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Li Y, Gao W, Yang Z, Hu Z, Li J. Multi-omics pan-cancer analyses identify MCM4 as a promising prognostic and diagnostic biomarker. Sci Rep 2024; 14:6517. [PMID: 38499612 PMCID: PMC10948783 DOI: 10.1038/s41598-024-57299-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 03/16/2024] [Indexed: 03/20/2024] Open
Abstract
Minichromosome Maintenance Complex Component 4 (MCM4) is a vital component of the mini-chromosome maintenance complex family, crucial for initiating the replication of eukaryotic genomes. Recently, there has been a growing interest in investigating the significance of MCM4 in different types of cancer. Despite the existing research on this topic, a comprehensive analysis of MCM4 across various cancer types has been lacking. This study aims to bridge this knowledge gap by presenting a thorough pan-cancer analysis of MCM4, shedding light on its functional implications and potential clinical applications. The study utilized multi-omics samples from various databases. Bioinformatic tools were employed to explore the expression profiles, genetic alterations, phosphorylation states, immune cell infiltration patterns, immune subtypes, functional enrichment, disease prognosis, as well as the diagnostic potential of MCM4 and its responsiveness to drugs in a range of cancers. Our research demonstrates that MCM4 is closely associated with the oncogenesis, prognosis and diagnosis of various tumors and proposes that MCM4 may function as a potential biomarker in pan-cancer, providing a deeper understanding of its potential role in cancer development and treatment.
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Affiliation(s)
- Yanxing Li
- Xi'an Jiaotong University Health Science Center, Xi'an, 710000, Shaanxi, People's Republic of China
| | - Wentao Gao
- Xi'an Jiaotong University Health Science Center, Xi'an, 710000, Shaanxi, People's Republic of China
| | - Zhen Yang
- Xi'an Jiaotong University Health Science Center, Xi'an, 710000, Shaanxi, People's Republic of China
| | - Zhenwei Hu
- Xi'an Jiaotong University Health Science Center, Xi'an, 710000, Shaanxi, People's Republic of China
| | - Jianjun Li
- Department of Cardiology, Jincheng People's Hospital Affiliated to Changzhi Medical College, Jincheng, Shanxi, People's Republic of China.
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Tan Y, Ding L, Li G. MCM4 acts as a biomarker for LUAD prognosis. J Cell Mol Med 2023; 27:3354-3362. [PMID: 37817427 PMCID: PMC10623528 DOI: 10.1111/jcmm.17819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 04/16/2023] [Accepted: 06/14/2023] [Indexed: 10/12/2023] Open
Abstract
MCM4 forms the pre-replication complex (MCM2-7) with five other minichromosome maintenance (MCM) proteins. This complex binds to replication origins at G1 stage in cell cycle process, playing a critical role in DNA replication initiation. Recently, MCM4 is reported to have a complex interaction with multiple cancer progression, including gastric, ovarian and cervical cancer. Here, this study mainly focused on the expression of MCM4 and its values in lung adenocarcinoma (LUAD). MCM4 was highly expressed in LUAD tumours and cells, and had an important effect on the overall survival. Overexpression of MCM4 promoted the proliferation, and suppressed the apoptosis in LUAD cells. However, MCM4 silence led to the opposite results. In vivo, knockdown of MCM4 inhibited tumour volume and weight in xenograft mouse model. As a member of DNA helicase, knockdown of MCM4 caused cell cycle arrest at G1 stage through inducing the expression of P21, a CDK inhibitor. These findings indicate that MCM4 may be a possible new therapeutic target for LUAD in the future.
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Affiliation(s)
- Yue Tan
- Branch of Minhang, Department of Medical OncologyFudan University Shanghai Cancer CenterShanghaiChina
| | - Lei Ding
- Department of Ultrasonic DiagnosisSecond Affiliated Hospital of Anhui Medical UniversityHefeiChina
| | - Guiyuan Li
- Department of Oncology, School of Medicine, Tongji HospitalTongji UniversityShanghaiChina
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Kim SM, Forsburg SL. Determinants of RPA megafoci localization to the nuclear periphery in response to replication stress. G3 (Bethesda) 2022; 12:jkac116. [PMID: 35567482 PMCID: PMC9258583 DOI: 10.1093/g3journal/jkac116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
Upon replication stress, ssDNA, coated by the ssDNA-binding protein RPA, accumulates and generates a signal to activate the replication stress response. Severe replication stress induced by the loss of minichromosome maintenance helicase subunit Mcm4 in the temperature-sensitive Schizosaccharomyces pombe degron mutant (mcm4-dg) results in the formation of a large RPA focus that is translocated to the nuclear periphery. We show that resection and repair processes and chromatin remodeler Swr1/Ino80 are involved in the large RPA foci formation and its relocalization to nuclear periphery. This concentrated accumulation of RPA increases the recruitment of Cds1 to chromatin and results in an aberrant cell cycle that lacks MBF-mediated G1/S accumulation of Tos4. These findings reveal a distinct replication stress response mediated by localized accumulation of RPA that allows the evasion of cell cycle arrest.
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Affiliation(s)
- Seong Min Kim
- Molecular & Computational Biology, University of Southern California, Los Angeles, CA 90007, USA
| | - Susan L Forsburg
- Corresponding author: Molecular & Computational Biology, University of Southern California, Los Angeles, CA 90007, USA.
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Ikui AE, Ueki N, Pecani K, Cross FR. Control of pre-replicative complex during the division cycle in Chlamydomonas reinhardtii. PLoS Genet 2021; 17:e1009471. [PMID: 33909603 PMCID: PMC8081180 DOI: 10.1371/journal.pgen.1009471] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 03/07/2021] [Indexed: 12/31/2022] Open
Abstract
DNA replication is fundamental to all living organisms. In yeast and animals, it is triggered by an assembly of pre-replicative complex including ORC, CDC6 and MCMs. Cyclin Dependent Kinase (CDK) regulates both assembly and firing of the pre-replicative complex. We tested temperature-sensitive mutants blocking Chlamydomonas DNA replication. The mutants were partially or completely defective in DNA replication and did not produce mitotic spindles. After a long G1, wild type Chlamydomonas cells enter a division phase when it undergoes multiple rapid synchronous divisions ('multiple fission'). Using tagged transgenic strains, we found that MCM4 and MCM6 were localized to the nucleus throughout the entire multiple fission division cycle, except for transient cytoplasmic localization during each mitosis. Chlamydomonas CDC6 was transiently localized in nucleus in early division cycles. CDC6 protein levels were very low, probably due to proteasomal degradation. CDC6 levels were severely reduced by inactivation of CDKA1 (CDK1 ortholog) but not the plant-specific CDKB1. Proteasome inhibition did not detectably increase CDC6 levels in the cdka1 mutant, suggesting that CDKA1 might upregulate CDC6 at the transcriptional level. All of the DNA replication proteins tested were essentially undetectable until late G1. They accumulated specifically during multiple fission and then were degraded as cells completed their terminal divisions. We speculate that loading of origins with the MCM helicase may not occur until the end of the long G1, unlike in the budding yeast system. We also developed a simple assay for salt-resistant chromatin binding of MCM4, and found that tight MCM4 loading was dependent on ORC1, CDC6 and MCM6, but not on RNR1 or CDKB1. These results provide a microbial framework for approaching replication control in the plant kingdom.
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Affiliation(s)
- Amy E. Ikui
- Department of Biology, Brooklyn College, The City University of New York, New York City, New York, United States of America
- * E-mail: (AEI); (FRC)
| | - Noriko Ueki
- Department of Biology, Brooklyn College, The City University of New York, New York City, New York, United States of America
| | - Kresti Pecani
- Laboratory of Cell Cycle Genetics, The Rockefeller University, New York City, New York, United States of America
| | - Frederick R. Cross
- Laboratory of Cell Cycle Genetics, The Rockefeller University, New York City, New York, United States of America
- * E-mail: (AEI); (FRC)
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Byun WS, Kim S, Shin YH, Kim WK, Oh DC, Lee SK. Antitumor Activity of Ohmyungsamycin A through the Regulation of the Skp2-p27 Axis and MCM4 in Human Colorectal Cancer Cells. J Nat Prod 2020; 83:118-126. [PMID: 31894983 DOI: 10.1021/acs.jnatprod.9b00918] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Ohmyungsamycin A (1), a novel cyclic peptide discovered from a marine Streptomyces sp., was previously reported with antibacterial and anticancer activities. However, the antitumor activities and the underlying molecular mechanisms of 1 remain to be elucidated. Compound 1 inhibited the proliferation and tumor growth of HCT116 human colorectal cancer cells based on both in vitro cell cultures and an in vivo animal model. A cDNA microarray analysis revealed that 1 downregulated genes involved in cell cycle checkpoint control. Compound 1 also induced G0/G1 cell cycle arrest that was mediated by the regulation of S-phase kinase-associated protein 2 (Skp2)-p27 axis and minichromosome maintenance protein 4 (MCM4). Furthermore, a longer exposure of 1 exhibited an accumulation of a sub-G1 phase cell population, which is characteristic of apoptotic cells. The induction of apoptosis by 1 was also associated with the modulation of caspase family proteins. Compound 1 effectively suppressed tumor growth in a xenograft mouse model subcutaneously implanted with HCT116 cells. In addition, analysis of tumors revealed that 1 upregulated the expression of the CDK inhibitor p27 but downregulated the expression of Skp2 and MCM4. These findings demonstrate the involvement of 1 in cell cycle regulation and the induction of apoptosis in human colorectal cancer cells.
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Affiliation(s)
- Woong Sub Byun
- College of Pharmacy, Natural Products Research Institute , Seoul National University , Seoul 08826 , Republic of Korea
| | - Sunghwa Kim
- College of Pharmacy, Natural Products Research Institute , Seoul National University , Seoul 08826 , Republic of Korea
| | - Yern-Hyerk Shin
- College of Pharmacy, Natural Products Research Institute , Seoul National University , Seoul 08826 , Republic of Korea
| | - Won Kyung Kim
- College of Pharmacy, Natural Products Research Institute , Seoul National University , Seoul 08826 , Republic of Korea
| | - Dong-Chan Oh
- College of Pharmacy, Natural Products Research Institute , Seoul National University , Seoul 08826 , Republic of Korea
| | - Sang Kook Lee
- College of Pharmacy, Natural Products Research Institute , Seoul National University , Seoul 08826 , Republic of Korea
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Issac MSM, Yousef E, Tahir MR, Gaboury LA. MCM2, MCM4, and MCM6 in Breast Cancer: Clinical Utility in Diagnosis and Prognosis. Neoplasia 2019; 21:1015-1035. [PMID: 31476594 PMCID: PMC6726925 DOI: 10.1016/j.neo.2019.07.011] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/24/2019] [Accepted: 07/29/2019] [Indexed: 12/25/2022] Open
Abstract
Breast cancer is a heterogeneous disease comprising the estrogen receptor (ER)-positive luminal subtype which is subdivided into luminal A and luminal B and ER-negative breast cancer which includes the triple-negative subtype. This study has four aims: 1) to examine whether Minichromosome Maintenance (MCM)2, MCM4, and MCM6 can be used as markers to differentiate between luminal A and luminal B subtypes; 2) to study whether MCM2, MCM4, and MCM6 are highly expressed in triple-negative breast cancer, as there is an urgent need to search for surrogate markers in this aggressive subtype, for drug development purposes; 3) to compare the prognostic values of these markers in predicting relapse-free survival; and 4) to compare the three approaches used for scoring the protein expression of these markers by immunohistochemistry (IHC). MCM2, MCM4, MCM6, and MKI67 mRNA expression was first studied using in silico analysis of available breast cancer datasets. We next used IHC to evaluate their protein expression on tissue microarrays using three scoring methods. MCM2, MCM4, and MCM6 can help in distinction between luminal A and luminal B whose therapeutic management and clinical outcomes are different. MCM2, MCM4, MCM6, and Ki-67 are highly expressed in breast cancer of high histological grades that comprise clinically aggressive tumors such as luminal B, HER2-positive, and triple-negative subtypes. Low transcript expression of these markers is associated with increased probability of relapse-free survival. A positive relationship exists among the three scoring methods of each of the four markers. An independent validation cohort is needed to confirm their clinical utility.
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Affiliation(s)
- Marianne Samir Makboul Issac
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, Quebec, Canada H3T 1J4
| | - Einas Yousef
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, Quebec, Canada H3T 1J4
| | - Muhammad Ramzan Tahir
- The University of Montreal Hospital Research Centre, Montréal, Quebec, Canada H2X 0A9
| | - Louis A Gaboury
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Montréal, Quebec, Canada H3T 1J4; Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montréal, Quebec, Canada H3T 1J4.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Tatsumi R, Ishimi Y. An MCM4 mutation detected in cancer cells affects MCM4/6/7 complex formation. J Biochem 2017; 161:259-268. [PMID: 27794528 DOI: 10.1093/jb/mvw065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 09/20/2016] [Indexed: 02/01/2023] Open
Abstract
An MCM4 mutation detected in human cancer cells from endometrium was characterized. The mutation of G486D is located within MCM-box and the glycine at 486 in human MCM4 is conserved in Saccharomyces cerevisiae MCM4 and Sulfolobus solfataricus MCM. This MCM4 mutation affected human MCM4/6/7 complex formation, since the complex containing the mutant MCM4 protein is unstable and the mutant MCM4 protein is tend to be degraded. It is likely that the MCM4 mutation affects the interaction with MCM7 to destabilize the MCM4/6/7 complex. Cells with abnormal nuclear morphology were detected when the mutant MCM4 was expressed in HeLa cells, suggesting that DNA replication was perturbed in the presence of the mutant MCM4. Role of the conserved amino acid in MCM4 function is discussed.
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Xie L, Li T, Yang LH. E2F2 induces MCM4, CCNE2 and WHSC1 upregulation in ovarian cancer and predicts poor overall survival. Eur Rev Med Pharmacol Sci 2017; 21:2150-2156. [PMID: 28537669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
OBJECTIVE To explore the genes co-upregulated with E2F2 in ovarian cancer and their association with survival outcomes in ovarian cancer patients. MATERIALS AND METHODS The raw data of GDS3592 was downloaded from GEO datasets for reanalysis. The overlapping subset between the top 150 upregulated genes in ovarian cancer epithelial cells (CEPIs) and the E2F2 positively correlated genes (Pearson's r≥0.5) in ovarian cancer cohort in TCGA was identified. The association between E2F2, MCM4, CCNE2 and WHSC1 and overall survival (OS) and recurrence-free survival (RFS) in ovarian cancer patients were assessed using Kaplan-Meier plotter. RESULTS E2F2 is a significantly upregulated transcription factor in CEPIs. MCM4, CCNE2, and WHSC1 are co-upregulated with E2F2 among the 308 ovarian cancer samples (Pearson's r=0.5159, 0.3963 and 0.4941 respectively). Enforced E2F2 expression significantly enhanced MCM4, CCNE2 and WHSC1 transcription in SKOV3 and A2780 cells. High E2F2 and CCNE2 expression are associated with worse OS (high E2F2, HR: 1.48, 95%CI: 1.17-1.85, p<0.01; high CCNE2, HR: 1.36, 95%CI: 1.15-1.6, p<0.01). High MCM expression might be associated with worse RFS at the margin of significance (HR: 1.18, 95%CI: 1.00-1.39, p=0.055). CONCLUSIONS MCM4, CCNE2, and WHSC1 are co-upregulated with E2F2 in ovarian cancer. Enforced E2F2 expression significantly increased MCM4, CCNE2, and WHSC1 expression in ovarian cancer cells. High E2F2 and CCNE2 expression are associated with worse OS among ovarian cancer patients.
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Affiliation(s)
- L Xie
- Department of Gynecology, the First Hospital of Hebei Medical University, Shijiazhuang, Hebei, China.
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Wu R, Wang Z, Zhang H, Gan H, Zhang Z. H3K9me3 demethylase Kdm4d facilitates the formation of pre-initiative complex and regulates DNA replication. Nucleic Acids Res 2017; 45:169-180. [PMID: 27679476 PMCID: PMC5224507 DOI: 10.1093/nar/gkw848] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/13/2016] [Accepted: 09/14/2016] [Indexed: 11/30/2022] Open
Abstract
DNA replication is tightly regulated to occur once and only once per cell cycle. How chromatin, the physiological substrate of DNA replication machinery, regulates DNA replication remains largely unknown. Here we show that histone H3 lysine 9 demethylase Kdm4d regulates DNA replication in eukaryotic cells. Depletion of Kdm4d results in defects in DNA replication, which can be rescued by the expression of H3K9M, a histone H3 mutant transgene that reverses the effect of Kdm4d on H3K9 methylation. Kdm4d interacts with replication proteins, and its recruitment to DNA replication origins depends on the two pre-replicative complex components (origin recognition complex [ORC] and minichromosome maintenance [MCM] complex). Depletion of Kdm4d impairs the recruitment of Cdc45, proliferating cell nuclear antigen (PCNA), and polymerase δ, but not ORC and MCM proteins. These results demonstrate a novel mechanism by which Kdm4d regulates DNA replication by reducing the H3K9me3 level to facilitate formation of pre-initiative complex.
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Affiliation(s)
- Rentian Wu
- Department of Biochemistry and Molecular Biology, Mayo Clinic Cancer Center, Mayo Clinic, Rochester, MN 55902, USA
| | - Zhiquan Wang
- Department of Biochemistry and Molecular Biology, Mayo Clinic Cancer Center, Mayo Clinic, Rochester, MN 55902, USA
| | - Honglian Zhang
- Institute for Cancer Genetics, Department of Pediatric and Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Haiyun Gan
- Institute for Cancer Genetics, Department of Pediatric and Department of Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Zhiguo Zhang
- Institute for Cancer Genetics, Department of Pediatric and Department of Genetics and Development, Columbia University, New York, NY 10032, USA
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Nan YL, Hu YL, Liu ZK, Duan FF, Xu Y, Li S, Li T, Chen DF, Zeng XY. Relationships between cell cycle pathway gene polymorphisms and risk of hepatocellular carcinoma. World J Gastroenterol 2016; 22:5558-5567. [PMID: 27350734 PMCID: PMC4917616 DOI: 10.3748/wjg.v22.i24.5558] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 04/29/2016] [Accepted: 05/23/2016] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the associiations between the polymorphisms of cell cycle pathway genes and the risk of hepatocellular carcinoma (HCC).
METHODS: We enrolled 1127 cases newly diagnosed with HCC from the Tumor Hospital of Guangxi Medical University and 1200 non-tumor patients from the First Affiliated Hospital of Guangxi Medical University. General demographic characteristics, behavioral information, and hematological indices were collected by unified questionnaires. Genomic DNA was isolated from peripheral venous blood using Phenol-Chloroform. The genotyping was performed using the Sequenom MassARRAY iPLEX genotyping method. The association between genetic polymorphisms and risk of HCC was shown by P-value and the odd ratio (OR) with 95% confidence interval (CI) using the unconditional logistic regression after adjusting for age, sex, nationality, smoking, drinking, family history of HCC, and hepatitis B virus (HBV) infection. Moreover, stratified analysis was conducted on the basis of the status of HBV infection, smoking, and alcohol drinking.
RESULTS: The HCC risk was lower in patients with the MCM4 rs2305952 CC (OR = 0.22, 95%CI: 0.08-0.63, P = 0.01) and with the CHEK1 rs515255 TC, TT, TC/TT (OR = 0.73, 95%CI: 0.56-0.96, P = 0.02; OR = 0.67, 95%CI: 0.46-0.97, P = 0.04; OR = 0.72, 95%CI: 0.56-0.92, P = 0.01, respectively). Conversely, the HCC risk was higher in patients with the KAT2B rs17006625 GG (OR = 1.64, 95%CI: 1.01-2.64, P = 0.04). In addition, the risk was markedly lower for those who were carriers of MCM4 rs2305952 CC and were also HBsAg-positive and non-drinking and non-smoking (P < 0.05, respectively) and for those who were carriers of CHEK1 rs515255 TC, TT, TC/TT and were also HBsAg-negative and non-drinking (P < 0.05, respectively). Moreover, the risk was higher for those who were carriers of KAT2B rs17006625 GG and were also HBsAg-negative (P < 0.05).
CONCLUSION: Of 12 cell cycle pathway genes, MCM4, CHEK1 and KAT2B polymorphisms may be associated with the risk of HCC.
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Sugimoto N, Maehara K, Yoshida K, Yasukouchi S, Osano S, Watanabe S, Aizawa M, Yugawa T, Kiyono T, Kurumizaka H, Ohkawa Y, Fujita M. Cdt1-binding protein GRWD1 is a novel histone-binding protein that facilitates MCM loading through its influence on chromatin architecture. Nucleic Acids Res 2015; 43:5898-911. [PMID: 25990725 PMCID: PMC4499137 DOI: 10.1093/nar/gkv509] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 05/04/2015] [Accepted: 05/05/2015] [Indexed: 12/16/2022] Open
Abstract
Efficient pre-replication complex (pre-RC) formation on chromatin templates is crucial for the maintenance of genome integrity. However, the regulation of chromatin dynamics during this process has remained elusive. We found that a conserved protein, GRWD1 (glutamate-rich WD40 repeat containing 1), binds to two representative replication origins specifically during G1 phase in a CDC6- and Cdt1-dependent manner, and that depletion of GRWD1 reduces loading of MCM but not CDC6 and Cdt1. Furthermore, chromatin immunoprecipitation coupled with high-throughput sequencing (Seq) revealed significant genome-wide co-localization of GRWD1 with CDC6. We found that GRWD1 has histone-binding activity. To investigate the effect of GRWD1 on chromatin architecture, we used formaldehyde-assisted isolation of regulatory elements (FAIRE)-seq or FAIRE-quantitative PCR analyses, and the results suggest that GRWD1 regulates chromatin openness at specific chromatin locations. Taken together, these findings suggest that GRWD1 may be a novel histone-binding protein that regulates chromatin dynamics and MCM loading at replication origins.
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Affiliation(s)
- Nozomi Sugimoto
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kazumitsu Maehara
- Faculty of Medicine, Division of Epigenetics, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kazumasa Yoshida
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Shuhei Yasukouchi
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Satoko Osano
- Division of Virology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Shinya Watanabe
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Masahiro Aizawa
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Takashi Yugawa
- Division of Virology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Tohru Kiyono
- Division of Virology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Yasuyuki Ohkawa
- Faculty of Medicine, Division of Epigenetics, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Masatoshi Fujita
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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Turnbull AK, Arthur LM, Renshaw L, Larionov AA, Kay C, Dunbier AK, Thomas JS, Dowsett M, Sims AH, Dixon JM. Accurate Prediction and Validation of Response to Endocrine Therapy in Breast Cancer. J Clin Oncol 2015; 33:2270-8. [PMID: 26033813 DOI: 10.1200/jco.2014.57.8963] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
PURPOSE Aromatase inhibitors (AIs) have an established role in the treatment of breast cancer. Response rates are only 50% to 70% in the neoadjuvant setting and lower in advanced disease. Accurate biomarkers are urgently needed to predict response in these settings and to determine which individuals will benefit from adjuvant AI therapy. PATIENTS AND METHODS Pretreatment and on-treatment (after 2 weeks and 3 months) biopsies were obtained from 89 postmenopausal women who had estrogen receptor-alpha positive breast cancer and were receiving neoadjuvant letrozole for transcript profiling. Dynamic clinical response was assessed with use of three-dimensional ultrasound measurements. RESULTS The molecular response to letrozole was characterized and a four-gene classifier of clinical response was established (accuracy of 96%) on the basis of the level of two genes before treatment (one gene [IL6ST] was associated with immune signaling, and the other [NGFRAP1] was associated with apoptosis) and the level of two proliferation genes (ASPM, MCM4) after 2 weeks of therapy. The four-gene signature was found to be 91% accurate in a blinded, completely independent validation data set of patients treated with anastrozole. Matched 2-week on-treatment biopsies were associated with improved predictive power as compared with pretreatment biopsies alone. This signature also significantly predicted recurrence-free survival (P = .029) and breast cancer -specific survival (P = .009). We demonstrate that the test can also be performed with use of quantitative polymerase chain reaction or immunohistochemistry. CONCLUSION A four-gene predictive model of clinical response to AIs by 2 weeks has been generated and validated. Deregulated immune and apoptotic responses before treatment and cell proliferation that is not reduced 2 weeks after initiation of treatment are functional characteristics of breast tumors that do not respond to AIs.
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Affiliation(s)
- Arran K Turnbull
- Arran K. Turnbull, Laura M. Arthur, Lorna Renshaw, Alexey A. Larionov, Charlene Kay, Jeremy S. Thomas, Andrew H. Sims, J. Michael Dixon, University of Edinburgh Cancer Research UK Centre, Edinburgh; Anita K. Dunbier, Mitch Dowsett, Institute of Cancer Research, London, United Kingdom; and Anita K. Dunbier, University of Otago, Dunedin, New Zealand
| | - Laura M Arthur
- Arran K. Turnbull, Laura M. Arthur, Lorna Renshaw, Alexey A. Larionov, Charlene Kay, Jeremy S. Thomas, Andrew H. Sims, J. Michael Dixon, University of Edinburgh Cancer Research UK Centre, Edinburgh; Anita K. Dunbier, Mitch Dowsett, Institute of Cancer Research, London, United Kingdom; and Anita K. Dunbier, University of Otago, Dunedin, New Zealand
| | - Lorna Renshaw
- Arran K. Turnbull, Laura M. Arthur, Lorna Renshaw, Alexey A. Larionov, Charlene Kay, Jeremy S. Thomas, Andrew H. Sims, J. Michael Dixon, University of Edinburgh Cancer Research UK Centre, Edinburgh; Anita K. Dunbier, Mitch Dowsett, Institute of Cancer Research, London, United Kingdom; and Anita K. Dunbier, University of Otago, Dunedin, New Zealand
| | - Alexey A Larionov
- Arran K. Turnbull, Laura M. Arthur, Lorna Renshaw, Alexey A. Larionov, Charlene Kay, Jeremy S. Thomas, Andrew H. Sims, J. Michael Dixon, University of Edinburgh Cancer Research UK Centre, Edinburgh; Anita K. Dunbier, Mitch Dowsett, Institute of Cancer Research, London, United Kingdom; and Anita K. Dunbier, University of Otago, Dunedin, New Zealand
| | - Charlene Kay
- Arran K. Turnbull, Laura M. Arthur, Lorna Renshaw, Alexey A. Larionov, Charlene Kay, Jeremy S. Thomas, Andrew H. Sims, J. Michael Dixon, University of Edinburgh Cancer Research UK Centre, Edinburgh; Anita K. Dunbier, Mitch Dowsett, Institute of Cancer Research, London, United Kingdom; and Anita K. Dunbier, University of Otago, Dunedin, New Zealand
| | - Anita K Dunbier
- Arran K. Turnbull, Laura M. Arthur, Lorna Renshaw, Alexey A. Larionov, Charlene Kay, Jeremy S. Thomas, Andrew H. Sims, J. Michael Dixon, University of Edinburgh Cancer Research UK Centre, Edinburgh; Anita K. Dunbier, Mitch Dowsett, Institute of Cancer Research, London, United Kingdom; and Anita K. Dunbier, University of Otago, Dunedin, New Zealand
| | - Jeremy S Thomas
- Arran K. Turnbull, Laura M. Arthur, Lorna Renshaw, Alexey A. Larionov, Charlene Kay, Jeremy S. Thomas, Andrew H. Sims, J. Michael Dixon, University of Edinburgh Cancer Research UK Centre, Edinburgh; Anita K. Dunbier, Mitch Dowsett, Institute of Cancer Research, London, United Kingdom; and Anita K. Dunbier, University of Otago, Dunedin, New Zealand
| | - Mitch Dowsett
- Arran K. Turnbull, Laura M. Arthur, Lorna Renshaw, Alexey A. Larionov, Charlene Kay, Jeremy S. Thomas, Andrew H. Sims, J. Michael Dixon, University of Edinburgh Cancer Research UK Centre, Edinburgh; Anita K. Dunbier, Mitch Dowsett, Institute of Cancer Research, London, United Kingdom; and Anita K. Dunbier, University of Otago, Dunedin, New Zealand
| | - Andrew H Sims
- Arran K. Turnbull, Laura M. Arthur, Lorna Renshaw, Alexey A. Larionov, Charlene Kay, Jeremy S. Thomas, Andrew H. Sims, J. Michael Dixon, University of Edinburgh Cancer Research UK Centre, Edinburgh; Anita K. Dunbier, Mitch Dowsett, Institute of Cancer Research, London, United Kingdom; and Anita K. Dunbier, University of Otago, Dunedin, New Zealand.
| | - J Michael Dixon
- Arran K. Turnbull, Laura M. Arthur, Lorna Renshaw, Alexey A. Larionov, Charlene Kay, Jeremy S. Thomas, Andrew H. Sims, J. Michael Dixon, University of Edinburgh Cancer Research UK Centre, Edinburgh; Anita K. Dunbier, Mitch Dowsett, Institute of Cancer Research, London, United Kingdom; and Anita K. Dunbier, University of Otago, Dunedin, New Zealand
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Zhang W, Gong W, Ai H, Tang J, Shen C. Gene expression analysis of lung adenocarcinoma and matched adjacent non-tumor lung tissue. Tumori 2014; 100:338-45. [PMID: 25076248 DOI: 10.1700/1578.17222] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
AIMS AND BACKGROUND The aim of this study was to find disease-associated genes and gene functions in lung adenocarcinoma and matched adjacent non-tumor lung tissues with DNA microarray. METHODS We downloaded the gene expression profile GSE32863 from the Gene Expression Omnibus database including 58 lung adenocarcinoma and 58 adjacent non-tumor lung tissue samples. Data were preprocessed and the differentially expressed genes (DEGs) were identified using packages in the R computing language. The selected DEGs were further analyzed with bioinformatics methods. After the coexpression network of DEGs was constructed by STRING (Search Tool for the Retrieval of Interacting Genes/Proteins), we analyzed gene functions with DAVID (The Database for Annotation, Visualization and Integrated Discovery) and WebGestalt (WEB-based Gene Set Analysis Toolkit). RESULTS A total of 1429 genes were filtered as DEGs, including 873 downregulated genes and 556 upregulated genes, and the DEGs including CDC45, CCNB2, CDC20, MCM2, PTTG1, MCM4 and FEN1 were most significantly related to cell cycle and DNA replication. CONCLUSION The discovery of featured genes which were significantly related to cell cycle and DNA replication has potential for use in the clinic for the diagnosis of lung adenocarcinoma in the future. However, further experiments will be needed to confirm our result.
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Guo W, Wu Z, Song J, Jiang F, Wang Z, Deng S, Walker VK, Zhou S. Juvenile hormone-receptor complex acts on mcm4 and mcm7 to promote polyploidy and vitellogenesis in the migratory locust. PLoS Genet 2014; 10:e1004702. [PMID: 25340846 PMCID: PMC4207617 DOI: 10.1371/journal.pgen.1004702] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 08/23/2014] [Indexed: 11/18/2022] Open
Abstract
Juvenile hormone (JH), a sesquiterpenoid produced by the corpora allata, coordinates insect growth, metamorphosis, and reproduction. While JH action for the repression of larval metamorphosis has been well studied, the molecular basis of JH in promoting adult reproduction has not been fully elucidated. Methoprene-tolerant (Met), the JH receptor, has been recently shown to mediate JH action during metamorphosis as well as in vitellogenesis, but again, the precise mechanism underlying the latter has been lacking. We have now demonstrated using Met RNAi to phenocopy a JH-deprived condition in migratory locusts, that JH stimulates DNA replication and increases ploidy in preparation for vitellogenesis. Mcm4 and Mcm7, two genes in the DNA replication pathway were expressed in the presence of JH and Met. Depletion of Mcm4 or Mcm7 inhibited de novo DNA synthesis and polyploidization, and resulted in the substantial reduction of vitellogenin mRNA levels as well as severely impaired oocyte maturation and ovarian growth. By using luciferase reporter and electrophoretic mobility shift assays, we have shown that Met directly regulates the transcription of Mcm4 and Mcm7 by binding to upstream consensus sequences with E-box or E-box-like motifs. Our work suggests that the JH-receptor complex acts on Mcm4 and Mcm7 to regulate DNA replication and polyploidy for vitellogenesis and oocyte maturation.
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Affiliation(s)
- Wei Guo
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zhongxia Wu
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Jiasheng Song
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Feng Jiang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Zhiming Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Shun Deng
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | | | - Shutang Zhou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- * E-mail:
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