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Yan M, Jiao G, Shao G, Chen Y, Zhu M, Yang L, Xie L, Hu P, Tang S. Chalkiness and premature controlled by energy homeostasis in OsNAC02 Ko-mutant during vegetative endosperm development. BMC PLANT BIOLOGY 2024; 24:196. [PMID: 38494545 PMCID: PMC10946104 DOI: 10.1186/s12870-024-04845-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/21/2024] [Indexed: 03/19/2024]
Abstract
BACKGROUND Chalkiness is a common phenotype induced by various reasons, such as abiotic stress or the imbalance of starch synthesis and metabolism during the development period. However, the reason mainly for one gene losing its function such as NAC (TFs has a large family in rice) which may cause premature is rarely known to us. RESULTS The Ko-Osnac02 mutant demonstrated an obviously early maturation stage compared to the wild type (WT) with 15 days earlier. The result showed that the mature endosperm of Ko-Osnac02 mutant exhibited chalkiness, characterized by white-core and white-belly in mature endosperm. As grain filling rate is a crucial factor in determining the yield and quality of rice (Oryza sativa, ssp. japonica), it's significant that mutant has a lower amylose content (AC) and higher soluble sugar content in the mature endosperm. Interestingly among the top DEGs in the RNA sequencing of N2 (3DAP) and WT seeds revealed that the OsBAM2 (LOC_Os10g32810) expressed significantly high in N2 mutant, which involved in Maltose up-regulated by the starch degradation. As Prediction of Protein interaction showed in the chalky endosperm formation in N2 seeds (3 DAP), seven genes were expressed at a lower-level which should be verified by a heatmap diagrams based on DEGs of N2 versus WT. The Tubulin genes controlling cell cycle are downregulated together with the MCM family genes MCM4 ( ↓), MCM7 ( ↑), which may cause white-core in the early endosperm development. In conclusion, the developing period drastically decreased in the Ko-Osnac02 mutants, which might cause the chalkiness in seeds during the early endosperm development. CONCLUSIONS The gene OsNAC02 which controls a great genetic co-network for cell cycle regulation in early development, and KO-Osnac02 mutant shows prematurity and white-core in endosperm.
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Affiliation(s)
- Mei Yan
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding of Ministry of Agriculture, China National Rice Research Institute, Hangzhou, 311400, China
| | - Guiai Jiao
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding of Ministry of Agriculture, China National Rice Research Institute, Hangzhou, 311400, China
| | - Gaoneng Shao
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding of Ministry of Agriculture, China National Rice Research Institute, Hangzhou, 311400, China
| | - Ying Chen
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding of Ministry of Agriculture, China National Rice Research Institute, Hangzhou, 311400, China
| | - Maodi Zhu
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding of Ministry of Agriculture, China National Rice Research Institute, Hangzhou, 311400, China
| | - Lingwei Yang
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding of Ministry of Agriculture, China National Rice Research Institute, Hangzhou, 311400, China
| | - Lihong Xie
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding of Ministry of Agriculture, China National Rice Research Institute, Hangzhou, 311400, China
| | - Peisong Hu
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding of Ministry of Agriculture, China National Rice Research Institute, Hangzhou, 311400, China
| | - Shaoqing Tang
- State Key Laboratory of Rice Biology, Key Laboratory of Rice Biology and Breeding of Ministry of Agriculture, China National Rice Research Institute, Hangzhou, 311400, China.
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Mouery BL, Baker EM, Mills CA, Herring LE, Fleifel D, Cook JG. APC/C prevents non-canonical order of cyclin/CDK activity to maintain CDK4/6 inhibitor-induced arrest. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.566394. [PMID: 37986787 PMCID: PMC10659421 DOI: 10.1101/2023.11.09.566394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Regulated cell cycle progression ensures homeostasis and prevents cancer. In proliferating cells, premature S phase entry is avoided by the E3 ubiquitin ligase APC/C (anaphase promoting complex/cyclosome), although the APC/C substrates whose degradation restrains G1-S progression are not fully known. The APC/C is also active in arrested cells that exited the cell cycle, but it is not clear if APC/C maintains all types of arrest. Here by expressing the APC/C inhibitor, EMI1, we show that APC/C activity is essential to prevent S phase entry in cells arrested by pharmacological CDK4/6 inhibition (Palbociclib). Thus, active protein degradation is required for arrest alongside repressed cell cycle gene expression. The mechanism of rapid and robust arrest bypass from inhibiting APC/C involves cyclin-dependent kinases acting in an atypical order to inactivate RB-mediated E2F repression. Inactivating APC/C first causes mitotic cyclin B accumulation which then promotes cyclin A expression. We propose that cyclin A is the key substrate for maintaining arrest because APC/C-resistant cyclin A, but not cyclin B, is sufficient to induce S phase entry. Cells bypassing arrest from CDK4/6 inhibition initiate DNA replication with severely reduced origin licensing. The simultaneous accumulation of S phase licensing inhibitors, such as cyclin A and geminin, with G1 licensing activators disrupts the normal order of G1-S progression. As a result, DNA synthesis and cell proliferation are profoundly impaired. Our findings predict that cancers with elevated EMI1 expression will tend to escape CDK4/6 inhibition into a premature, underlicensed S phase and suffer enhanced genome instability.
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Affiliation(s)
- Brandon L Mouery
- Curriculum in Genetics and Molecular Biology. The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599, USA
| | - Eliyambuya M Baker
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599
- Immuno-Oncology, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Christine A Mills
- UNC Proteomics Core Facility, Department of Pharmacology. The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599, USA
- Department of Pharmacology. The University of North Carolina at Chapel Hill. Chapel Hill NC, 27599, USA
| | - Laura E Herring
- UNC Proteomics Core Facility, Department of Pharmacology. The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center. The University of North Carolina at Chapel Hill. Chapel Hill NC 27599, USA
- Department of Pharmacology. The University of North Carolina at Chapel Hill. Chapel Hill NC, 27599, USA
| | - Dalia Fleifel
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599
| | - Jeanette Gowen Cook
- Curriculum in Genetics and Molecular Biology. The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599, USA
- Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill. Chapel Hill, NC 27599
- Lineberger Comprehensive Cancer Center. The University of North Carolina at Chapel Hill. Chapel Hill NC 27599, USA
- Department of Pharmacology. The University of North Carolina at Chapel Hill. Chapel Hill NC, 27599, USA
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3
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Weng HP, Ke CH, Tung CW, Tani A, Wang CC, Yang WY, Wang YS, Han W, Liao CH, Tomiyasu H, Lin CS. Canine diffuse large b-cell lymphoma downregulates the activity of CD8 + T-cells through tumor-derived extracellular vesicles. Cancer Cell Int 2023; 23:252. [PMID: 37884996 PMCID: PMC10601183 DOI: 10.1186/s12935-023-03104-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 10/16/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Tumor-derived extracellular vesicles (EVs) have been proposed as the essential mediator between host immunity and cancer development. These EVs conduct cellular communication to facilitate tumor growth, enable invasion and metastasis, and shape the favorable tumor microenvironment. Lymphoma is one of the most common hematological malignancies in humans and dogs. Effective T-cell responses are required for the control of these malignancies. However, the immune crosstalk between CD8 + T-cells, which dominates anti-tumor responses, and canine lymphoma has rarely been described. METHODS This study investigates the immune manipulating effects of EVs, produced from the clinical cases and cell line of canine B cell lymphoma, on CD8 + T-cells isolated from canine donors. RESULTS Lymphoma-derived EVs lead to the apoptosis of CD8 + T-cells. Furthermore, EVs trigger the overexpression of CTLA-4 on CD8 + T-cells, which indicates that EV blockade could serve as a potential therapeutic strategy for lymphoma patients. Notably, EVs transform the CD8 + T-cells into regulatory phenotypes by upregulating their PD-1, PD-L1, and FoxP3 mRNA expression. The regulatory CD8 + T-cells secret the panel of inhibitory cytokines and angiogenic factors and thus create a pro-tumorigenic microenvironment. CONCLUSION In summary, the current study demonstrated that the EVs derived from canine B cell lymphoma impaired the anti-tumor activity of CD8 + T-cells and manipulated the possible induction of regulatory CD8 + T-cells to fail the activation of host cellular immunity.
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Affiliation(s)
- Hsin-Pei Weng
- Department of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, No.1 Sec.4 Roosevelt Rd, Taipei, 10617, Taiwan ROC
| | - Chiao-Hsu Ke
- Department of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, No.1 Sec.4 Roosevelt Rd, Taipei, 10617, Taiwan ROC
| | - Chun-Wei Tung
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, 35053, Miaoli, Taiwan
- Graduate Institute of Data Science, College of Management, Taipei Medical University, 106, Taipei, Taiwan
- Doctoral Degree Program in Toxicology, College of Pharmacy, Kaohsiung Medical University, 80708, Kaohsiung, Taiwan
| | - Akiyoshi Tani
- Department of Veterinary Internal Medicine, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-Ku, Tokyo, 113-8657, Japan
| | - Chia-Chi Wang
- Department of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, No.1 Sec.4 Roosevelt Rd, Taipei, 10617, Taiwan ROC
| | - Wen-Yuan Yang
- Department of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, No.1 Sec.4 Roosevelt Rd, Taipei, 10617, Taiwan ROC
- Zoonoses Research Center and School of Veterinary Medicine, National Taiwan University, Taipei, 106, Taiwan
| | - Yu-Shan Wang
- Lab. 2612, Rekiin Biotech Inc, Taipei, 114737, Taiwan
| | - Winston Han
- Lab. 2612, Rekiin Biotech Inc, Taipei, 114737, Taiwan
| | - Chi-Hsun Liao
- Department of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, No.1 Sec.4 Roosevelt Rd, Taipei, 10617, Taiwan ROC
| | - Hirotaka Tomiyasu
- Department of Veterinary Internal Medicine, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-Ku, Tokyo, 113-8657, Japan.
| | - Chen-Si Lin
- Department of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, No.1 Sec.4 Roosevelt Rd, Taipei, 10617, Taiwan ROC.
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Sinha S, Das S, Mohiyuddin SA. Evaluation of Cyclin D1 and Human Epidermal Growth Factor Receptor 2 Neu Protein Expression in Head and Neck Squamous Cell Carcinoma. Cureus 2023; 15:e35526. [PMID: 37007344 PMCID: PMC10058519 DOI: 10.7759/cureus.35526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2023] [Indexed: 03/03/2023] Open
Abstract
Background Head and neck cancers are highly aggressive, frequently occurring cancers that are prevalent worldwide. The mainstay of their treatment is surgery, followed by adjuvant therapy. Various studies have documented the usefulness of molecular markers in carcinogenesis and have proven helpful in the diagnosis and treatment of head and neck cancers. Cyclin D1 is a proto‑oncogene, overexpression of which leads to the accelerated entry of cells in the S phase of the cell cycle, causing uncontrolled proliferation of the cells. The dysregulation of human epidermal growth factor receptor 2 (HER2) neu is also related to multiple features of malignancy, including loss of cell cycle control, induction of angiogenesis, and resistance to apoptotic stimuli. This study seeks to identify a subset of patients with a bad prognosis who may require aggressive treatment strategies. Aim This study aims to determine the proportion of the expression of cyclin D1 and HER2 neu in head and neck squamous cell carcinoma (HNSCC) and analyze the association between the expression of cyclin D1 and HER2 neu using histological grading, tumor, node, and metastasis (TNM) staging, and nodal status of the tumor. Furthermore, this study also aims to document clinical outcomes, such as locoregional control, depth of invasion (DOI), and regional metastasis regarding the expression of cyclin D1 and HER2 neu in HNSCC. Setting and design This study is a laboratory-based observational study. Materials and methods Seventy histologically proven cases of HNSCC were studied for various histopathological parameters, and further immunohistochemistry (IHC) was performed for cyclin D1 and HER2 neu. The expression and intensity of cyclin D1 were multiplied, and the total score was derived. The College of American Pathologists/American Society of Clinical Oncology (CAP/ASCO) guidelines for HER2 neu testing in breast cancer were used for scoring. Result Out of 70 cases, 52 (75%) demonstrated strong and moderate positivity for cyclin D1, and the p-values were 0.017, 0.001, and 0.032 for depth of invasion, TNM stage, and lymph node metastases, respectively, for cyclin D1, which was considered statistically significant. For HER2 neu, five out of 70 cases were positive, and the p-value was significant for depth of invasion (0.008). Conclusion The expression of the above marker cyclin D1 increases with stage, DOI, and positive lymph node status. Hence, cyclin D1 immunoexpression can be helpful in the early assessment of HNSCC behavior and can serve as an independent prognostic marker. Furthermore, it was observed that HER2 neu was significant with an increase in depth of invasion of tumor, which, in the American Joint Committee on Cancer (AJCC) eighth edition, is considered an important factor for determining the stage of the tumor. Further research is needed to examine whether HER2 neu can act as a prognostic factor for HNSCC and if it can be targeted for treatment options.
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5
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Matsukawa T, Yin M, Baslan T, Chung YJ, Cao D, Bertoli R, Zhu YJ, Walker RL, Freeland A, Knudsen E, Lowe SW, Meltzer PS, Aplan PD. Mcm2 hypomorph leads to acute leukemia or hematopoietic stem cell failure, dependent on genetic context. FASEB J 2022; 36:e22430. [PMID: 35920299 PMCID: PMC9377154 DOI: 10.1096/fj.202200061rr] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 06/07/2022] [Accepted: 06/13/2022] [Indexed: 11/11/2022]
Abstract
Minichromosome maintenance proteins (Mcm2-7) form a hexameric complex that unwinds DNA ahead of a replicative fork. The deficiency of Mcm proteins leads to replicative stress and consequent genomic instability. Mice with a germline insertion of a Cre cassette into the 3'UTR of the Mcm2 gene (designated Mcm2Cre ) have decreased Mcm2 expression and invariably develop precursor T-cell lymphoblastic leukemia/lymphoma (pre-T LBL), due to 100-1000 kb deletions involving important tumor suppressor genes. To determine whether mice that were protected from pre-T LBL would develop non-T-cell malignancies, we used two approaches. Mice engrafted with Mcm2Cre/Cre Lin- Sca-1+ Kit+ hematopoietic stem/progenitor cells did not develop hematologic malignancy; however, these mice died of hematopoietic stem cell failure by 6 months of age. Placing the Mcm2Cre allele onto an athymic nu/nu background completely prevented pre-T LBL and extended survival of these mice three-fold (median 296.5 vs. 80.5 days). Ultimately, most Mcm2Cre/Cre ;nu/nu mice developed B-cell precursor acute lymphoblastic leukemia (BCP-ALL). We identified recurrent deletions of 100-1000 kb that involved genes known or suspected to be involved in BCP-ALL, including Pax5, Nf1, Ikzf3, and Bcor. Moreover, whole-exome sequencing identified recurrent mutations of genes known to be involved in BCP-ALL progression, such as Jak1/Jak3, Ptpn11, and Kras. These findings demonstrate that an Mcm2Cre/Cre hypomorph can induce hematopoietic dysfunction via hematopoietic stem cell failure as well as a "deletor" phenotype affecting known or suspected tumor suppressor genes.
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Affiliation(s)
- Toshihiro Matsukawa
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- These authors contributed equally to this work
| | - Mianmian Yin
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- These authors contributed equally to this work
| | - Timour Baslan
- Cancer Biology and Genetics Program, Sloan-Kettering Institute, NY, USA
| | - Yang Jo Chung
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dengchao Cao
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ryan Bertoli
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yuelin J. Zhu
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Robert L. Walker
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Amy Freeland
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Erik Knudsen
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Scott W. Lowe
- Cancer Biology and Genetics Program, Sloan-Kettering Institute, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Paul S. Meltzer
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Peter D. Aplan
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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6
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Limas JC, Littlejohn AN, House AM, Kedziora KM, Mouery BL, Ma B, Fleifel D, Walens A, Aleman MM, Dominguez D, Cook JG. Quantitative profiling of adaptation to cyclin E overproduction. Life Sci Alliance 2022; 5:5/5/e202201378. [PMID: 35173014 PMCID: PMC8860095 DOI: 10.26508/lsa.202201378] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 01/28/2022] [Accepted: 01/31/2022] [Indexed: 01/03/2023] Open
Abstract
Cyclin E/CDK2 drives cell cycle progression from G1 to S phase. Despite the toxicity of cyclin E overproduction in mammalian cells, the cyclin E gene is overexpressed in some cancers. To further understand how cells can tolerate high cyclin E, we characterized non-transformed epithelial cells subjected to chronic cyclin E overproduction. Cells overproducing cyclin E, but not cyclins D or A, briefly experienced truncated G1 phases followed by a transient period of DNA replication origin underlicensing, replication stress, and impaired proliferation. Individual cells displayed substantial intercellular heterogeneity in cell cycle dynamics and CDK activity. Each phenotype improved rapidly despite high cyclin E-associated activity. Transcriptome analysis revealed adapted cells down-regulated a cohort of G1-regulated genes. Withdrawing cyclin E from adapted cells only partially reversed underlicensing indicating that adaptation is at least partly non-genetic. This study provides evidence that mammalian cyclin E/CDK inhibits origin licensing indirectly through premature S phase onset and provides mechanistic insight into the relationship between CDKs and licensing. It serves as an example of oncogene adaptation that may recapitulate molecular changes during tumorigenesis.
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Affiliation(s)
- Juanita C Limas
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Amiee N Littlejohn
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Amy M House
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Katarzyna M Kedziora
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Bioinformatics and Analytics Research Collaborative (BARC), University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Brandon L Mouery
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Boyang Ma
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Dalia Fleifel
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Andrea Walens
- Lineberger Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Maria M Aleman
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Daniel Dominguez
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeanette Gowen Cook
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA .,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Lineberger Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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7
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Zhang R, Liu Z, Zhang G. CDC45 modulates MCM7 expression and inhibits cell proliferation by suppressing the PI3K/AKT pathway in acute myeloid leukemia. Am J Transl Res 2021; 13:10218-10232. [PMID: 34650692 PMCID: PMC8507005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 07/28/2021] [Indexed: 06/13/2023]
Abstract
Acute myeloid leukemia (AML) is a heterogenous hematologic disease that has a poor prognosis. This study aimed to identify new targets for the diagnosis and treatment of AML. The GSE65409 and GSE90062 were selected from the AML database of the Gene Expression Omnibus and compared using the GEO2R tool to identify differentially expressed genes (DEGs). The Database for Annotation, Visualization, and Integrated Discovery was used to perform gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses of the DEGs. Protein-protein interactions were visualized using the Search Tool for the Retrieval of Interacting Genes, which identified two potential hub genes that encode CDC45 and MCM7. Relative to AML specimens, normal specimens had higher expression levels of CDC45 and MCM7 based on the Gene Expression Omnibus and The Cancer Genome Atlas databases. Furthermore, Pearson's correlation analysis revealed a significant relationship between CDC45 and MCM7. High expression of CDC45 was positively correlated with complete remission and negatively correlated with white blood cell count, hemoglobin concentration, platelet count, and bone marrow blasts. Moreover, high expression of MCM7 was negatively correlated with white blood cell count, hemoglobin concentration, platelet count, bone marrow blasts, and unfavorable cytogenetics. Overexpression of CDC45 increased the expressions of CDC45 and MCM7, while overexpression of MCM7 increased the expression of MCM7 but not CDC45. Overexpression of CDC45 or MCM7 led to impaired AML cell proliferation and blockage at the G1/S phase transition. Overexpression of CDC45 or MCM7 also attenuated the phosphorylation of PI3K, AKT, and mTOR, while simultaneous down-regulation of MCM7 expression abolished the effects of CDC45 overexpression. These findings suggest a functional relationship between CDC45 and MCM7, which might have use in the diagnosis and treatment of AML.
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Affiliation(s)
- Rong Zhang
- Department of Hematology, Shenjing Hospital of China Medical University Shenyang, Liaoning Province, People's Republic of China
| | - Zhuogang Liu
- Department of Hematology, Shenjing Hospital of China Medical University Shenyang, Liaoning Province, People's Republic of China
| | - Guojun Zhang
- Department of Hematology, Shenjing Hospital of China Medical University Shenyang, Liaoning Province, People's Republic of China
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8
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Munisha M, Schimenti JC. Genome maintenance during embryogenesis. DNA Repair (Amst) 2021; 106:103195. [PMID: 34358805 DOI: 10.1016/j.dnarep.2021.103195] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 12/25/2022]
Abstract
Genome maintenance during embryogenesis is critical, because defects during this period can be perpetuated and thus have a long-term impact on individual's health and longevity. Nevertheless, genome instability is normal during certain aspects of embryonic development, indicating that there is a balance between the exigencies of timely cell proliferation and mutation prevention. In particular, early embryos possess unique cellular and molecular features that underscore the challenge of having an appropriate balance. Here, we discuss genome instability during embryonic development, the mechanisms used in various cell compartments to manage genomic stress and address outstanding questions regarding the balance between genome maintenance mechanisms in key cell types that are important for adulthood and progeny.
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Affiliation(s)
- Mumingjiang Munisha
- Dept. of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY 14853, United States
| | - John C Schimenti
- Dept. of Biomedical Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY 14853, United States.
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9
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Chen WC, To MD, Westcott PMK, Delrosario R, Kim IJ, Philips M, Tran Q, Bollam SR, Goodarzi H, Bayani N, Mirzoeva O, Balmain A. Targeting KRAS4A splicing through the RBM39/DCAF15 pathway inhibits cancer stem cells. Nat Commun 2021; 12:4288. [PMID: 34257283 PMCID: PMC8277813 DOI: 10.1038/s41467-021-24498-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 06/14/2021] [Indexed: 12/30/2022] Open
Abstract
The commonly mutated human KRAS oncogene encodes two distinct KRAS4A and KRAS4B proteins generated by differential splicing. We demonstrate here that coordinated regulation of both isoforms through control of splicing is essential for development of Kras mutant tumors. The minor KRAS4A isoform is enriched in cancer stem-like cells, where it responds to hypoxia, while the major KRAS4B is induced by ER stress. KRAS4A splicing is controlled by the DCAF15/RBM39 pathway, and deletion of KRAS4A or pharmacological inhibition of RBM39 using Indisulam leads to inhibition of cancer stem cells. Our data identify existing clinical drugs that target KRAS4A splicing, and suggest that levels of the minor KRAS4A isoform in human tumors can be a biomarker of sensitivity to some existing cancer therapeutics.
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Affiliation(s)
- Wei-Ching Chen
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Minh D To
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Peter M K Westcott
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
- MIT Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Reyno Delrosario
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Il-Jin Kim
- Guardant Health, Redwood City, California, USA
| | - Mark Philips
- NYU Cancer Institute, NYU School of Medicine, New York, NY, USA
| | - Quan Tran
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Saumya R Bollam
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Nora Bayani
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Olga Mirzoeva
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Allan Balmain
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA.
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
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10
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Mahmoud SS, Hussein S, Rashed H, Abdelghany EMA, Ali AI. Anticancer Effects of Tacrolimus on Induced Hepatocellular Carcinoma in Mice. Curr Mol Pharmacol 2021; 15:434-445. [PMID: 34061012 DOI: 10.2174/1874467214666210531164546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 02/12/2021] [Accepted: 02/17/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Tacrolimus is a calcineurin inhibitor widely used for immunological disorders. However, there is a significant controversy regarding its effect on the liver. The present study was conducted to evaluate the anticancer effects of tacrolimus on an induced murine hepatocellular carcinoma (HCC) model and its possible hepatotoxicity at standard therapeutic doses. METHODS Fifty-four male mice were divided into five groups: a control healthy group, control HCC group, tacrolimus-treated group, doxorubicin (DOXO)-treated group, and combined tacrolimus- and DOXO-treated group. The activity of liver enzymes, including alkaline phosphatase, gamma-glutamyl transferase, lactate dehydrogenase, alanine transaminase, and aspartate transaminase, was determined. Serum vascular endothelial growth factor (VEGF) was measured using an enzyme-linked immunosorbent assay. A quantitative real-time polymerase chain reaction (qRT-PCR) was conducted to measure the expression of proliferating cell nuclear antigen (PCNA), Bax, and p53 mRNA. Immunohistochemical staining for cyclin D1 and VEGF was performed. RESULTS Mice that received combined treatment with tacrolimus and DOXO exhibited the best improvement in all parameters when compared with the groups that received DOXO or tacrolimus alone (p < 0.001). CONCLUSION The combination of DOXO and tacrolimus was more effective in the management of HCC compared with either agent alone. This improvement was detected by the reduction of liver enzymes and the improvement of the histopathological picture. The involved mechanisms included significant apoptosis induction demonstrated by upregulation of bax along with a reduction in angiogenesis demonstrated by downregulation of VEGF. This was accompanied by inhibition of cell cycle progression mediated by upregulated p53 and downregulated PCNA and cyclin D1.
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Affiliation(s)
- Shireen Sami Mahmoud
- Clinical Pharmacology Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Samia Hussein
- Medical Biochemistry & Molecular Biology Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Hayam Rashed
- Pathology Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Eman M A Abdelghany
- Anatomy and Embryology Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Alaa I Ali
- Clinical Pharmacology Department, Faculty of Medicine, Zagazig University, Zagazig, Egypt
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11
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Marescal O, Cheeseman IM. Cellular Mechanisms and Regulation of Quiescence. Dev Cell 2021; 55:259-271. [PMID: 33171109 DOI: 10.1016/j.devcel.2020.09.029] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/25/2020] [Accepted: 09/29/2020] [Indexed: 02/06/2023]
Abstract
Quiescence is a state of reversible proliferative arrest in which cells are not actively dividing and yet retain the capacity to reenter the cell cycle upon receiving an appropriate stimulus. Quiescent cells are remarkably diverse-they reside in different locations throughout the body, serve distinct roles, and are activated by a variety of signals. Despite this diversity, all quiescent cells must be able to persist in a nondividing state without compromising their proliferative potential, which requires changes to core cellular programs. How drastically different cell types are able to implement extensive changes to their gene-expression programs, metabolism, and cellular structures to induce a common cellular state is a fascinating question in cell and developmental biology. In this review, we explore the diversity of quiescent cells and highlight the unifying characteristics that define the quiescent state.
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Affiliation(s)
- Océane Marescal
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Iain M Cheeseman
- Whitehead Institute for Biomedical Research, 455 Main Street, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
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12
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Montalto FI, De Amicis F. Cyclin D1 in Cancer: A Molecular Connection for Cell Cycle Control, Adhesion and Invasion in Tumor and Stroma. Cells 2020; 9:cells9122648. [PMID: 33317149 PMCID: PMC7763888 DOI: 10.3390/cells9122648] [Citation(s) in RCA: 180] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/04/2020] [Accepted: 12/06/2020] [Indexed: 12/11/2022] Open
Abstract
Cyclin D1, an important regulator of cell cycle, carries out a central role in the pathogenesis of cancer determining uncontrolled cellular proliferation. In normal cells, Cyclin D1 expression levels are strictly regulated, conversely, in cancer, its activity is intensified in various manners. Different studies demonstrate that CCDN1 gene is amplified in several tumor types considering it as a negative prognostic marker of this pathology. Cyclin D1 is known for its role in the nucleus, but recent clinical studies associate the amount located in the cytoplasmic membrane with tumor invasion and metastasis. Cyclin D1 has also other functions: it governs the expression of specific miRNAs and it plays a crucial role in the tumor-stroma interactions potentiating most of the cancer hallmarks. In the present review, we will summarize the current scientific evidences that highlight the involvement of Cyclin D1 in the pathogenesis of different types of cancer, best of all in breast cancer. We will also focus on recent insights regarding the Cyclin D1 as molecular bridge between cell cycle control, adhesion, invasion, and tumor/stroma/immune-system interplay in cancer.
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Affiliation(s)
- Francesca Ida Montalto
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy;
- Health Center, University of Calabria, 87036 Rende, Italy
| | - Francesca De Amicis
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy;
- Health Center, University of Calabria, 87036 Rende, Italy
- Correspondence: ; Tel.: +39-984-496204
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13
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Sedlackova H, Rask MB, Gupta R, Choudhary C, Somyajit K, Lukas J. Equilibrium between nascent and parental MCM proteins protects replicating genomes. Nature 2020; 587:297-302. [PMID: 33087936 DOI: 10.1038/s41586-020-2842-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 07/27/2020] [Indexed: 12/14/2022]
Abstract
Minichromosome maintenance proteins (MCMs) are DNA-dependent ATPases that bind to replication origins and license them to support a single round of DNA replication. A large excess of MCM2-7 assembles on chromatin in G1 phase as pre-replication complexes (pre-RCs), of which only a fraction become the productive CDC45-MCM-GINS (CMG) helicases that are required for genome duplication1-4. It remains unclear why cells generate this surplus of MCMs, how they manage to sustain it across multiple generations, and why even a mild reduction in the MCM pool compromises the integrity of replicating genomes5,6. Here we show that, for daughter cells to sustain error-free DNA replication, their mother cells build up a nuclear pool of MCMs both by recycling chromatin-bound (parental) MCMs and by synthesizing new (nascent) MCMs. Although all MCMs can form pre-RCs, it is the parental pool that is inherently stable and preferentially matures into CMGs. By contrast, nascent MCM3-7 (but not MCM2) undergo rapid proteolysis in the cytoplasm, and their stabilization and nuclear translocation require interaction with minichromosome-maintenance complex-binding protein (MCMBP), a distant MCM paralogue7,8. By chaperoning nascent MCMs, MCMBP safeguards replicating genomes by increasing chromatin coverage with pre-RCs that do not participate on replication origins but adjust the pace of replisome movement to minimize errors during DNA replication. Consequently, although the paucity of pre-RCs in MCMBP-deficient cells does not alter DNA synthesis overall, it increases the speed and asymmetry of individual replisomes, which leads to DNA damage. The surplus of MCMs therefore increases the robustness of genome duplication by restraining the speed at which eukaryotic cells replicate their DNA. Alterations in physiological fork speed might thus explain why even a minor reduction in MCM levels destabilizes the genome and predisposes to increased incidence of tumour formation.
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Affiliation(s)
- Hana Sedlackova
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Maj-Britt Rask
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rajat Gupta
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Chunaram Choudhary
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kumar Somyajit
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Jiri Lukas
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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14
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Yin M, Baslan T, Walker RL, Zhu YJ, Freeland A, Matsukawa T, Sridharan S, Nussenzweig A, Pruitt SC, Lowe SW, Meltzer PS, Aplan PD. A unique mutator phenotype reveals complementary oncogenic lesions leading to acute leukemia. JCI Insight 2019; 4:131434. [PMID: 31622281 PMCID: PMC6962024 DOI: 10.1172/jci.insight.131434] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 10/10/2019] [Indexed: 12/30/2022] Open
Abstract
Mice homozygous for a hypomorphic allele of DNA replication factor minichromosome maintenance protein 2 (designated Mcm2cre/cre) develop precursor T cell lymphoblastic leukemia/lymphoma (pre-T LBL) with 4-32 small interstitial deletions per tumor. Mice that express a NUP98-HOXD13 (NHD13) transgene develop multiple types of leukemia, including myeloid and T and B lymphocyte. All Mcm2cre/cre NHD13+ mice develop pre-T LBL, and 26% develop an unrelated, concurrent B cell precursor acute lymphoblastic leukemia (BCP-ALL). Copy number alteration (CNA) analysis demonstrated that pre-T LBLs were characterized by homozygous deletions of Pten and Tcf3 and partial deletions of Notch1 leading to Notch1 activation. In contrast, BCP-ALLs were characterized by recurrent deletions involving Pax5 and Ptpn1 and copy number gain of Abl1 and Nup214 resulting in a Nup214-Abl1 fusion. We present a model in which Mcm2 deficiency leads to replicative stress, DNA double strand breaks (DSBs), and resultant CNAs due to errors in DNA DSB repair. CNAs that involve critical oncogenic pathways are then selected in vivo as malignant lymphoblasts because of a fitness advantage. Some CNAs, such as those involving Abl1 and Notch1, represent attractive targets for therapy.
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Affiliation(s)
- Mianmian Yin
- Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Timour Baslan
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Robert L Walker
- Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Yuelin J Zhu
- Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Amy Freeland
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Toshihiro Matsukawa
- Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Sriram Sridharan
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Steven C Pruitt
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Scott W Lowe
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Paul S Meltzer
- Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Peter D Aplan
- Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
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15
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Matson JP, House AM, Grant GD, Wu H, Perez J, Cook JG. Intrinsic checkpoint deficiency during cell cycle re-entry from quiescence. J Cell Biol 2019; 218:2169-2184. [PMID: 31186278 PMCID: PMC6605788 DOI: 10.1083/jcb.201902143] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/08/2019] [Accepted: 05/17/2019] [Indexed: 12/19/2022] Open
Abstract
To maintain tissue homeostasis, cells transition between cell cycle quiescence and proliferation. An essential G1 process is minichromosome maintenance complex (MCM) loading at DNA replication origins to prepare for S phase, known as origin licensing. A p53-dependent origin licensing checkpoint normally ensures sufficient MCM loading before S phase entry. We used quantitative flow cytometry and live cell imaging to compare MCM loading during the long first G1 upon cell cycle entry and the shorter G1 phases in the second and subsequent cycles. We discovered that despite the longer G1 phase, the first G1 after cell cycle re-entry is significantly underlicensed. Consequently, the first S phase cells are hypersensitive to replication stress. This underlicensing results from a combination of slow MCM loading with a severely compromised origin licensing checkpoint. The hypersensitivity to replication stress increases over repeated rounds of quiescence. Thus, underlicensing after cell cycle re-entry from quiescence distinguishes a higher-risk first cell cycle that likely promotes genome instability.
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Affiliation(s)
- Jacob Peter Matson
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Amy M House
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Gavin D Grant
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Huaitong Wu
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Joanna Perez
- Biochemistry, Cell and Developmental Biology Program, Emory University, Atlanta, GA
| | - Jeanette Gowen Cook
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
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16
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Wallis ABA, Nieduszynski CA. Investigating the role of Rts1 in DNA replication initiation. Wellcome Open Res 2018; 3:23. [PMID: 29721551 PMCID: PMC5897792 DOI: 10.12688/wellcomeopenres.13884.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2018] [Indexed: 11/22/2022] Open
Abstract
Background: Understanding DNA replication initiation is essential to understand the mis-regulation of replication seen in cancer and other human disorders. DNA replication initiates from DNA replication origins. In eukaryotes, replication is dependent on cell cycle kinases which function during S phase. Dbf4-dependent kinase (DDK) and cyclin-dependent kinase (CDK) act to phosphorylate the DNA helicase (composed of mini chromosome maintenance proteins: Mcm2-7) and firing factors to activate replication origins. It has recently been found that Rif1 can oppose DDK phosphorylation. Rif1 can recruit protein phosphatase 1 (PP1) to dephosphorylate MCM and restricts origin firing. In this study, we investigate a potential role for another phosphatase, protein phosphatase 2A (PP2A), in regulating DNA replication initiation. The PP2A regulatory subunit Rts1 was previously identified in a large-scale genomic screen to have a genetic interaction with
ORC2 (a DNA replication licensing factor). Deletion of
RTS1 synthetically rescued the temperature-sensitive (ts-) phenotype of
ORC2 mutants. Methods: We deleted
RTS1 in multiple ts-replication factor
Saccharomyces cerevisiae strains, including
ORC2. Dilution series assays were carried out to compare qualitatively the growth of double mutant
∆rts1 ts-replication factor strains relative to the respective single mutant strains. Results: No synthetic rescue of temperature-sensitivity was observed. Instead we found an additive phenotype, indicating gene products function in separate biological processes. These findings are in agreement with a recent genomic screen which found that
RTS1 deletion in several ts-replication factor strains led to increased temperature-sensitivity. Conclusions: We find no evidence that Rts1 is involved in the dephosphorylation of DNA replication initiation factors.
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Affiliation(s)
- Ana B A Wallis
- Sir William Dunn School of Pathology, University of Oxford, Oxford, Oxfordshire, OX1 3RE, UK
| | - Conrad A Nieduszynski
- Sir William Dunn School of Pathology, University of Oxford, Oxford, Oxfordshire, OX1 3RE, UK
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17
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Luo CT, Osmanbeyoglu HU, Do MH, Bivona MR, Toure A, Kang D, Xie Y, Leslie CS, Li MO. Ets transcription factor GABP controls T cell homeostasis and immunity. Nat Commun 2017; 8:1062. [PMID: 29051483 PMCID: PMC5648787 DOI: 10.1038/s41467-017-01020-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 08/11/2017] [Indexed: 01/08/2023] Open
Abstract
Peripheral T cells are maintained in the absence of vigorous stimuli, and respond to antigenic stimulation by initiating cell cycle progression and functional differentiation. Here we show that depletion of the Ets family transcription factor GA-binding protein (GABP) in T cells impairs T-cell homeostasis. In addition, GABP is critically required for antigen-stimulated T-cell responses in vitro and in vivo. Transcriptome and genome-wide GABP-binding site analyses identify GABP direct targets encoding proteins involved in cellular redox balance and DNA replication, including the Mcm replicative helicases. These findings show that GABP has a nonredundant role in the control of T-cell homeostasis and immunity. T cells need to undergo rapid proliferation in response to antigenic stimulation. Here the authors show that the Ets family transcription factor GABP is required for T-cell homeostasis and response to infection by inducing Mcm3 and Mcm5 expression and enabling S-phase entry.
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Affiliation(s)
- Chong T Luo
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.,Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Hatice U Osmanbeyoglu
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Mytrang H Do
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Michael R Bivona
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Ahmed Toure
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Davina Kang
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Yuchen Xie
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Christina S Leslie
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Ming O Li
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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18
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Neves H, Kwok HF. In sickness and in health: The many roles of the minichromosome maintenance proteins. Biochim Biophys Acta Rev Cancer 2017; 1868:295-308. [DOI: 10.1016/j.bbcan.2017.06.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 05/29/2017] [Accepted: 06/01/2017] [Indexed: 01/09/2023]
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19
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Shima N, Pederson KD. Dormant origins as a built-in safeguard in eukaryotic DNA replication against genome instability and disease development. DNA Repair (Amst) 2017; 56:166-173. [PMID: 28641940 PMCID: PMC5547906 DOI: 10.1016/j.dnarep.2017.06.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
DNA replication is a prerequisite for cell proliferation, yet it can be increasingly challenging for a eukaryotic cell to faithfully duplicate its genome as its size and complexity expands. Dormant origins now emerge as a key component for cells to successfully accomplish such a demanding but essential task. In this perspective, we will first provide an overview of the fundamental processes eukaryotic cells have developed to regulate origin licensing and firing. With a special focus on mammalian systems, we will then highlight the role of dormant origins in preventing replication-associated genome instability and their functional interplay with proteins involved in the DNA damage repair response for tumor suppression. Lastly, deficiencies in the origin licensing machinery will be discussed in relation to their influence on stem cell maintenance and human diseases.
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Affiliation(s)
- Naoko Shima
- The University of Minnesota, Twin Cities, Department of Genetics, Cell Biology and Development, Masonic Cancer Center, 6-160 Jackson Hall, 321 Church St SE., Minneapolis, MN 55455, United States.
| | - Kayla D Pederson
- The University of Minnesota, Twin Cities, Department of Genetics, Cell Biology and Development, Masonic Cancer Center, 6-160 Jackson Hall, 321 Church St SE., Minneapolis, MN 55455, United States
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20
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MCM7 promotes cancer progression through cyclin D1-dependent signaling and serves as a prognostic marker for patients with hepatocellular carcinoma. Cell Death Dis 2017; 8:e2603. [PMID: 28182015 PMCID: PMC5386449 DOI: 10.1038/cddis.2016.352] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 09/23/2016] [Accepted: 09/28/2016] [Indexed: 12/13/2022]
Abstract
DNA replication is a central procedure of cell proliferation, whereas aberrant DNA replication is indicated to be a driving force of oncogenesis. Minichromosome maintenance complex component 7 (MCM7) plays an essential role in initiating DNA replication. To investigate the potential oncogenic properties and prognostic value of MCM7 in hepatocellular carcinoma (HCC), we conducted immunohistochemistry staining of MCM7 in 153 HCC samples and found that MCM7 high expression level was associated with worse overall survival (OS) of HCC patients. Mechanistically, knockdown of MCM7 significantly inhibited cellular proliferation in vitro and HCC tumorigenicity in vivo. Cyclin D1 was proved to be regulated by MCM7–MAPK signaling pathway. Clinically, high expression of both MCM7 and cyclin D1 exhibited a relatively high sensitivity and specificity to predict worse outcome of HCC patients. Taken together, our results suggest that MCM7–cyclin D1 pathway may participate in cancer progression and serve as a biomarker for prognosis in HCC.
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21
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Sugimoto N, Fujita M. Molecular Mechanism for Chromatin Regulation During MCM Loading in Mammalian Cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1042:61-78. [PMID: 29357053 DOI: 10.1007/978-981-10-6955-0_3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
DNA replication is a fundamental process required for the accurate and timely duplication of chromosomes. During late mitosis to G1 phase, the MCM2-7 complex is loaded onto chromatin in a manner dependent on ORC, CDC6, and Cdt1, and chromatin becomes licensed for replication. Although every eukaryotic organism shares common features in replication control, there are also some differences among species. For example, in higher eukaryotic cells including human cells, no strict sequence specificity has been observed for replication origins, unlike budding yeast or bacterial replication origins. Therefore, elements other than beyond DNA sequences are important for regulating replication. For example, the stability and precise positioning of nucleosomes affects replication control. However, little is known about how nucleosome structure is regulated when replication licensing occurs. During the last decade, histone acetylation enzyme HBO1, chromatin remodeler SNF2H, and histone chaperone GRWD1 have been identified as chromatin-handling factors involved in the promotion of replication licensing. In this review, we discuss how the rearrangement of nucleosome formation by these factors affects replication licensing.
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Affiliation(s)
- Nozomi Sugimoto
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan.
| | - Masatoshi Fujita
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan.
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22
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Krause CJ, Popp O, Thirunarayanan N, Dittmar G, Lipp M, Müller G. MicroRNA-34a promotes genomic instability by a broad suppression of genome maintenance mechanisms downstream of the oncogene KSHV-vGPCR. Oncotarget 2016; 7:10414-32. [PMID: 26871287 PMCID: PMC4891129 DOI: 10.18632/oncotarget.7248] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 01/17/2016] [Indexed: 12/18/2022] Open
Abstract
The Kaposi's sarcoma-associated herpesvirus (KSHV)-encoded chemokine receptor vGPCR acts as an oncogene in Kaposi's sarcomagenesis. Until now, the molecular mechanisms by which the vGPCR contributes to tumor development remain incompletely understood. Here, we show that the KSHV-vGPCR contributes to tumor progression through microRNA (miR)-34a-mediated induction of genomic instability. Large-scale analyses on the DNA, gene and protein level of cell lines derived from a mouse model of vGPCR-driven tumorigenesis revealed that a vGPCR–induced upregulation of miR-34a resulted in a broad suppression of genome maintenance genes. A knockdown of either the vGPCR or miR-34a largely restored the expression of these genes and confirmed miR-34a as a downstream effector of the KSHV-vGPCR that compromises genome maintenance mechanisms. This novel, protumorigenic role of miR-34a questions the use of miR-34a mimetics in cancer therapy as they could impair genome stability.
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Affiliation(s)
- Claudia J Krause
- Molecular Tumor Genetics and Immunogenetics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Laboratory of Molecular Radiology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Oliver Popp
- Mass Spectrometry Group, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Nanthakumar Thirunarayanan
- Molecular Tumor Genetics and Immunogenetics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Gunnar Dittmar
- Mass Spectrometry Group, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Martin Lipp
- Molecular Tumor Genetics and Immunogenetics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Gerd Müller
- Molecular Tumor Genetics and Immunogenetics, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
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23
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Kordasti S, Costantini B, Seidl T, Perez Abellan P, Martinez Llordella M, McLornan D, Diggins KE, Kulasekararaj A, Benfatto C, Feng X, Smith A, Mian SA, Melchiotti R, de Rinaldis E, Ellis R, Petrov N, Povoleri GAM, Chung SS, Thomas NSB, Farzaneh F, Irish JM, Heck S, Young NS, Marsh JCW, Mufti GJ. Deep phenotyping of Tregs identifies an immune signature for idiopathic aplastic anemia and predicts response to treatment. Blood 2016; 128:1193-205. [PMID: 27281795 PMCID: PMC5009512 DOI: 10.1182/blood-2016-03-703702] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 06/01/2016] [Indexed: 11/20/2022] Open
Abstract
Idiopathic aplastic anemia (AA) is an immune-mediated and serious form of bone marrow failure. Akin to other autoimmune diseases, we have previously shown that in AA regulatory T cells (Tregs) are reduced in number and function. The aim of this study was to further characterize Treg subpopulations in AA and investigate the potential correlation between specific Treg subsets and response to immunosuppressive therapy (IST) as well as their in vitro expandability for potential clinical use. Using mass cytometry and an unbiased multidimensional analytical approach, we identified 2 specific human Treg subpopulations (Treg A and Treg B) with distinct phenotypes, gene expression, expandability, and function. Treg B predominates in IST responder patients, has a memory/activated phenotype (with higher expression of CD95, CCR4, and CD45RO within FOXP3(hi), CD127(lo) Tregs), expresses the interleukin-2 (IL-2)/STAT5 pathway and cell-cycle commitment genes. Furthermore, in vitro-expanded Tregs become functional and take on the characteristics of Treg B. Collectively, this study identifies human Treg subpopulations that can be used as predictive biomarkers for response to IST in AA and potentially other autoimmune diseases. We also show that Tregs from AA patients are IL-2-sensitive and expandable in vitro, suggesting novel therapeutic approaches such as low-dose IL-2 therapy and/or expanded autologous Tregs and meriting further exploration.
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Affiliation(s)
- Shahram Kordasti
- Department of Haematological Medicine, King's College London, London, United Kingdom; Haematological Medicine, King's College Hospital, London, United Kingdom
| | - Benedetta Costantini
- Department of Haematological Medicine, King's College London, London, United Kingdom; Haematological Medicine, King's College Hospital, London, United Kingdom
| | - Thomas Seidl
- Department of Haematological Medicine, King's College London, London, United Kingdom
| | | | - Marc Martinez Llordella
- Division of Transplantation Immunology & Mucosal Biology, King's College London, London, United Kingdom
| | - Donal McLornan
- Haematological Medicine, King's College Hospital, London, United Kingdom
| | | | | | - Cinzia Benfatto
- Department of Haematological Medicine, King's College London, London, United Kingdom
| | - Xingmin Feng
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD; and
| | - Alexander Smith
- Department of Haematological Medicine, King's College London, London, United Kingdom; Haematological Medicine, King's College Hospital, London, United Kingdom
| | - Syed A Mian
- Department of Haematological Medicine, King's College London, London, United Kingdom
| | - Rossella Melchiotti
- National Institute for Health Research Biomedical Research Centre, King's College London, London, United Kingdom
| | - Emanuele de Rinaldis
- National Institute for Health Research Biomedical Research Centre, King's College London, London, United Kingdom
| | - Richard Ellis
- National Institute for Health Research Biomedical Research Centre, King's College London, London, United Kingdom
| | - Nedyalko Petrov
- National Institute for Health Research Biomedical Research Centre, King's College London, London, United Kingdom
| | - Giovanni A M Povoleri
- Division of Transplantation Immunology & Mucosal Biology, King's College London, London, United Kingdom
| | - Sun Sook Chung
- Department of Haematological Medicine, King's College London, London, United Kingdom
| | - N Shaun B Thomas
- Department of Haematological Medicine, King's College London, London, United Kingdom
| | - Farzin Farzaneh
- Department of Haematological Medicine, King's College London, London, United Kingdom
| | - Jonathan M Irish
- Department of Cancer Biology, Vanderbilt University, Nashville, TN
| | - Susanne Heck
- National Institute for Health Research Biomedical Research Centre, King's College London, London, United Kingdom
| | - Neal S Young
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD; and
| | - Judith C W Marsh
- Department of Haematological Medicine, King's College London, London, United Kingdom; Haematological Medicine, King's College Hospital, London, United Kingdom
| | - Ghulam J Mufti
- Department of Haematological Medicine, King's College London, London, United Kingdom; Haematological Medicine, King's College Hospital, London, United Kingdom
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Parplys AC, Seelbach JI, Becker S, Behr M, Wrona A, Jend C, Mansour WY, Joosse SA, Stuerzbecher HW, Pospiech H, Petersen C, Dikomey E, Borgmann K. High levels of RAD51 perturb DNA replication elongation and cause unscheduled origin firing due to impaired CHK1 activation. Cell Cycle 2016; 14:3190-202. [PMID: 26317153 DOI: 10.1080/15384101.2015.1055996] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
In response to replication stress ATR signaling through CHK1 controls the intra-S checkpoint and is required for the maintenance of genomic integrity. Homologous recombination (HR) comprises a series of interrelated pathways that function in the repair of DNA double strand breaks and interstrand crosslinks. In addition, HR, with its key player RAD51, provides critical support for the recovery of stalled forks during replication. High levels of RAD51 are regularly found in various cancers, yet little is known about the effect of the increased RAD51 expression on intra-S checkpoint signaling. Here, we describe a role for RAD51 in driving genomic instability caused by impaired replication and intra-S mediated CHK1 signaling by studying an inducible RAD51 overexpression model as well as 10 breast cancer cell lines. We demonstrate that an excess of RAD51 decreases I-Sce-I mediated HR despite formation of more RAD51 foci. Cells with high RAD51 levels display reduced elongation rates and excessive dormant origin firing during undisturbed growth and after damage, likely caused by impaired CHK1 activation. In consequence, the inability of cells with a surplus of RAD51 to properly repair complex DNA damage and to resolve replication stress leads to higher genomic instability and thus drives tumorigenesis.
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Affiliation(s)
- Ann Christin Parplys
- a Laboratory of Radiobiology & Experimental Radiooncology; University Medical Center Hamburg-Eppendorf ; Hamburg , Germany
| | - Jasna Irena Seelbach
- a Laboratory of Radiobiology & Experimental Radiooncology; University Medical Center Hamburg-Eppendorf ; Hamburg , Germany
| | - Saskia Becker
- a Laboratory of Radiobiology & Experimental Radiooncology; University Medical Center Hamburg-Eppendorf ; Hamburg , Germany
| | - Matthias Behr
- a Laboratory of Radiobiology & Experimental Radiooncology; University Medical Center Hamburg-Eppendorf ; Hamburg , Germany
| | - Agnieszka Wrona
- a Laboratory of Radiobiology & Experimental Radiooncology; University Medical Center Hamburg-Eppendorf ; Hamburg , Germany
| | - Camilla Jend
- a Laboratory of Radiobiology & Experimental Radiooncology; University Medical Center Hamburg-Eppendorf ; Hamburg , Germany
| | - Wael Yassin Mansour
- a Laboratory of Radiobiology & Experimental Radiooncology; University Medical Center Hamburg-Eppendorf ; Hamburg , Germany.,b Tumor Biology Department; National Cancer Institute; Cairo University ; Cairo , Egypt
| | - Simon Andreas Joosse
- d Department of Tumor Biology ; University Medical Center Hamburg-Eppendorf ; Hamburg , Germany
| | | | - Helmut Pospiech
- f Leibniz Institute for Age Research - Fritz Lipmann Institute ; Jena , Germany.,g Faculty of Biochemistry and Molecular Medicine; University of Oulu ; Oulu , Finland
| | - Cordula Petersen
- c Department of Radiotherapy and Radiooncology ; University Medical Center Hamburg-Eppendorf ; Hamburg , Germany
| | - Ekkehard Dikomey
- a Laboratory of Radiobiology & Experimental Radiooncology; University Medical Center Hamburg-Eppendorf ; Hamburg , Germany
| | - Kerstin Borgmann
- a Laboratory of Radiobiology & Experimental Radiooncology; University Medical Center Hamburg-Eppendorf ; Hamburg , Germany
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25
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Karavias D, Maroulis I, Papadaki H, Gogos C, Kakkos S, Karavias D, Bravou V. Overexpression of CDT1 Is a Predictor of Poor Survival in Patients with Hepatocellular Carcinoma. J Gastrointest Surg 2016; 20:568-79. [PMID: 26408331 DOI: 10.1007/s11605-015-2960-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 09/16/2015] [Indexed: 01/31/2023]
Abstract
BACKGROUND Genomic instability is a common feature in hepatocellular carcinoma. Deregulation of replication licensing factors has been shown to trigger DNA damage response contributing to genomic instability. Overexpression of DNA replication licensing factors chromatin licensing and DNA replication factor 1 (CDT1) and minichromosome maintenance complex component 7 (MCM7) has been previously reported in several human cancers. The aim of the present study was to evaluate the expression and prognostic significance of CDT1 and MCM7 in association with DNA damage response markers and p53 in patients with hepatocellular carcinoma. METHODS Expression of CDT1, MCM7, p-H2A histone family member X (H2AX), phospho-ataxia telangiectasia-mutated (ATM)/ataxia telangiectasia rad3-related (ATR) substrate, and p53 was evaluated by immunohistochemistry on formalin-fixed paraffin-embedded surgical specimens from 111 patients who underwent hepatectomy for hepatocellular carcinoma. Statistical analysis was performed to evaluate associations between the studied proteins, clinicopathological parameters, and patient survival. RESULTS CDT1 expression correlated with p-H2AX (p = 0.038), while MCM7 correlated with p-H2AX and phospho-ATM/ATR substrate (p < 0.001). Increased CDT1 expression was associated with higher tumor grade (p = 0.006) and tumor-node-metastasis (TNM) stage (p = 0.033). High CDT1 expression correlated significantly with reduced overall survival (60.8 and 26.5 % vs 82.8 and 53.0 %, for low CDT1 expression, at 2 and 5 years, respectively, p = 0.012) and was identified by multivariate analysis as an independent predictor of poor overall survival (p = 0.049). CONCLUSIONS Overexpression of CDT1 and MCM7 in hepatocellular carcinoma correlates with DNA damage response, and CDT1 overexpression is a significant prognostic biomarker in hepatocellular carcinoma.
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Affiliation(s)
- Dimitrios Karavias
- Department of Surgery, University Hospital of Patras, Rio, 26500, Greece.
| | - Ioannis Maroulis
- Department of Surgery, University Hospital of Patras, Rio, 26500, Greece
| | - Helen Papadaki
- Department of Anatomy, Histology and Embryology, School of Medicine, University of Patras, Rio, Greece
| | - Charalambos Gogos
- Department of Internal Medicine, University Hospital of Patras, Rio, Greece
| | - Stavros Kakkos
- Department of Vascular Surgery, University Hospital of Patras, Rio, Greece
| | | | - Vasiliki Bravou
- Department of Anatomy, Histology and Embryology, School of Medicine, University of Patras, Rio, Greece
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26
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Kunnev D, Freeland A, Qin M, Leach RW, Wang J, Shenoy RM, Pruitt SC. Effect of minichromosome maintenance protein 2 deficiency on the locations of DNA replication origins. Genome Res 2015; 25:558-69. [PMID: 25762552 PMCID: PMC4381527 DOI: 10.1101/gr.176099.114] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 01/26/2015] [Indexed: 12/27/2022]
Abstract
Minichromosome maintenance (MCM) proteins are loaded onto chromatin during G1-phase and define potential locations of DNA replication initiation. MCM protein deficiency results in genome instability and high rates of cancer in mouse models. Here we develop a method of nascent strand capture and release and show that MCM2 deficiency reduces DNA replication initiation in gene-rich regions of the genome. DNA structural properties are shown to correlate with sequence motifs associated with replication origins and with locations that are preferentially affected by MCM2 deficiency. Reduced nascent strand density correlates with sites of recurrent focal CNVs in tumors arising in MCM2-deficient mice, consistent with a direct relationship between sites of reduced DNA replication initiation and genetic damage. Between 10% and 90% of human tumors, depending on type, carry heterozygous loss or mutation of one or more MCM2-7 genes, which is expected to compromise DNA replication origin licensing and result in elevated rates of genome damage at a subset of gene-rich locations.
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Affiliation(s)
| | | | - Maochun Qin
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, New York 14263, USA
| | - Robert W Leach
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, New York 14263, USA
| | - Jianmin Wang
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, New York 14263, USA
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27
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Abstract
DNA replication must be tightly regulated to ensure that the genome is accurately duplicated during each cell cycle. When these regulatory mechanisms fail, replicative stress and DNA damage ensue. Activated oncogenes promote replicative stress, inducing a DNA damage response (DDR) early in tumorigenesis. Senescence or apoptosis result, forming a barrier against tumour progression. This may provide a selective pressure for acquisition of mutations in the DDR pathway during tumorigenesis. Despite its potential importance in early cancer development, the precise nature of oncogene-induced replicative stress remains poorly understood. Here, we review our current understanding of replication initiation and its regulation, describe mechanisms by which activated oncogenes might interfere with these processes and discuss how replicative stress might contribute to the genomic instability seen in cancers.
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Affiliation(s)
- Stephanie A Hills
- Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms, Herts, EN6 3LD, UK
| | - John F X Diffley
- Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms, Herts, EN6 3LD, UK.
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28
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Whole-genome sequencing identifies genomic heterogeneity at a nucleotide and chromosomal level in bladder cancer. Proc Natl Acad Sci U S A 2014; 111:E672-81. [PMID: 24469795 DOI: 10.1073/pnas.1313580111] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Using complete genome analysis, we sequenced five bladder tumors accrued from patients with muscle-invasive transitional cell carcinoma of the urinary bladder (TCC-UB) and identified a spectrum of genomic aberrations. In three tumors, complex genotype changes were noted. All three had tumor protein p53 mutations and a relatively large number of single-nucleotide variants (SNVs; average of 11.2 per megabase), structural variants (SVs; average of 46), or both. This group was best characterized by chromothripsis and the presence of subclonal populations of neoplastic cells or intratumoral mutational heterogeneity. Here, we provide evidence that the process of chromothripsis in TCC-UB is mediated by nonhomologous end-joining using kilobase, rather than megabase, fragments of DNA, which we refer to as "stitchers," to repair this process. We postulate that a potential unifying theme among tumors with the more complex genotype group is a defective replication-licensing complex. A second group (two bladder tumors) had no chromothripsis, and a simpler genotype, WT tumor protein p53, had relatively few SNVs (average of 5.9 per megabase) and only a single SV. There was no evidence of a subclonal population of neoplastic cells. In this group, we used a preclinical model of bladder carcinoma cell lines to study a unique SV (translocation and amplification) of the gene glutamate receptor ionotropic N-methyl D-aspertate as a potential new therapeutic target in bladder cancer.
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29
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Proteomic and protein interaction network analysis of human T lymphocytes during cell-cycle entry. Mol Syst Biol 2012; 8:573. [PMID: 22415777 PMCID: PMC3321526 DOI: 10.1038/msb.2012.5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Accepted: 01/30/2012] [Indexed: 12/23/2022] Open
Abstract
Proteomic analysis of T cells emerging from quiescence identifies dynamic network-level changes in key cellular processes. Disruption of two such processes, ribosome biogenesis and RNA splicing, reveals that the programs controlling cell growth and cell-cycle entry are separable. ![]()
The authors conduct a proteomic and protein interaction network analysis of human T lymphocytes during entry into the first cell cycle. Inhibiting the induction of eIF6 (60S ribosome biogenesis) causes T cells to enter the cell cycle without growing in size. Inhibiting the induction of SF3B2/SF3B4 (U2/U12-dependent RNA splicing) allows an increase in cell size without entering the cell cycle. These results provide proof of principle that blastogenesis and proliferation programs are separable in primary human T cells.
Regulating the transition of cells such as T lymphocytes from quiescence (G0) into an activated, proliferating state involves initiation of cellular programs resulting in entry into the cell cycle (proliferation), the growth cycle (blastogenesis, cell size) and effector (functional) activation. We show the first proteomic analysis of protein interaction networks activated during entry into the first cell cycle from G0. We also provide proof of principle that blastogenesis and proliferation programs are separable in primary human T cells. We employed a proteomic profiling method to identify large-scale changes in chromatin/nuclear matrix-bound and unbound proteins in human T lymphocytes during the transition from G0 into the first cell cycle and mapped them to form functionally annotated, dynamic protein interaction networks. Inhibiting the induction of two proteins involved in two of the most significantly upregulated cellular processes, ribosome biogenesis (eIF6) and hnRNA splicing (SF3B2/SF3B4), showed, respectively, that human T cells can enter the cell cycle without growing in size, or increase in size without entering the cell cycle.
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30
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Chuang CH, Yang D, Bai G, Freeland A, Pruitt SC, Schimenti JC. Post-transcriptional homeostasis and regulation of MCM2-7 in mammalian cells. Nucleic Acids Res 2012; 40:4914-24. [PMID: 22362746 PMCID: PMC3367205 DOI: 10.1093/nar/gks176] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The MiniChromosome Maintenance 2-7 (MCM2-7) complex provides essential replicative helicase function. Insufficient MCMs impair the cell cycle and cause genomic instability (GIN), leading to cancer and developmental defects in mice. Remarkably, depletion or mutation of one Mcm can decrease all Mcm levels. Here, we use mice and cells bearing a GIN-causing hypomophic allele of Mcm4 (Chaos3), in conjunction with disruption alleles of other Mcms, to reveal two new mechanisms that regulate MCM protein levels and pre-RC formation. First, the Mcm4Chaos3 allele, which disrupts MCM4:MCM6 interaction, triggers a Dicer1 and Drosha-dependent ∼40% reduction in Mcm2–7 mRNAs. The decreases in Mcm mRNAs coincide with up-regulation of the miR-34 family of microRNAs, which is known to be Trp53-regulated and target Mcms. Second, MCM3 acts as a negative regulator of the MCM2–7 helicase in vivo by complexing with MCM5 in a manner dependent upon a nuclear-export signal-like domain, blocking the recruitment of MCMs onto chromatin. Therefore, the stoichiometry of MCM components and their localization is controlled post-transcriptionally at both the mRNA and protein levels. Alterations to these pathways cause significant defects in cell growth reflected by disease phenotypes in mice.
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Affiliation(s)
- Chen-Hua Chuang
- Department of Biomedical Sciences and Center for Vertebrate Genomics, Cornell University College of Veterinary Medicine, Ithaca, NY 14853, USA
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31
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Rusiniak ME, Kunnev D, Freeland A, Cady GK, Pruitt SC. Mcm2 deficiency results in short deletions allowing high resolution identification of genes contributing to lymphoblastic lymphoma. Oncogene 2011; 31:4034-44. [PMID: 22158038 PMCID: PMC3309111 DOI: 10.1038/onc.2011.566] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mini-chromosome maintenance (Mcm) proteins are part of the replication licensing complex that is loaded onto chromatin during the G1-phase of the cell cycle and required for initiation of DNA replication in the subsequent S-phase. Mcm proteins are typically loaded in excess of the number of locations that are utilized during S-phase. Nonetheless, partial depletion of Mcm proteins leads to cancers and stem cell deficiencies. Mcm2 deficient mice, on a 129Sv genetic background, display a high rate of thymic lymphoblastic lymphoma. Here array comparative genomic hybridization (aCGH) is utilized to characterize the genetic damage accruing in these tumors. The predominant events are deletions averaging less than 0.5 Mb, considerably shorter than observed in prior studies using alternative mouse lymphoma models or human tumors. Such deletions facilitate identification of specific genes and pathways responsible for the tumors. Mutations in many genes that have been implicated in human lymphomas are recapitulated in this mouse model. These features, and the fact that the mutation underlying the accelerated genetic damage does not target a specific gene or pathway a priori, are valuable features of this mouse model for identification of tumor suppressor genes. Genes affected in all tumors include Pten, Tcfe2a, Mbd3 and Setd1b. Notch1 and additional genes are affected in subsets of tumors. The high frequency of relatively short deletions is consistent with elevated recombination between nearby stalled replication forks in Mcm2 deficient mice.
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Affiliation(s)
- M E Rusiniak
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA
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32
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Maki K, Inoue T, Onaka A, Hashizume H, Somete N, Kobayashi Y, Murakami S, Shigaki C, Takahashi TS, Masukata H, Nakagawa T. Abundance of prereplicative complexes (Pre-RCs) facilitates recombinational repair under replication stress in fission yeast. J Biol Chem 2011; 286:41701-41710. [PMID: 21971174 DOI: 10.1074/jbc.m111.285619] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mcm2-7 complexes are loaded onto chromatin with the aid of Cdt1 and Cdc18/Cdc6 and form prereplicative complexes (pre-RCs) at multiple sites on each chromosome. Pre-RCs are essential for DNA replication and surviving replication stress. However, the mechanism by which pre-RCs contribute to surviving replication stress is largely unknown. Here, we isolated the fission yeast mcm6-S1 mutant that was hypersensitive to methyl methanesulfonate (MMS) and camptothecin (CPT), both of which cause forks to collapse. The mcm6-S1 mutation impaired the interaction with Cdt1 and decreased the binding of minichromosome maintenance (MCM) proteins to replication origins. Overexpression of Cdt1 restored MCM binding and suppressed the sensitivity to MMS and CPT, suggesting that the Cdt1-Mcm6 interaction is important for the assembly of pre-RCs and the repair of collapsed forks. MMS-induced Chk1 phosphorylation and Rad22/Rad52 focus formation occurred normally, whereas cells containing Rhp54/Rad54 foci, which are involved in DNA strand exchange and dissociation of the joint molecules, were increased. Remarkably, G(1) phase extension through deletion of an S phase cyclin, Cig2, as well as Cdt1 overexpression restored pre-RC assembly and suppressed Rhp54 accumulation. A cdc18 mutation also caused hypersensitivity to MMS and CPT and accumulation of Rhp54 foci. These data suggest that an abundance of pre-RCs facilitates a late step in the recombinational repair of collapsed forks in the following S phase.
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Affiliation(s)
- Kentaro Maki
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan; Graduate School of Frontier Biosciences, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Takahiro Inoue
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Atsushi Onaka
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Hiroko Hashizume
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Naoko Somete
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Yuko Kobayashi
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Shigefumi Murakami
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan; Graduate School of Frontier Biosciences, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Chikako Shigaki
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Tatsuro S Takahashi
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Hisao Masukata
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan; Graduate School of Frontier Biosciences, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Takuro Nakagawa
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan.
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Sugimoto N, Yugawa T, Iizuka M, Kiyono T, Fujita M. Chromatin remodeler sucrose nonfermenting 2 homolog (SNF2H) is recruited onto DNA replication origins through interaction with Cdc10 protein-dependent transcript 1 (Cdt1) and promotes pre-replication complex formation. J Biol Chem 2011; 286:39200-10. [PMID: 21937426 DOI: 10.1074/jbc.m111.256123] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
From late mitosis to the G(1) phase of the cell cycle, ORC, CDC6, and Cdt1 form the machinery necessary to load MCM2-7 complexes onto DNA. Here, we show that SNF2H, a member of the ATP-dependent chromatin-remodeling complex, is recruited onto DNA replication origins in human cells in a Cdt1-dependent manner and positively regulates MCM loading. SNF2H physically interacted with Cdt1. ChIP assays indicated that SNF2H associates with replication origins specifically during the G(1) phase. Binding of SNF2H at origins was decreased by Cdt1 silencing and, conversely, enhanced by Cdt1 overexpression. Furthermore, SNF2H silencing prevented MCM loading at origins and moderately inhibited S phase progression. Although neither SNF2H overexpression nor SNF2H silencing appeared to impact rereplication induced by Cdt1 overexpression, Cdt1-induced checkpoint activation was inhibited by SNF2H silencing. Collectively, these data suggest that SNF2H may promote MCM loading at DNA replication origins via interaction with Cdt1 in human cells. Because efficient loading of excess MCM complexes is thought to be required for cells to tolerate replication stress, Cdt1- and SNF2H-mediated promotion of MCM loading may be biologically relevant for the regulation of DNA replication.
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Affiliation(s)
- Nozomi Sugimoto
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashiku, Fukuoka 812-8582, Japan
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34
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How dormant origins promote complete genome replication. Trends Biochem Sci 2011; 36:405-14. [PMID: 21641805 DOI: 10.1016/j.tibs.2011.05.002] [Citation(s) in RCA: 172] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Revised: 04/26/2011] [Accepted: 05/04/2011] [Indexed: 01/21/2023]
Abstract
Many replication origins that are licensed by loading MCM2-7 complexes in G1 are not normally used. Activation of these dormant origins during S phase provides a first line of defence for the genome if replication is inhibited. When replication forks fail, dormant origins are activated within regions of the genome currently engaged in replication. At the same time, DNA damage-response kinases activated by the stalled forks preferentially suppress the assembly of new replication factories, thereby ensuring that chromosomal regions experiencing replicative stress complete synthesis before new regions of the genome are replicated. Mice expressing reduced levels of MCM2-7 have fewer dormant origins, are cancer-prone and are genetically unstable, demonstrating the importance of dormant origins for preserving genome integrity. We review the function of dormant origins, the molecular mechanism of their regulation and their physiological implications.
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35
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Kawabata T, Luebben SW, Yamaguchi S, Ilves I, Matise I, Buske T, Botchan MR, Shima N. Stalled fork rescue via dormant replication origins in unchallenged S phase promotes proper chromosome segregation and tumor suppression. Mol Cell 2011; 41:543-53. [PMID: 21362550 DOI: 10.1016/j.molcel.2011.02.006] [Citation(s) in RCA: 156] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Revised: 11/24/2010] [Accepted: 12/21/2010] [Indexed: 01/25/2023]
Abstract
Eukaryotic cells license far more origins than are actually used for DNA replication, thereby generating a large number of dormant origins. Accumulating evidence suggests that such origins play a role in chromosome stability and tumor suppression, though the underlying mechanism is largely unknown. Here, we show that a loss of dormant origins results in an increased number of stalled replication forks, even in unchallenged S phase in primary mouse fibroblasts derived from embryos homozygous for the Mcm4(Chaos3) allele. We found that this allele reduces the stability of the MCM2-7 complex, but confers normal helicase activity in vitro. Despite the activation of multiple fork recovery pathways, replication intermediates in these cells persist into M phase, increasing the number of abnormal anaphase cells with lagging chromosomes and/or acentric fragments. These findings suggest that dormant origins constitute a major pathway for stalled fork recovery, contributing to faithful chromosome segregation and tumor suppression.
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Affiliation(s)
- Tsuyoshi Kawabata
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
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