis of transitional cell carcinoma-like variant of tubo-ovarian high-grade serous carcinoma. Hum Pathol 2020; 101:40-52. [PMID: 32360491 PMCID: PMC8204941 DOI: 10.1016/j.humpath.2020.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 02/18/2020] [Accepted: 02/23/2020] [Indexed: 02/06/2023]
Abstract
The current World Health Organization classification does not distinguish transitional cell carcinoma of the ovary (TCC) from conventional tubo-ovarian high-grade serous carcinoma (HGSC), despite evidence suggesting improved prognosis for patients with TCC; instead, it is considered a morphologic variant of HGSC. The immunohistochemical (IHC) markers applied to date do not distinguish between TCC and HGSC. Therefore, we sought to compare the proteomic profiles of TCC and conventional HGSC to identify proteins enriched in TCC. Prognostic biomarkers in HGSC have proven to be elusive, and our aim was to identify biomarkers of TCC as a way of reliably and reproducibly identifying patients with a favorable prognosis and better response to chemotherapy compared with those with conventional HGSC. Quantitative global proteome analysis was performed on archival material of 12 cases of TCC and 16 cases of HGSC using SP3 (single-pot, solid phase-enhanced, sample preparation)-Clinical Tissue Proteomics, a recently described protocol for full-proteome analysis from formalin-fixed paraffin-embedded tissues. We identified 430 proteins that were significantly enriched in TCC over HGSC. Unsupervised co-clustering perfectly distinguished TCC from HGSC based on protein expression. Pathway analysis showed that proteins associated with cell death, necrosis, and apoptosis were highly expressed in TCCs, whereas proteins associated with DNA homologous recombination, cell mitosis, proliferation and survival, and cell cycle progression pathways had reduced expression. From the proteomic analysis, three potential biomarkers for TCC were identified, claudin-4 (CLDN4), ubiquitin carboxyl-terminal esterase L1 (UCHL1), and minichromosome maintenance protein 7 (MCM7), and tested by IHC analysis on tissue microarrays. In agreement with the proteomic analysis, IHC expression of those proteins was stronger in TCC than in HGSC (p < 0.0001). Using global proteomic analysis, we are able to distinguish TCC from conventional HGSC. Follow-up studies will be necessary to confirm that these molecular and morphologic differences are clinically significant.
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Affiliation(s)
- Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, BC, Canada; Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - Dawn R Cochrane
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
| | - Anthony N Karnezis
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, UC Davis Medical Center, Sacramento, CA, United States
| | - Shane Colborne
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Jamie Magrill
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
| | - Aline Talhouk
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
| | - Jonathan Zhang
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
| | - Samuel Leung
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
| | | | - Anna Piskorz
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK
| | - Angela S Cheng
- Genetic Pathology Evaluation Centre, The University of British Columbia, Vancouver, Canada
| | - Kendall Greening
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
| | | | | | - Robert A Soslow
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Stefan Kommoss
- Department of Obstetrics and Gynecology, Tübingen University Hospital, Tübingen, Germany
| | - James D Brenton
- Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Cambridge, UK
| | - Gregg B Morin
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - C Blake Gilks
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - David G Huntsman
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
| | - Friedrich Kommoss
- Institute of Pathology, Medizin Campus Bodensee, Friedrichshafen, Germany.
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Li X, Ren Z, Xiong C, Geng J, Li Y, Liu C, Ren C, Liu H. Minichromosome maintenance 6 complex component identified by bioinformatics analysis and experimental validation in esophageal squamous cell carcinoma. Oncol Rep 2020; 44:987-1002. [PMID: 32583000 PMCID: PMC7388536 DOI: 10.3892/or.2020.7658] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 06/05/2020] [Indexed: 12/12/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC), the main subtype of esophageal cancer (EC), is a common lethal type of cancer with a high mortality rate. The aim of the present study was to select key relevant genes and identify potential mechanisms involved in the development of ESCC based on bioinformatics analysis. Minichromosome maintenance 6 complex component (MCM6) has been identified to be upregulated in multiple malignancies; however, its contributions to ESCC remain unclear. For the purposes of the present study, four datasets were downloaded from the Gene Expression Omnibus (GSE63941, GSE26886, GSE17351 and GSE77861), and the intersection of the differentially expressed genes was obtained using a Venn diagram. The protein‑protein interaction was then constructed, and the modules were verified by Cytoscape, in which the key genes have a high connectivity degree with other genes. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway were subsequently filtered out to analyze the development of ESCC. MCM6, an upregulated gene, was selected and connected with most of the other genes, for further research validation. The expression levels of MCM6 were then assessed using the Oncomine, GEPIA and UALCAN databases and validated in both ESCC tissues samples and cell lines by immunohistochemistry and RT‑qPCR. Cell counting kit‑8 (CCK‑8), flow cytometry, wound healing and Transwell assays were used to determine the proliferation, apoptosis, cell cycle, migration and invasion of ESCC cells. A total of 24 genes were identified by a series of bioinformatics analyses and the results revealed that the genes were associated with DNA replication and cell cycle. Experimental validation revealed that MCM6 expression was significantly elevated in both ESCC tissues and cell lines. The results were consistent with those of bioinformatics analysis. Furthermore, the knockdown of MCM6 inhibited cell proliferation, migration and invasion and promoted cell apoptosis, and made cells arrested in S stage. In summary, the findings of bioinformatics analysis provided a novel hypothesis for ESCC progression. In particular, the aberrantly elevated expression of MCM6 is a potential biomarker for ESCC diagnosis and treatment.
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Affiliation(s)
- Xuebing Li
- Department of Medical Laboratory, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Zhenzhen Ren
- Department of Medical Laboratory, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Chao Xiong
- Department of Medical Laboratory, The Second Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, Henan 450000, P.R. China
| | - Jie Geng
- Department of Medical Laboratory, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Yuqing Li
- Department of Medical Laboratory, The Second Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, Henan 450000, P.R. China
| | - Cong Liu
- Department of Medical Laboratory, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Chunfeng Ren
- Department of Medical Laboratory, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Hongchun Liu
- Department of Medical Laboratory, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
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71
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Zhang S, Han B, Wu F, Huang H. Quantitative proteomic analysis provides insights into the algicidal mechanism of Halobacillus sp. P1 against the marine diatom Skeletonema costatum. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 717:137048. [PMID: 32070889 DOI: 10.1016/j.scitotenv.2020.137048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/30/2020] [Accepted: 01/30/2020] [Indexed: 06/10/2023]
Abstract
Algicidal behavior is a common interaction between marine microalgae and bacteria, especially in the dissipation phase of algal blooms. The marine bacterium Halobacillus sp. P1 was previously isolated and exhibits high algicidal activity against the diatom Skeletonema costatum. However, little is known about the mechanism underlying this algicidal process. Here, a tandem mass tag (TMT)-based proteomic approach was coupled with physiological analysis to investigate the cellular responses of S. costatum when treated with P1 culture supernatant. Among the 4582 proteins identified, 82 and 437 proteins were differentially expressed after treatment for 12 and 24 h, respectively. The proteomic results were in accordance with the results of verification by parallel reaction monitoring (PRM) assays. Proteins involved in reactive oxygen species scavenging, protein degradation and transport were upregulated, while proteins participating in nitrogen metabolism, protein translation, photosynthetic pigment biosynthesis and cell cycle regulation were significantly downregulated (p-value ≤0.05), corresponding to the increasing malondialdehyde content and the decreasing nitrogen, protein and chlorophyll a contents. A nutrient competitive relationship might exist between the bacterium P1 and S. costatum, and the inhibition of nitrogen metabolism by the P1 culture supernatant might be the key lethal factor that results in the dysfunction of S. costatum metabolism. Our study sheds light on the algicidal mechanism of P1 at the molecular level and provides new insights into algae-bacteria interactions.
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Affiliation(s)
- Shufei Zhang
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Beibei Han
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Fengxia Wu
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
| | - Honghui Huang
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China.
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Concurrent Control of the Kaposi's Sarcoma-Associated Herpesvirus Life Cycle through Chromatin Modulation and Host Hedgehog Signaling: a New Prospect for the Therapeutic Potential of Lipoxin A4. J Virol 2020; 94:JVI.02177-19. [PMID: 32102879 DOI: 10.1128/jvi.02177-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 02/14/2020] [Indexed: 02/07/2023] Open
Abstract
Lipoxin A4 (LXA4) is an endogenous lipid mediator with compelling anti-inflammatory and proresolution properties. Studies done to assess the role of arachidonic acid pathways of the host in Kaposi's sarcoma-associated herpesvirus (KSHV) biology helped discover that KSHV infection hijacks the proinflammatory cyclooxygenase-2 (COX-2) and 5-lipoxygenase (5-LO) pathways and concurrently reduces anti-inflammatory LXA4 secretion to maintain KSHV latency in infected cells. Treatment of KSHV-infected cells with LXA4 minimizes the activation of inflammatory and proliferative signaling pathways, including the NF-κB, AKT, and extracellular signal-regulated kinase 1/2 (ERK1/2) pathways, but the exact mechanism of action of LXA4 remains unexplored. Here, using mass spectrometry analysis, we identified components from the minichromosome maintenance (MCM) protein and chromatin-remodeling complex SMARCB1 and SMARCC2 to be LXA4-interacting host proteins in KSHV-infected cells. We identified a higher level of nuclear aryl hydrocarbon receptor (AhR) in LXA4-treated KSHV-infected cells than in untreated KSHV-infected cells, which probably facilitates the affinity interaction of the nucleosome complex protein with LXA4. We demonstrate that SMARCB1 regulates both replication and transcription activator (RTA) activity and host hedgehog (hh) signaling in LXA4-treated KSHV-infected cells. Host hedgehog signaling was modulated in an AMP-activated protein kinase (AMPK)-mammalian target of rapamycin (mTOR)-S6 kinase-dependent manner in LXA4-treated KSHV-infected cells. Since anti-inflammatory drugs are beneficial as adjuvants to conventional and immune-based therapies, we evaluated the potential of LXA4 treatment in regulating programmed death-ligand 1 (PD-L1) on KSHV-carrying tumor cells. Overall, our study identified LXA4-interacting host factors in KSHV-infected cells, which could help provide an understanding of the mode of action of LXA4 and its therapeutic potential against KSHV.IMPORTANCE The latent-to-lytic switch in KSHV infection is one of the critical events regulated by the major replication and transcription activator KSHV protein called RTA. Chromatin modification of the viral genome determines the phase of the viral life cycle in the host. Here, we report that LXA4 interacts with a host chromatin modulator, especially SMARCB1, which upregulates the KSHV ORF50 promoter. SMARCB1 has also been recognized to be a tumor suppressor protein which controls many tumorigenic events associated with the hedgehog (hh) signaling pathway. We also observed that LXA4 treatment reduces PD-L1 expression and that PD-L1 expression is an important immune evasion strategy used by KSHV for its survival and maintenance in the host. Our study underscores the role of LXA4 in KSHV biology and emphasizes that KSHV is strategic in downregulating LXA4 secretion in the host to establish latency. This study also uncovers the therapeutic potential of LXA4 and its targetable receptor, AhR, in KSHV's pathogenesis.
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74
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Hulke ML, Massey DJ, Koren A. Genomic methods for measuring DNA replication dynamics. Chromosome Res 2020; 28:49-67. [PMID: 31848781 PMCID: PMC7131883 DOI: 10.1007/s10577-019-09624-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/30/2019] [Accepted: 12/03/2019] [Indexed: 12/27/2022]
Abstract
Genomic DNA replicates according to a defined temporal program in which early-replicating loci are associated with open chromatin, higher gene density, and increased gene expression levels, while late-replicating loci tend to be heterochromatic and show higher rates of genomic instability. The ability to measure DNA replication dynamics at genome scale has proven crucial for understanding the mechanisms and cellular consequences of DNA replication timing. Several methods, such as quantification of nucleotide analog incorporation and DNA copy number analyses, can accurately reconstruct the genomic replication timing profiles of various species and cell types. More recent developments have expanded the DNA replication genomic toolkit to assays that directly measure the activity of replication origins, while single-cell replication timing assays are beginning to reveal a new level of replication timing regulation. The combination of these methods, applied on a genomic scale and in multiple biological systems, promises to resolve many open questions and lead to a holistic understanding of how eukaryotic cells replicate their genomes accurately and efficiently.
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Affiliation(s)
- Michelle L Hulke
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Dashiell J Massey
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA.
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Prognostic role of minichromosome maintenance family in multiple myeloma. Cancer Gene Ther 2020; 27:819-829. [PMID: 31959909 DOI: 10.1038/s41417-020-0162-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/31/2019] [Accepted: 01/07/2020] [Indexed: 12/29/2022]
Abstract
Multiple myeloma (MM) is a plasma cell malignancy. The minichromosome maintenance (MCM) family involve in DNA replication and is vital in limiting replication in cell cycle. The prognostic role of MCMs in MM is still unclear. We took four independent GEO datasets to analyze the relationship between the expression of MCMs and myeloma progression and survival. The expression of MCMs showed an upward trend with myeloma progression in 205 patients. High MCM2/3/4/6/8 expression was associated with both poor EFS and OS (all p < 0.050). Multivariate analysis demonstrated that high MCM2 expression, B2M, and LDH were independent risk factors. Moreover, the combination of MCM2/B2M and MCM2/LDH was a better tool in prognostication. In conclusion, high MCM2 expression is an independent adverse prognostic factor and could be used as a prognostic biomarker in MM.
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76
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Zi Z, Zhang Y, Zhang P, Ding Q, Chu M, Chen Y, Minna JD, Yu Y. A Proteomic Connectivity Map for Characterizing the Tumor Adaptive Response to Small Molecule Chemical Perturbagens. ACS Chem Biol 2020; 15:140-150. [PMID: 31846293 DOI: 10.1021/acschembio.9b00694] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A powerful means to understand the cellular function of corrupt oncogenic signaling programs requires perturbing the system and monitoring the downstream consequences. Here, using a unique pair of non-small cell lung cancer (NSCLC)/normal lung epithelial patient-derived cell lines (HCC4017/HBEC30KT), we systematically interrogated the remodeling of the NSCLC proteome upon treatment with 35 chemical perturbagens targeting a diverse array of mechanistic classes. HCC4017 and HBEC30KT cells differ significantly in their proteomic response to the same compound treatment. Using protein covariance analyses, we identified a large number of functional protein networks. For example, we found that a poorly studied protein, C5orf22, is a novel component of the WBP11/PQBP1 splicing complex. Depletion of C5orf22 leads to the aberrant splicing and expression of genes involved in cell growth and immunomodulation. In summary, we show that by systematically measuring the tumor adaptive responses at the proteomic level, an understanding could be generated that provides critical circuit-level biological insights for these pharmacologic perturbagens.
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Affiliation(s)
- Zhenzhen Zi
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Yajie Zhang
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Peng Zhang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Qing Ding
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Michael Chu
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Yiwen Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - John D. Minna
- Hamon Center for Therapeutic Oncology Research, Departments of Internal Medicine and Pharmacology, Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Yonghao Yu
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas 75390, United States
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Alqahtani FM, Arivett BA, Taylor ZE, Handy ST, Farone AL, Farone MB. Chemogenomic profiling to understand the antifungal action of a bioactive aurone compound. PLoS One 2019; 14:e0226068. [PMID: 31825988 PMCID: PMC6905557 DOI: 10.1371/journal.pone.0226068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 11/18/2019] [Indexed: 12/15/2022] Open
Abstract
Every year, more than 250,000 invasive candidiasis infections are reported with 50,000 deaths worldwide. The limited number of antifungal agents necessitates the need for alternative antifungals with potential novel targets. The 2-benzylidenebenzofuran-3-(2H)-ones have become an attractive scaffold for antifungal drug design. This study aimed to determine the antifungal activity of a synthetic aurone compound and characterize its mode of action. Using the broth microdilution method, aurone SH1009 exhibited inhibition against C. albicans, including resistant isolates, as well as C. glabrata, and C. tropicalis with IC50 values of 4-29 μM. Cytotoxicity assays using human THP-1, HepG2, and A549 human cell lines showed selective toxicity toward fungal cells. The mode of action for SH1009 was characterized using chemical-genetic interaction via haploinsufficiency (HIP) and homozygous (HOP) profiling of a uniquely barcoded Saccharomyces cerevisiae mutant collection. Approximately 5300 mutants were competitively treated with SH1009 followed by DNA extraction, amplification of unique barcodes, and quantification of each mutant using multiplexed next-generation sequencing. Barcode post-sequencing analysis revealed 238 sensitive and resistant mutants that significantly (FDR P values ≤ 0.05) responded to aurone SH1009. The enrichment analysis of KEGG pathways and gene ontology demonstrated the cell cycle pathway as the most significantly enriched pathway along with DNA replication, cell division, actin cytoskeleton organization, and endocytosis. Phenotypic studies of these significantly enriched responses were validated in C. albicans. Flow cytometric analysis of SH1009-treated C. albicans revealed a significant accumulation of cells in G1 phase, indicating cell cycle arrest. Fluorescence microscopy detected abnormally interrupted actin dynamics, resulting in enlarged, unbudded cells. RT-qPCR confirmed the effects of SH1009 in differentially expressed cell cycle, actin polymerization, and signal transduction genes. These findings indicate the target of SH1009 as a cell cycle-dependent organization of the actin cytoskeleton, suggesting a novel mode of action of the aurone compound as an antifungal inhibitor.
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Affiliation(s)
- Fatmah M. Alqahtani
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, United States of America
| | - Brock A. Arivett
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, United States of America
| | - Zachary E. Taylor
- Department of Chemistry, Middle Tennessee State University, Murfreesboro, Tennessee, United States of America
| | - Scott T. Handy
- Department of Chemistry, Middle Tennessee State University, Murfreesboro, Tennessee, United States of America
| | - Anthony L. Farone
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, United States of America
| | - Mary B. Farone
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, United States of America
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78
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Dynamics of trophoblast differentiation in peri-implantation-stage human embryos. Proc Natl Acad Sci U S A 2019; 116:22635-22644. [PMID: 31636193 DOI: 10.1073/pnas.1911362116] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Single-cell RNA sequencing of cells from cultured human blastocysts has enabled us to define the transcriptomic landscape of placental trophoblast (TB) that surrounds the epiblast and associated embryonic tissues during the enigmatic day 8 (D8) to D12 peri-implantation period before the villous placenta forms. We analyzed the transcriptomes of 3 early placental cell types, cytoTB (CTB), syncytioTB (STB), and migratoryTB (MTB), picked manually from cultured embryos dissociated with trypsin and were able to follow sublineages that emerged from proliferating CTB at the periphery of the conceptus. A unique form of CTB with some features of STB was detectable at D8, while mature STB was at its zenith at D10. A form of MTB with a mixed MTB/CTB phenotype arose around D10. By D12, STB generation was in decline, CTB had entered a new phase of proliferation, and mature MTB cells had begun to move from the main body of the conceptus. Notably, the MTB transcriptome at D12 indicated enrichment of transcripts associated with IFN signaling, migration, and invasion and up-regulation of HLA-C, HLA-E, and HLA-G. The STB, which is distinct from the STB of later villous STB, had a phenotype consistent with intense protein export and placental hormone production, as well as migration and invasion. The studies show that TB associated with human embryos is in rapid developmental flux during peri-implantation period when it must invade, signal robustly to the mother to ensure that the pregnancy continues, and make first contact with the maternal immune system.
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79
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Down-regulation of CK2α correlates with decreased expression levels of DNA replication minichromosome maintenance protein complex (MCM) genes. Sci Rep 2019; 9:14581. [PMID: 31601942 PMCID: PMC6787000 DOI: 10.1038/s41598-019-51056-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 06/12/2019] [Indexed: 11/12/2022] Open
Abstract
Protein kinase CK2 is a serine/threonine kinase composed of two catalytic subunits (CK2α and/or CK2α’) and two regulatory subunits (CK2β). It is implicated in every stage of the cell cycle and in the regulation of various intracellular pathways associated with health and disease states. The catalytic subunits have similar biochemical activity, however, their functions may differ significantly in cells and in vivo. In this regard, homozygous deletion of CK2α leads to embryonic lethality in mid-gestation potentially due to severely impaired cell proliferation. To determine the CK2α-dependent molecular mechanisms that control cell proliferation, we established a myoblast-derived cell line with inducible silencing of CK2α and carried out a comprehensive RNA-Seq analysis of gene expression. We report evidence that CK2α depletion causes delayed cell cycle progression through the S-phase and defective response to replication stress. Differential gene expression analysis revealed that the down-regulated genes were enriched in pathways implicated in cell cycle regulation, DNA replication and DNA damage repair. Interestingly, the genes coding for the minichromosome maintenance proteins (MCMs), which constitute the core of the replication origin recognition complex, were among the most significantly down-regulated genes. These findings were validated in cells and whole mouse embryos. Taken together, our study provides new evidence for a critical role of protein kinase CK2 in controlling DNA replication initiation and the expression levels of replicative DNA helicases, which ensure maintenance of proliferative potential and genome integrity in eukaryotic cells.
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80
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Zeng Y, Liu C, Gong Y, Bai Z, Hou S, He J, Bian Z, Li Z, Ni Y, Yan J, Huang T, Shi H, Ma C, Chen X, Wang J, Bian L, Lan Y, Liu B, Hu H. Single-Cell RNA Sequencing Resolves Spatiotemporal Development of Pre-thymic Lymphoid Progenitors and Thymus Organogenesis in Human Embryos. Immunity 2019; 51:930-948.e6. [PMID: 31604687 DOI: 10.1016/j.immuni.2019.09.008] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/25/2019] [Accepted: 09/11/2019] [Indexed: 02/05/2023]
Abstract
Generation of the first T lymphocytes in the human embryo involves the emergence, migration, and thymus seeding of lymphoid progenitors together with concomitant thymus organogenesis, which is the initial step to establish the entire adaptive immune system. However, the cellular and molecular programs regulating this process remain unclear. We constructed a single-cell transcriptional landscape of human early T lymphopoiesis by using cells from multiple hemogenic and hematopoietic sites spanning embryonic and fetal stages. Among heterogenous early thymic progenitors, one subtype shared common features with a subset of lymphoid progenitors in fetal liver that are known as thymus-seeding progenitors. Unbiased bioinformatics analysis identified a distinct type of pre-thymic lymphoid progenitors in the aorta-gonad-mesonephros (AGM) region. In parallel, we investigated thymic epithelial cell development and potential cell-cell interactions during thymus organogenesis. Together, our data provide insights into human early T lymphopoiesis that prospectively direct T lymphocyte regeneration, which might lead to development of clinical applications.
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Affiliation(s)
- Yang Zeng
- State Key Laboratory of Experimental Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Chen Liu
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing 100071, China
| | - Yandong Gong
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing 100071, China
| | - Zhijie Bai
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing 100071, China
| | - Siyuan Hou
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing 100071, China
| | - Jian He
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing 100071, China
| | - Zhilei Bian
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou 510632, China; Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Guangzhou 510530, China
| | - Zongcheng Li
- State Key Laboratory of Experimental Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Yanli Ni
- State Key Laboratory of Experimental Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Jing Yan
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing 100071, China
| | - Tao Huang
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing 100071, China
| | - Hui Shi
- State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing 100071, China
| | - Chunyu Ma
- Department of Gynecology, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Xueying Chen
- Department of Rheumatology and Immunology, Rare Disease Center, the State Key Laboratory of Biotherapy, West China Hospital, Sichuan University. Collaboration and Innovation Center for Biotherapy. Chengdu 610041, China
| | - Jinyong Wang
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Lihong Bian
- Department of Gynecology, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China
| | - Yu Lan
- Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou 510632, China; Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Guangzhou 510530, China.
| | - Bing Liu
- State Key Laboratory of Experimental Hematology, Fifth Medical Center of Chinese PLA General Hospital, Beijing 100071, China; State Key Laboratory of Proteomics, Academy of Military Medical Sciences, Academy of Military Sciences, Beijing 100071, China; Key Laboratory for Regenerative Medicine of Ministry of Education, Institute of Hematology, School of Medicine, Jinan University, Guangzhou 510632, China; State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences, Tianjin 300020, China.
| | - Hongbo Hu
- Department of Rheumatology and Immunology, Rare Disease Center, the State Key Laboratory of Biotherapy, West China Hospital, Sichuan University. Collaboration and Innovation Center for Biotherapy. Chengdu 610041, China.
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81
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Li S, Jiang Z, Li Y, Xu Y. Prognostic significance of minichromosome maintenance mRNA expression in human lung adenocarcinoma. Oncol Rep 2019; 42:2279-2292. [PMID: 31545501 PMCID: PMC6826304 DOI: 10.3892/or.2019.7330] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 08/09/2019] [Indexed: 12/21/2022] Open
Abstract
The minichromosome maintenance (MCM) gene family plays an essential role in DNA replication and cell cycle progression. However, MCM gene expression has not been well-studied in lung adenocarcinoma (LUAD). In the present study, the expression, prognostic value and functions of MCMs in LUAD were investigated using several databases and bioinformatic tools, including Oncomine, GEPIA, cBioPortal, CancerSEA and Kaplan-Meier plotter. It was demonstrated that the mRNA expression of MCM2, MCM4 and MCM10 were significantly increased in patients with LUAD. High mRNA expression of MCM2-5, MCM8 and MCM10 were associated with poor overall survival and progression-free survival. High MCM4 expression was associated with adverse post-progression survival. In addition, the Human Protein Atlas database showed that MCM protein expression was consistent with the mRNA expression. These results demonstrate that MCM2, MCM4 and MCM10 are potential prognostic markers and therapeutic targets for LUAD.
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Affiliation(s)
- Shu Li
- Department of Hematology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
| | - Zhou Jiang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
| | - Yirun Li
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, P.R. China
| | - Yang Xu
- Department of Hematology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, P.R. China
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5-hydroxymethylcytosine Marks Mammalian Origins Acting as a Barrier to Replication. Sci Rep 2019; 9:11065. [PMID: 31363131 PMCID: PMC6667497 DOI: 10.1038/s41598-019-47528-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 07/15/2019] [Indexed: 01/07/2023] Open
Abstract
In most mammalian cells, DNA replication occurs once, and only once between cell divisions. Replication initiation is a highly regulated process with redundant mechanisms that prevent errant initiation events. In lower eukaryotes, replication is initiated from a defined consensus sequence, whereas a consensus sequence delineating mammalian origin of replication has not been identified. Here we show that 5-hydroxymethylcytosine (5hmC) is present at mammalian replication origins. Our data support the hypothesis that 5hmC has a role in cell cycle regulation. We show that 5hmC level is inversely proportional to proliferation; indeed, 5hmC negatively influences cell division by increasing the time a cell resides in G1. Our data suggest that 5hmC recruits replication-licensing factors, then is removed prior to or during origin firing. Later we propose that TET2, the enzyme catalyzing 5mC to 5hmC conversion, acts as barrier to rereplication. In a broader context, our results significantly advance the understating of 5hmC involvement in cell proliferation and disease states.
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83
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Liu K, Kang M, Liao X, Wang R. Genome-wide investigation of the clinical significance and prospective molecular mechanism of minichromosome maintenance protein family genes in patients with Lung Adenocarcinoma. PLoS One 2019; 14:e0219467. [PMID: 31323040 PMCID: PMC6641114 DOI: 10.1371/journal.pone.0219467] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 06/24/2019] [Indexed: 12/24/2022] Open
Abstract
Our current study is to identify clinical significance of minichromosome maintenance (MCM) gene expression in Lung Adenocarcinoma (LUAD) using genome-wide RNA sequencing (RNA-seq) dataset and bioinformatics analysis tools. The biological function and potential process for function of the MCM1-10 were identified by multiple bioinformatics analysis tools. Clinical significance and molecular mechanism of the MCM1-10 were investigated by the RNA-seq dataset of LUAD from The Cancer Genome Atlas. Functional assessment substantiated involvement of MCM1-10 in cell cycle progression and DNA replication, and co-expressed with each other. We also observed that the MCM1-10 were dysregulation in LUAD tumor tissues, and may be have diagnostic implications in LUAD. Prognosis analysis in TCGA and KM plotter cohorts suggest that high abundance of MCM5, MCM8 and MCM4 notably correlated to poor LUAD overall survival. Mechanistic exploration of MCM4, MCM5, and MCM8 by gene set enrichment analysis suggests that these genes may influence the LUAD prognosis by regulating the cell cycle, DNA replication and other multiple biological processes and pathways. In comclusion, our study suggests that MCM1-10 can serve as diagnostic biomarkers for LUAD patients. Of them, MCM4, MCM5, and MCM8 may act as potential prognostic indicators for LUAD.
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Affiliation(s)
- Kang Liu
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Min Kang
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Xiwen Liao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Rensheng Wang
- Department of Radiation Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, People's Republic of China
- * E-mail:
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84
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Meagher M, Epling LB, Enemark EJ. DNA translocation mechanism of the MCM complex and implications for replication initiation. Nat Commun 2019; 10:3117. [PMID: 31308367 PMCID: PMC6629641 DOI: 10.1038/s41467-019-11074-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 06/18/2019] [Indexed: 12/12/2022] Open
Abstract
The DNA translocation activity of the minichromosome maintenance (MCM) complex powers DNA strand separation of the replication forks of eukaryotes and archaea. Here we illustrate an atomic level mechanism for this activity with a crystal structure of an archaeal MCM hexamer bound to single-stranded DNA and nucleotide cofactors. Sequence conservation indicates this rotary mechanism is fully possible for all eukaryotes and archaea. The structure definitively demonstrates the ring orients during translocation with the N-terminal domain leading, indicating that the translocation activity could also provide the physical basis of replication initiation where a double-hexamer idly encircling double-stranded DNA transforms to single-hexamers that encircle only one strand. In this mechanism, each strand binds to the N-terminal tier of one hexamer and the AAA+ tier of the other hexamer such that one ring pulls on the other, aligning equivalent interfaces to enable each hexamer to pull its translocation strand outside of the opposing hexamer.
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Affiliation(s)
- Martin Meagher
- Department of Structural Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 311, Memphis, TN, 38105, USA
| | - Leslie B Epling
- Department of Structural Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 311, Memphis, TN, 38105, USA.,Incyte Research Institute, 1801 Augustine Cut-off, Wilmington, DE, 19803, USA
| | - Eric J Enemark
- Department of Structural Biology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 311, Memphis, TN, 38105, USA.
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85
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Gong B, Ma M, Yang X, Xie W, Luo Y, Sun T. MCM5 promotes tumour proliferation and correlates with the progression and prognosis of renal cell carcinoma. Int Urol Nephrol 2019; 51:1517-1526. [PMID: 31190295 DOI: 10.1007/s11255-019-02169-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 05/07/2019] [Indexed: 12/22/2022]
Abstract
BACKGROUND To investigate the role of Minichromosome maintenance protein 5 (MCM5) in the clinical prognosis and biological function of renal cell carcinoma (RCC). METHODS The Oncomine database was analysed to determine the differential expression of MCMs in RCC. A total of 50 RCC tissues were evaluated by immunohistochemistry (IHC), and the association between MCM5 and clinicopathologic features was determined. Kaplan-Meier curves and the log-rank test were applied for survival analysis. MCM5 expression in RCC tissues and cell lines was examined further by Western blotting. To explore the biological function of MCM5 in RCC, RCC cell lines (786-0, 769p) were transfected with shRNA-MCM5 or MCM5. Cell proliferation was assessed using MTT and colony-formation assays. Tumour xenografts were generated in nude mice to confirm the effects of MCM5 on tumour growth. RESULTS MCM5 was significantly overexpressed in RCC tissues; this outcome was confirmed by the Oncomine database, IHC and Western blotting. IHC and LinkedOmics analysis demonstrated that the MCM5 expression was significantly associated with pathological stage, lymph node status, distant metastasis, and TNM stage (p < 0.05) but not with sex, age, position, or tumour size (p > 0.05). Furthermore, high MCM5 levels correlated with unfavourable clinical outcomes in RCC (p < 0.05). Additionally, MCM5 silencing inhibited RCC cell line proliferation and reduced 786-0 xenograft tumour growth; in contrast, MCM5 upregulation promoted cell proliferation. CONCLUSION MCM5 overexpression is associated with malignant status and poor prognosis in RCC. Additionally, MCM5 plays an important role in proliferation and may be a potential prognostic marker and novel therapeutic target for RCC.
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Affiliation(s)
- Binbin Gong
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Ming Ma
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Xiaorong Yang
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Wenjie Xie
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Yanping Luo
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China.
| | - Ting Sun
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China.
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86
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Wu R, Amin A, Wang Z, Huang Y, Man-Hei Cheung M, Yu Z, Yang W, Liang C. The interaction networks of the budding yeast and human DNA replication-initiation proteins. Cell Cycle 2019; 18:723-741. [PMID: 30890025 DOI: 10.1080/15384101.2019.1586509] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
DNA replication is a stringently regulated cellular process. In proliferating cells, DNA replication-initiation proteins (RIPs) are sequentially loaded onto replication origins during the M-to-G1 transition to form the pre-replicative complex (pre-RC), a process known as replication licensing. Subsequently, additional RIPs are recruited to form the pre-initiation complex (pre-IC). RIPs and their regulators ensure that chromosomal DNA is replicated exactly once per cell cycle. Origin recognition complex (ORC) binds to, and marks replication origins throughout the cell cycle and recruits other RIPs including Noc3p, Ipi1-3p, Cdt1p, Cdc6p and Mcm2-7p to form the pre-RC. The detailed mechanisms and regulation of the pre-RC and its exact architecture still remain unclear. In this study, pairwise protein-protein interactions among 23 budding yeast and 16 human RIPs were systematically and comprehensively examined by yeast two-hybrid analysis. This study tested 470 pairs of yeast and 196 pairs of human RIPs, from which 113 and 96 positive interactions, respectively, were identified. While many of these interactions were previously reported, some were novel, including various ORC and MCM subunit interactions, ORC self-interactions, and the interactions of IPI3 and NOC3 with several pre-RC and pre-IC proteins. Ten of the novel interactions were further confirmed by co-immunoprecipitation assays. Furthermore, we identified the conserved interaction networks between the yeast and human RIPs. This study provides a foundation and framework for further understanding the architectures, interactions and functions of the yeast and human pre-RC and pre-IC.
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Affiliation(s)
- Rentian Wu
- a Division of Life Science, Center for Cancer Research and State Key Lab for Molecular Neuroscience , Hong Kong University of Science and Technology , Hong Kong , China.,b Guangzhou HKUST Fok Ying Tung Research Institute , Guangzhou , China
| | - Aftab Amin
- a Division of Life Science, Center for Cancer Research and State Key Lab for Molecular Neuroscience , Hong Kong University of Science and Technology , Hong Kong , China.,b Guangzhou HKUST Fok Ying Tung Research Institute , Guangzhou , China.,c School of Chinese Medicine , Hong Kong Baptist University , Guangzhou , China
| | - Ziyi Wang
- a Division of Life Science, Center for Cancer Research and State Key Lab for Molecular Neuroscience , Hong Kong University of Science and Technology , Hong Kong , China
| | - Yining Huang
- a Division of Life Science, Center for Cancer Research and State Key Lab for Molecular Neuroscience , Hong Kong University of Science and Technology , Hong Kong , China
| | - Marco Man-Hei Cheung
- a Division of Life Science, Center for Cancer Research and State Key Lab for Molecular Neuroscience , Hong Kong University of Science and Technology , Hong Kong , China.,b Guangzhou HKUST Fok Ying Tung Research Institute , Guangzhou , China
| | - Zhiling Yu
- c School of Chinese Medicine , Hong Kong Baptist University , Guangzhou , China
| | - Wei Yang
- a Division of Life Science, Center for Cancer Research and State Key Lab for Molecular Neuroscience , Hong Kong University of Science and Technology , Hong Kong , China.,d Guangdong Lewwin Pharmaceutical Research Institute Co., Ltd , Hong Kong , China
| | - Chun Liang
- a Division of Life Science, Center for Cancer Research and State Key Lab for Molecular Neuroscience , Hong Kong University of Science and Technology , Hong Kong , China.,b Guangzhou HKUST Fok Ying Tung Research Institute , Guangzhou , China.,e ntelgen Limited , Hong Kong-Guangzhou-Foshan , China
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87
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Pierre C, Agopiantz M, Brunaud L, Battaglia-Hsu SF, Max A, Pouget C, Nomine C, Lomazzi S, Vignaud JM, Weryha G, Oussalah A, Gauchotte G, Busby-Venner H. COPPS, a composite score integrating pathological features, PS100 and SDHB losses, predicts the risk of metastasis and progression-free survival in pheochromocytomas/paragangliomas. Virchows Arch 2019; 474:721-734. [DOI: 10.1007/s00428-019-02553-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 02/26/2019] [Accepted: 02/27/2019] [Indexed: 11/30/2022]
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88
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Zhu F, Qian X, Wang Z. Molecular characterization of minichromosome maintenance protein (MCM7) in Scylla paramamosain and its role in white spot syndrome virus and Vibrio alginolyticus infection. FISH & SHELLFISH IMMUNOLOGY 2018; 83:104-114. [PMID: 30205202 DOI: 10.1016/j.fsi.2018.09.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 09/03/2018] [Accepted: 09/07/2018] [Indexed: 06/08/2023]
Abstract
The minichromosome maintenance protein (MCM7) is a member of the MCM protein family which participates in the MCM complex by playing a role in the cell replication cycle and chromosome initiation in eukaryotes. The 2270 bp cDNA sequence of MCM7, including a 2127-bp open reading frame (ORF) encoding a 709-aa protein, was cloned from Scylla paramamosain using RT-PCR and RACE. Data showed that MCM7 was highly expressed in the digestive organ and hepatopancreas of S. paramamosain. Furthermore, MCM7 expression was down-regulated by infection with white spot syndrome virus (WSSV) or Vibrio alginolyticus. When MCM7 was knocked down, immune genes such as Janus kinase (JAK) and crustin antimicrobial peptide (CAP) were down-regulated, and C-type-lectin (CTL) was up-regulated in hemocytes. The mortality of WSSV-infected or V. alginolyticus-infected crabs was enhanced following MCM7 knockdown. It was demonstrated that MCM7 is very important in the progression of WSSV and V. alginolyticus infection. We also investigated the effect of MCM7 on apoptosis rate and phagocytic rate in S. paramamosain. MCM7 knockdown caused higher levels of apoptosis in the hemocytes of the control, WSSV, and V. alginolyticus groups. MCM7 knockdown influenced the activity of phenoloxidase (PO) and superoxide dismutase (SOD), and total hemocyte count (THC) after infection with WSSV or V. alginolyticus, which indicated that MCM7 plays a regulatory role in innate immunity of crabs. Thus, we conclude that MCM7 may participate in the anti-WSSV and V. alginolyticus immune response in crabs by regulating apoptosis and the activity of PO and SOD.
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Affiliation(s)
- Fei Zhu
- College of Animal Science and Technology, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, China.
| | - Xiyi Qian
- College of Animal Science and Technology, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, China
| | - Ziyan Wang
- College of Animal Science and Technology, Zhejiang Agriculture and Forestry University, Hangzhou, 311300, China
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89
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Schumann M, Malešević M, Hinze E, Mathea S, Meleshin M, Schutkowski M, Haehnel W, Schiene-Fischer C. Regulation of the Minichromosome Maintenance Protein 3 (MCM3) Chromatin Binding by the Prolyl Isomerase Pin1. J Mol Biol 2018; 430:5169-5181. [PMID: 30316783 DOI: 10.1016/j.jmb.2018.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 09/26/2018] [Accepted: 10/04/2018] [Indexed: 01/16/2023]
Abstract
Human Pin1 is a peptidyl prolyl cis/trans isomerase with a unique preference for phosphorylated Ser/Thr-Pro substrate motifs. Here we report that MCM3 (minichromosome maintenance complex component 3) is a novel target of Pin1. MCM3 interacts directly with the WW domain of Pin1. Proline-directed phosphorylation of MCM3 at S112 and T722 are crucial for the interaction with Pin1. MCM3 as a subunit of the minichromosome maintenance heterocomplex MCM2-7 is part of the pre-replication complex responsible for replication licensing and is implicated in the formation of the replicative helicase during progression of replication. Our data suggest that Pin1 coordinates phosphorylation-dependently MCM3 loading onto chromatin and its unloading from chromatin, thereby mediating S phase control.
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Affiliation(s)
- Michael Schumann
- Department of Enzymology, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Center, Kurt-Mothes-Str. 3a, D-06120 Halle/Saale, Germany
| | - Miroslav Malešević
- Max Planck Research Unit for Enzymology of Protein Folding Halle, Weinbergweg 22, D-06120 Halle/Saale, Germany
| | - Erik Hinze
- Max Planck Research Unit for Enzymology of Protein Folding Halle, Weinbergweg 22, D-06120 Halle/Saale, Germany
| | - Sebastian Mathea
- Max Planck Research Unit for Enzymology of Protein Folding Halle, Weinbergweg 22, D-06120 Halle/Saale, Germany
| | - Marat Meleshin
- Department of Enzymology, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Center, Kurt-Mothes-Str. 3a, D-06120 Halle/Saale, Germany
| | - Mike Schutkowski
- Department of Enzymology, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Center, Kurt-Mothes-Str. 3a, D-06120 Halle/Saale, Germany
| | - Wolfgang Haehnel
- Institute of Biology II / Biochemistry, Albert-Ludwigs-Universität Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany
| | - Cordelia Schiene-Fischer
- Department of Enzymology, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Center, Kurt-Mothes-Str. 3a, D-06120 Halle/Saale, Germany.
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90
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Lu Z, Huang FY, Cao R, Tan GH, Yi G, He N, Xu L, Zhang L. Intrinsic, Cancer Cell-Selective Toxicity of Organic Photothermal Nanoagent: A Simple Formulation for Combined Photothermal Chemotherapy of Cancer. ACS APPLIED MATERIALS & INTERFACES 2018; 10:26028-26038. [PMID: 30004218 DOI: 10.1021/acsami.8b07801] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Nano-agent-mediated photothermal therapy (PTT) combined with chemotherapy has been proposed as an effective strategy against cancer. However, chemotherapeutic agents often cause serious side effects. Herein, a novel PTT nanoagent (Cy5.5-MSA-G250) with unanticipated intrinsic tumor-selective cytotoxicity is developed. The Cy5.5-MSA-G250 nanoparticles (NPs) are created by mixing mouse serum albumin (MSA) and coomassie brilliant blue (G250) and then conjugated with cyanine 5.5 (Cy5.5). As expected, Cy5.5-MSA-G250 NPs can efficiently kill cancer cells in vitro and in vivo by PTT. Meanwhile, we accidentally discover that Cy5.5-MSA-G250 have intrinsic specific cytotoxicity against tumor cells but not against normal cells. Moreover, the tumor-specific cytotoxicity of Cy5.5-MSA-G250 is much stronger than that of cytarabine, an FDA-approved anticancer drug. In vivo experiments also prove that Cy5.5-MSA-G250 NPs can effectively eliminate residual tumor cells and prevent metastasis. Further study indicates that selective induction of G1 cell cycle arrest and inhibition of DNA duplication in tumor cells may be the possible mechanism of the tumor cell-selective cytotoxicity of Cy5.5-MSA-G250 NPs. In addition, direct visualization, low systematic toxicity, good biodegradation, and efficient body excretion further make Cy5.5-MSA-G250 NPs attractive for in vivo applications. Taken together, Cy5.5-MSA-G250 NPs are proven to be a promising platform for combined photothermal chemotherapy.
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Affiliation(s)
- Zhuoxuan Lu
- Key Laboratory of Tropical Disease and Translational Medicine of the Ministry of Education & Hainan Provincial Key Laboratory of Tropical Medicine , Hainan Medical College , Haikou 571101 , P. R. China
| | - Feng-Ying Huang
- Key Laboratory of Tropical Disease and Translational Medicine of the Ministry of Education & Hainan Provincial Key Laboratory of Tropical Medicine , Hainan Medical College , Haikou 571101 , P. R. China
| | - Rong Cao
- Key Laboratory of Tropical Disease and Translational Medicine of the Ministry of Education & Hainan Provincial Key Laboratory of Tropical Medicine , Hainan Medical College , Haikou 571101 , P. R. China
| | - Guang-Hong Tan
- Key Laboratory of Tropical Disease and Translational Medicine of the Ministry of Education & Hainan Provincial Key Laboratory of Tropical Medicine , Hainan Medical College , Haikou 571101 , P. R. China
| | - Guohui Yi
- Key Laboratory of Tropical Disease and Translational Medicine of the Ministry of Education & Hainan Provincial Key Laboratory of Tropical Medicine , Hainan Medical College , Haikou 571101 , P. R. China
| | - Nongyue He
- Hunan Key Laboratory of Green Chemistry and Application of Biological Nanotechnology , Hunan University of Technology , Zhuzhou 412008 , P. R. China
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering , Southeast University , Nanjing 210096 , P. R. China
| | - Lingfeng Xu
- Key Laboratory of Tropical Disease and Translational Medicine of the Ministry of Education & Hainan Provincial Key Laboratory of Tropical Medicine , Hainan Medical College , Haikou 571101 , P. R. China
| | - Liming Zhang
- Key Laboratory of Tropical Disease and Translational Medicine of the Ministry of Education & Hainan Provincial Key Laboratory of Tropical Medicine , Hainan Medical College , Haikou 571101 , P. R. China
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91
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Zhai Y, Tye BK. Structure of the MCM2-7 Double Hexamer and Its Implications for the Mechanistic Functions of the Mcm2-7 Complex. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1042:189-205. [PMID: 29357059 DOI: 10.1007/978-981-10-6955-0_9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The eukaryotic minichromosome maintenance 2-7 complex is the core of the inactive MCM replication licensing complex and the catalytic core of the Cdc45-MCM-GINS replicative helicase. The years of effort to determine the structure of parts or the whole of the heterohexameric complex by X-ray crystallography and conventional cryo-EM produced limited success. Modern cryo-EM technology ushered in a new era of structural biology that allowed the determination of the structure of the inactive double hexamer at an unprecedented resolution of 3.8 Å. This review will focus on the fine details observed in the Mcm2-7 double hexameric complex and their implications for the function of the Mcm2-7 hexamer in its different roles during DNA replication.
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Affiliation(s)
- Yuanliang Zhai
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China
- Institute for Advanced Study, Hong Kong University of Science and Technology, Hong Kong, China
| | - Bik-Kwoon Tye
- Division of Life Science, Hong Kong University of Science and Technology, Hong Kong, China.
- Department of Molecular Biology and Genetics, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA.
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92
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Liao X, Liu X, Yang C, Wang X, Yu T, Han C, Huang K, Zhu G, Su H, Qin W, Huang R, Yu L, Deng J, Zeng X, Ye X, Peng T. Distinct Diagnostic and Prognostic Values of Minichromosome Maintenance Gene Expression in Patients with Hepatocellular Carcinoma. J Cancer 2018; 9:2357-2373. [PMID: 30026832 PMCID: PMC6036720 DOI: 10.7150/jca.25221] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 04/14/2018] [Indexed: 12/31/2022] Open
Abstract
Background: The aim of the present study was to identify diagnostic and prognostic values of minichromosome maintenance (MCM) gene expression in patients with hepatocellular carcinoma (HCC). Methods: The biological function of the MCM genes were investigated by bioinformatics analysis. The diagnostic and prognostic values of the MCM genes were investigated by using the data of HCC patients from the GSE14520 and The Cancer Genome Atlas (TCGA) databases. Results: Bioinformatics analysis of the MCM genes substantiated that MCM2-7 genes were significantly enriched in DNA replication and cell cycle, and co-expressed with each other. These genes also co-expressed in HCC tumor tissue in both the GSE14520 and TCGA cohort. We also observed that the expression of the MCM2-7 genes was increased in tumor tissue, and diagnostic receiver operating characteristic analysis of MCM2-7 indicated that these genes could serve as sensitive diagnostic markers in HCC. Survival analysis in the GSE14520 cohort suggested that expression of MCM2, MCM4, MCM5, and MCM6 were significantly associated with hepatitis B virus-related HCC overall survival (OS). However, none of the MCM genes were associated with recurrence-free survival in the GSE14520 cohort. The validation cohort of TCGA suggested that the expression of MCM2, MCM6, and MCM7 were significantly correlated with HCC OS. Conclusion: Our study indicated that MCM2-7 genes may be potential diagnostic biomarkers in patients with HCC. Among them, MCM2 and MCM6 may serve as potential prognostic biomarkers for HCC.
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Affiliation(s)
- Xiwen Liao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Xiaoguang Liu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China.,Department of Hepatobiliary Surgery, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, Guangdong Province, People's Republic of China
| | - Chengkun Yang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Xiangkun Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Tingdong Yu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Chuangye Han
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Ketuan Huang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Guangzhi Zhu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Hao Su
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Wei Qin
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Rui Huang
- Department of Hematology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Long Yu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China.,Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000, Henan, China
| | - Jianlong Deng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China.,Department of Hepatobiliary Surgery, The Sixth Affiliated Hospital of Guangxi Medical University, Yulin, 537000, Guangxi, China
| | - Xianmin Zeng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Xinping Ye
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Tao Peng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
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93
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BoxCar acquisition method enables single-shot proteomics at a depth of 10,000 proteins in 100 minutes. Nat Methods 2018; 15:440-448. [DOI: 10.1038/s41592-018-0003-5] [Citation(s) in RCA: 229] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 02/23/2018] [Indexed: 12/30/2022]
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94
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Güzel C, Govorukhina NI, Wisman GBA, Stingl C, Dekker LJM, Klip HG, Hollema H, Guryev V, Horvatovich PL, van der Zee AGJ, Bischoff R, Luider TM. Proteomic alterations in early stage cervical cancer. Oncotarget 2018; 9:18128-18147. [PMID: 29719595 PMCID: PMC5915062 DOI: 10.18632/oncotarget.24773] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 02/25/2018] [Indexed: 01/20/2023] Open
Abstract
Laser capture microdissection (LCM) allows the capture of cell types or well-defined structures in tissue. We compared in a semi-quantitative way the proteomes from an equivalent of 8,000 tumor cells from patients with squamous cell cervical cancer (SCC, n = 22) with healthy epithelial and stromal cells obtained from normal cervical tissue (n = 13). Proteins were enzymatically digested into peptides which were measured by high-resolution mass spectrometry and analyzed by “all-or-nothing” analysis, Bonferroni, and Benjamini-Hochberg correction for multiple testing. By comparing LCM cell type preparations, 31 proteins were exclusively found in early stage cervical cancer (n = 11) when compared with healthy epithelium and stroma, based on criteria that address specificity in a restrictive “all-or-nothing” way. By Bonferroni correction for multiple testing, 30 proteins were significantly up-regulated between early stage cervical cancer and healthy control, including six members of the MCM protein family. MCM proteins are involved in DNA repair and expected to be participating in the early stage of cancer. After a less stringent Benjamini-Hochberg correction for multiple testing, we found that the abundances of 319 proteins were significantly different between early stage cervical cancer and healthy controls. Four proteins were confirmed in digests of whole tissue lysates by Parallel Reaction Monitoring (PRM). Ingenuity Pathway Analysis using correction for multiple testing by permutation resulted in two networks that were differentially regulated in early stage cervical cancer compared with healthy tissue. From these networks, we learned that specific tumor mechanisms become effective during the early stage of cervical cancer.
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Affiliation(s)
- Coşkun Güzel
- Laboratory of Neuro-Oncology, Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Center Rotterdam, Rotterdam 3015 CN, The Netherlands
| | - Natalia I Govorukhina
- Department of Analytical Biochemistry, Center for Pharmacy, University of Groningen, Groningen 9713 AV, The Netherlands
| | - G Bea A Wisman
- Department of Gynecologic Oncology, Cancer Research Center Groningen, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, The Netherlands
| | - Christoph Stingl
- Laboratory of Neuro-Oncology, Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Center Rotterdam, Rotterdam 3015 CN, The Netherlands
| | - Lennard J M Dekker
- Laboratory of Neuro-Oncology, Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Center Rotterdam, Rotterdam 3015 CN, The Netherlands
| | - Harry G Klip
- Department of Gynecologic Oncology, Cancer Research Center Groningen, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, The Netherlands
| | - Harry Hollema
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen 9713 GZ, The Netherlands
| | - Victor Guryev
- Department of Analytical Biochemistry, Center for Pharmacy, University of Groningen, Groningen 9713 AV, The Netherlands
| | - Peter L Horvatovich
- Department of Analytical Biochemistry, Center for Pharmacy, University of Groningen, Groningen 9713 AV, The Netherlands
| | - Ate G J van der Zee
- Department of Gynecologic Oncology, Cancer Research Center Groningen, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, The Netherlands
| | - Rainer Bischoff
- Department of Analytical Biochemistry, Center for Pharmacy, University of Groningen, Groningen 9713 AV, The Netherlands
| | - Theo M Luider
- Laboratory of Neuro-Oncology, Clinical and Cancer Proteomics, Department of Neurology, Erasmus University Medical Center Rotterdam, Rotterdam 3015 CN, The Netherlands
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95
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Brand CL, Cattani MV, Kingan SB, Landeen EL, Presgraves DC. Molecular Evolution at a Meiosis Gene Mediates Species Differences in the Rate and Patterning of Recombination. Curr Biol 2018; 28:1289-1295.e4. [PMID: 29606420 DOI: 10.1016/j.cub.2018.02.056] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 02/15/2018] [Accepted: 02/20/2018] [Indexed: 10/17/2022]
Abstract
Crossing over between homologous chromosomes during meiosis repairs programmed DNA double-strand breaks, ensures proper segregation at meiosis I [1], shapes the genomic distribution of nucleotide variability in populations, and enhances the efficacy of natural selection among genetically linked sites [2]. Between closely related Drosophila species, large differences exist in the rate and chromosomal distribution of crossing over. Little, however, is known about the molecular genetic changes or population genetic forces that mediate evolved differences in recombination between species [3, 4]. Here, we show that a meiosis gene with a history of rapid evolution acts as a trans-acting modifier of species differences in crossing over. In transgenic flies, the dicistronic gene, mei-217/mei-218, recapitulates a large part of the species differences in the rate and chromosomal distribution of crossing over. These phenotypic differences appear to result from changes in protein sequence not gene expression. Our population genetics analyses show that the protein-coding sequence of mei-218, but not mei-217, has a history of recurrent positive natural selection. By modulating the intensity of centromeric and telomeric suppression of crossing over, evolution at mei-217/-218 has incidentally shaped gross differences in the chromosomal distribution of nucleotide variability between species. We speculate that recurrent bouts of adaptive evolution at mei-217/-218 might reflect a history of coevolution with selfish genetic elements.
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Affiliation(s)
- Cara L Brand
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - M Victoria Cattani
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Sarah B Kingan
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Emily L Landeen
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Daven C Presgraves
- Department of Biology, University of Rochester, Rochester, NY 14627, USA.
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96
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Seo YS, Kang YH. The Human Replicative Helicase, the CMG Complex, as a Target for Anti-cancer Therapy. Front Mol Biosci 2018; 5:26. [PMID: 29651420 PMCID: PMC5885281 DOI: 10.3389/fmolb.2018.00026] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 03/12/2018] [Indexed: 12/14/2022] Open
Abstract
DNA helicases unwind or rearrange duplex DNA during replication, recombination and repair. Helicases of many pathogenic organisms such as viruses, bacteria, and protozoa have been studied as potential therapeutic targets to treat infectious diseases, and human DNA helicases as potential targets for anti-cancer therapy. DNA replication machineries perform essential tasks duplicating genome in every cell cycle, and one of the important functions of these machineries are played by DNA helicases. Replicative helicases are usually multi-subunit protein complexes, and the minimal complex active as eukaryotic replicative helicase is composed of 11 subunits, requiring a functional assembly of two subcomplexes and one protein. The hetero-hexameric MCM2-7 helicase is activated by forming a complex with Cdc45 and the hetero-tetrameric GINS complex; the Cdc45-Mcm2-7-GINS (CMG) complex. The CMG complex can be a potential target for a treatment of cancer and the feasibility of this replicative helicase as a therapeutic target has been tested recently. Several different strategies have been implemented and are under active investigations to interfere with helicase activity of the CMG complex. This review focuses on the molecular function of the CMG helicase during DNA replication and its relevance to cancers based on data published in the literature. In addition, current efforts made to identify small molecules inhibiting the CMG helicase to develop anti-cancer therapeutic strategies were summarized, with new perspectives to advance the discovery of the CMG-targeting drugs.
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Affiliation(s)
- Yeon-Soo Seo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Young-Hoon Kang
- Core Protein Resources Center, Daegu Gyeongbuk Institute of Science and Technology, Daegu, South Korea
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97
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Wang D, Li Q, Li Y, Wang H. The role of MCM5 expression in cervical cancer: Correlation with progression and prognosis. Biomed Pharmacother 2017; 98:165-172. [PMID: 29253764 DOI: 10.1016/j.biopha.2017.12.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 11/29/2017] [Accepted: 12/04/2017] [Indexed: 12/12/2022] Open
Abstract
Minichromosome maintenance protein 5 (MCM5) has been suggested overexpressed in cervical cancer, but the clinical value and biological function of MCM5 in cervical cancer is still unknown. In our study, MCM5 mRNA and protein were significantly overexpressed in cervical cancer tissues and cell lines compared with normal cervical tissues and cell lines, and were obviously increased in cervical adenocarcinoma tissues and cell lines in comparison to cervical squamous cell carcinoma tissues and cell lines. In cervical adenocarcinoma patients, we firstly found that MCM5 expression was closely correlated with clinical stage, lymph node metastasis, distant metastasis and histological grade. Univariate and multivariate analysis showed MCM5 high-expression was an independent unfavorable prognostic factor. In conclusion, MCM5 is associated with the malignant status and poor prognosis in cervical adenocarcinoma patients, and modulates cervical adenocarcinoma cells proliferation.
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Affiliation(s)
- Dan Wang
- Department of Gynecology, Jining No. 1 People's Hospital, Jining, 272000, Shandong, China
| | - Qian Li
- Department of Gynecology, Jining No. 1 People's Hospital, Jining, 272000, Shandong, China
| | - Yichun Li
- Department of Hepatobiliary Surgery, Jining No. 1 People's Hospital, Jining, 272000, Shandong, China
| | - Hongyan Wang
- Department of Gynecology, Jining No. 1 People's Hospital, Jining, 272000, Shandong, China.
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98
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Lopez Aguilar A, Gao Y, Hou X, Lauvau G, Yates JR, Wu P. Profiling of Protein O-GlcNAcylation in Murine CD8 + Effector- and Memory-like T Cells. ACS Chem Biol 2017; 12:3031-3038. [PMID: 29125738 DOI: 10.1021/acschembio.7b00869] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
During an acute infection, antigenic stimulation leads to activation, expansion, and differentiation of naïve CD8+ T cells, first into cytotoxic effector cells and eventually into long-lived memory cells. T cell antigen receptors (TCRs) detect antigens on antigen-presenting cells (APCs) in the form of antigenic peptides bound to major histocompatibility complex I (MHC-I)-encoded molecules and initiate TCR signal transduction network. This process is mediated by phosphorylation of many intracellular signaling proteins. Protein O-GlcNAc modification is another post-translational modification involved in this process, which often has either reciprocal or synergistic roles with phosphorylation. In this study, using a chemoenzymatic glycan labeling technique and proteomics analysis, we compared protein O-GlcNAcylation of murine effector and memory-like CD8+ T cells differentiated in vitro. By quantitative proteomics analysis, we identified 445 proteins that are significantly regulated in either effector- or memory-like T cell subsets. Furthermore, qualitative and quantitative analysis identified highly regulated protein clusters that suggest involvement of this post-translational modification in specific cellular processes. In effector-like T cells, protein O-GlcNAcylation is heavily involved in transcriptional and translational processes that drive fast effector T cells proliferation. During the formation of memory-like T cells, protein O-GlcNAcylation is involved in a more specific, perhaps more targeted regulation of transcription, mRNA processing, and translation. Significantly, O-GlcNAc plays a critical role as part of the "histone code" in both CD8+ T cells subgroups.
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Affiliation(s)
- Aime Lopez Aguilar
- Department
of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Yu Gao
- Department
of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Xiaomeng Hou
- Department
of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Gregoire Lauvau
- Department
of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| | - John R. Yates
- Department
of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Peng Wu
- Department
of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
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99
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Minichromosome maintenance complex component 6 (MCM6) expression correlates with histological grade and survival in endometrioid endometrial adenocarcinoma. Virchows Arch 2017; 472:623-633. [PMID: 29243125 DOI: 10.1007/s00428-017-2278-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/30/2017] [Accepted: 12/04/2017] [Indexed: 12/16/2022]
Abstract
Minichromosome maintenance complex component 6 (MCM6) is involved in initiating DNA replication and is upregulated during licensed G0 phase of the cell cycle. This early expression permits its labeling of more proliferating cells than those by Ki-67. Here using a cohort of 89 endometrioid adenocarcinoma, we report findings made on the prognostic value of MCM6 based on immunohistochemical labeling index (LI) of the protein in comparison with that of Ki67 as no such information is currently available. Additionally, we examined the prognostic values of these markers based on their mRNA expression using a cohort of uterine corpus endometrial carcinoma (UCEC, n = 307) taken from The Cancer Genome Atlas (TCGA) database. Our evidence indicated the presence of a positive correlation between the LI of MCM6 and the histological grade of endometrioid endometrial adenocarcinoma (grade I, 66.7%; grade II, 75.3%; grade III, 81.4%; p < 0.001) and an inverse correlation between the LI of MCM6 and the overall and progression-free survival (p = 0.02 for both). The LI of Ki-67 correlated with grade (p < 0.001), but not survival. The MCM6 and Ki-67 inter-observer intra-class correlation coefficients were excellent: 0.84 (95% confidence interval, 0.83-0.91) and 0.84 (0.77-0.90), respectively. For in silico analyses of the TCGA cohort, both univariate and multivariate Cox analyses (p = 0.003 and p = 0.03, respectively) revealed high MCM6 mRNA Z-scores associated with reduced overall survival. This association was absent for Ki-67. MCM6 is thus a highly reproducible marker of poor prognosis in endometrial cancer. Evaluation of MCM6 should thus be considered in daily practice for risk stratification.
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100
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Saavedra C, Milan M, Leite RB, Cordero D, Patarnello T, Cancela ML, Bargelloni L. A Microarray Study of Carpet-Shell Clam ( Ruditapes decussatus) Shows Common and Organ-Specific Growth-Related Gene Expression Differences in Gills and Digestive Gland. Front Physiol 2017; 8:943. [PMID: 29234285 PMCID: PMC5712350 DOI: 10.3389/fphys.2017.00943] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 11/07/2017] [Indexed: 01/04/2023] Open
Abstract
Growth rate is one of the most important traits from the point of view of individual fitness and commercial production in mollusks, but its molecular and physiological basis is poorly known. We have studied differential gene expression related to differences in growth rate in adult individuals of the commercial marine clam Ruditapes decussatus. Gene expression in the gills and the digestive gland was analyzed in 5 fast-growing and five slow-growing animals by means of an oligonucleotide microarray containing 14,003 probes. A total of 356 differentially expressed genes (DEG) were found. We tested the hypothesis that differential expression might be concentrated at the growth control gene core (GCGC), i.e., the set of genes that underlie the molecular mechanisms of genetic control of tissue and organ growth and body size, as demonstrated in model organisms. The GCGC includes the genes coding for enzymes of the insulin/insulin-like growth factor signaling pathway (IIS), enzymes of four additional signaling pathways (Raf/Ras/Mapk, Jnk, TOR, and Hippo), and transcription factors acting at the end of those pathways. Only two out of 97 GCGC genes present in the microarray showed differential expression, indicating a very little contribution of GCGC genes to growth-related differential gene expression. Forty eight DEGs were shared by both organs, with gene ontology (GO) annotations corresponding to transcription regulation, RNA splicing, sugar metabolism, protein catabolism, immunity, defense against pathogens, and fatty acid biosynthesis. GO term enrichment tests indicated that genes related to growth regulation, development and morphogenesis, extracellular matrix proteins, and proteolysis were overrepresented in the gills. In the digestive gland overrepresented GO terms referred to gene expression control through chromatin rearrangement, RAS-related small GTPases, glucolysis, and energy metabolism. These analyses suggest a relevant role of, among others, some genes related to the IIS, such as the ParaHox gene Xlox, CCAR and the CCN family of secreted proteins, in the regulation of growth in bivalves.
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Affiliation(s)
- Carlos Saavedra
- Instituto de Acuicultura Torre de la Sal, Consejo Superior de Investigaciones Científicas, Castelló de la Plana, Spain
| | - Massimo Milan
- Dipartimento di Biomedicina Comparata e Alimentazione, Universitá di Padova, Polo di Agripolis, Legnaro, Italy
| | - Ricardo B Leite
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Faro, Portugal
| | - David Cordero
- Instituto de Acuicultura Torre de la Sal, Consejo Superior de Investigaciones Científicas, Castelló de la Plana, Spain
| | - Tomaso Patarnello
- Dipartimento di Biomedicina Comparata e Alimentazione, Universitá di Padova, Polo di Agripolis, Legnaro, Italy
| | - M Leonor Cancela
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Faro, Portugal.,Department of Biomedical Sciences and Medicine and Academic Biomedical Centre, Universidade do Algarve, Faro, Portugal
| | - Luca Bargelloni
- Dipartimento di Biomedicina Comparata e Alimentazione, Universitá di Padova, Polo di Agripolis, Legnaro, Italy
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