1
|
Arakawa J, Kondoh H, Matsushita T, Ogino Y, Asai M, Tanuma SI, Uchiumi F. Induction of the human CDC45 gene promoter activity by natural compound trans‑resveratrol. Mol Med Rep 2024; 29:92. [PMID: 38577929 PMCID: PMC11025027 DOI: 10.3892/mmr.2024.13216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 03/13/2024] [Indexed: 04/06/2024] Open
Abstract
GGAA motifs in the human TP53 and HELB gene promoters play a part in responding to trans‑resveratrol (Rsv) in HeLa S3 cells. This sequence is also present in the 5'‑upstream region of the human CDC45 gene, which encodes a component of CMG DNA helicase protein complex. The cells were treated with Rsv (20 µM), then transcripts and the translated protein were analyzed by quantitative RT‑PCR and western blotting, respectively. The results showed that the CDC45 gene and protein expression levels were induced after the treatment. To examine whether they were due to the activation of transcription, a 5'‑upstream 556‑bp of the CDC45 gene was cloned and inserted into a multi‑cloning site of the Luciferase (Luc) expression vector. In the present study, various deletion/point mutation‑introduced Luc expression plasmids were constructed and they were used for the transient transfection assay. The results showed that the GGAA motif, which is included in a putative RELB protein recognizing sequence, plays a part in the promoter activity with response to Rsv in HeLa S3 cells.
Collapse
Affiliation(s)
- Jun Arakawa
- Department of Gene Regulation, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Hikaru Kondoh
- Department of Gene Regulation, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Tokiyoshi Matsushita
- Department of Gene Regulation, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Yoko Ogino
- Department of Gene Regulation, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Masashi Asai
- Department of Gene Regulation, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba 278-8510, Japan
- Laboratory of Kampo Pharmacology, Faculty of Pharmaceutical Sciences, Yokohama University of Pharmacy, Yokohama, Kanagawa 245-0066, Japan
| | - Sei-Ichi Tanuma
- Genomic Medicinal Science, Research Institute for Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Fumiaki Uchiumi
- Department of Gene Regulation, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| |
Collapse
|
2
|
Radhakrishnan A, Sharma C, Malviya VN, Srivastav R. Deciphering the molecular functionality of Cdc45 in replisomal complex. Biochem Biophys Rep 2024; 37:101643. [PMID: 38298211 PMCID: PMC10828582 DOI: 10.1016/j.bbrep.2024.101643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/09/2024] [Accepted: 01/09/2024] [Indexed: 02/02/2024] Open
Abstract
The members of DHH superfamily have been reported with diverse substrate spectrum and play pivotal roles in replication, repair, and RNA metabolism. This family comprises phosphatases, phosphoesterase and bifunctional enzymes having nanoRNase and phosphatase activities. Cell cycle factor Cdc45, a member of this superfamily, is crucial for movement of the replication fork during DNA replication and an important component of the replisome. The specific protein-protein interactions of Cdc45 with other factors along with helicase moderate the faithful DNA replication process. However, the exact biochemical functions of this factor are still unknown and need further investigation. Here, we studied the biochemical roles of Cdc45 and its molecular interactions within the replisomal complex. The alteration in the level of protein, observed when DNA damage is induced in-vivo, suggests its association with DNA replication stress. We analyzed protein Cdc45, providing new insights about the molecular and biochemical functionality of this replisomal factor.
Collapse
Affiliation(s)
| | - Chandresh Sharma
- Translational Health Science and Technology Institute, Haryana, India
| | - Viveka Nand Malviya
- Department of Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Gottingen, Germany
| | - Rajpal Srivastav
- Amity Institute of Biotechnology, Amity University Uttar Pardesh, Noida, India
- Department of Science & Technology, Ministry of Science & Technology, New Delhi, India
| |
Collapse
|
3
|
Yadav AK, Polasek-Sedlackova H. Quantity and quality of minichromosome maintenance protein complexes couple replication licensing to genome integrity. Commun Biol 2024; 7:167. [PMID: 38336851 PMCID: PMC10858283 DOI: 10.1038/s42003-024-05855-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Accurate and complete replication of genetic information is a fundamental process of every cell division. The replication licensing is the first essential step that lays the foundation for error-free genome duplication. During licensing, minichromosome maintenance protein complexes, the molecular motors of DNA replication, are loaded to genomic sites called replication origins. The correct quantity and functioning of licensed origins are necessary to prevent genome instability associated with severe diseases, including cancer. Here, we delve into recent discoveries that shed light on the novel functions of licensed origins, the pathways necessary for their proper maintenance, and their implications for cancer therapies.
Collapse
Affiliation(s)
- Anoop Kumar Yadav
- Department of Cell Biology and Epigenetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Hana Polasek-Sedlackova
- Department of Cell Biology and Epigenetics, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.
| |
Collapse
|
4
|
Tonozuka Y, Tanaka H, Nomura K, Sakaguchi K, Soeda J, Kakimoto Y. The combination of brentuximab vedotin and chidamide synergistically suppresses the proliferation of T-cell lymphoma cells through the enhancement of apoptosis. Cancer Chemother Pharmacol 2024; 93:137-149. [PMID: 37921901 PMCID: PMC10853311 DOI: 10.1007/s00280-023-04609-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 10/14/2023] [Indexed: 11/05/2023]
Abstract
PURPOSE Peripheral T-cell lymphoma (PTCL) is an aggressive disease with a poor prognosis. Brentuximab vedotin (BV), an anti-CD30 monoclonal antibody linked to a microtubule-disrupting agent, has been approved for the treatment of PTCL. We evaluated a new effective combination partner of BV using non-clinical approaches that could potentially identify agents capable of improving survival times for patients with PTCL. METHODS A high-throughput screening test was used to select the most synergistic partner of BV from 14 candidate drugs that were under development or available in clinical practice for PTCL. HH cells, originating from an aggressive cutaneous T-cell lymphoma, were used as an experimental model of PTCL. Apoptotic effects of the synergistic partner of BV were further investigated in vitro and in vivo using HH-cell xenograft mice. RESULTS Chidamide (tucidinostat), a novel histone deacetylase inhibitor, was found to have the greatest synergistic effect with BV on HH cells. The combined effects of chidamide and BV were demonstrated in a study of HH-cell xenograft mice; mean tumor size following combined treatment was 22% of that observed in the control group, compared with 71% and 58% following chidamide and BV monotherapy, respectively. Further investigations in vitro and in vivo revealed that the levels of an anti-apoptotic protein, Bcl-2, and a rate-limiting factor of DNA replication, CDC45, were reduced in HH cells treated with chidamide combined with BV compared with the control group. CONCLUSION The use of chidamide in conjunction with BV may positively affect and enhance T-cellular apoptotic pathways without offsetting each other.
Collapse
Affiliation(s)
- Yukio Tonozuka
- Japan Medical Affairs, Japan Oncology Business Unit, Takeda Pharmaceutical Company Limited, 1-1 Nihonbashi Honcho 2-chome, Chuo-ku, Tokyo, 103-8668, Japan.
| | - Hiroshi Tanaka
- Integrated Biology, Integrated & Translational Science, Axcelead Drug Discovery Partners, Inc., 26-1, Muraoka-Higashi 2-chome Fujisawa, Kanagawa, 251-0012, Japan
| | - Kazumi Nomura
- Japan Medical Affairs, Japan Oncology Business Unit, Takeda Pharmaceutical Company Limited, 1-1 Nihonbashi Honcho 2-chome, Chuo-ku, Tokyo, 103-8668, Japan
| | - Kazuya Sakaguchi
- Frontier Technology, Integrated & Translational Science, Axcelead Drug Discovery Partners, Inc., 26-1, Muraoka-Higashi 2-chome Fujisawa, Kanagawa, 251-0012, Japan
| | - Junpei Soeda
- Japan Medical Affairs, Japan Oncology Business Unit, Takeda Pharmaceutical Company Limited, 1-1 Nihonbashi Honcho 2-chome, Chuo-ku, Tokyo, 103-8668, Japan
| | - Yoshihide Kakimoto
- Japan Medical Affairs, Japan Oncology Business Unit, Takeda Pharmaceutical Company Limited, 1-1 Nihonbashi Honcho 2-chome, Chuo-ku, Tokyo, 103-8668, Japan
| |
Collapse
|
5
|
Guilz NC, Ahn YO, Seo S, Mace EM. Unwinding the Role of the CMG Helicase in Inborn Errors of Immunity. J Clin Immunol 2023; 43:847-861. [PMID: 36809597 PMCID: PMC10789183 DOI: 10.1007/s10875-023-01437-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/20/2023] [Indexed: 02/23/2023]
Abstract
Inborn errors of immunity (IEI) are a collection of diseases resulting from genetic causes that impact the immune system through multiple mechanisms. Natural killer cell deficiency (NKD) is one such IEI where natural killer (NK) cells are the main immune lineage affected. Though rare, the deficiency of several genes has been described as underlying causes of NKD, including MCM4, GINS1, MCM10 , and GINS4 , all of which are involved in the eukaryotic CMG helicase. The CMG helicase is made up of C DC45 – M CM – G INS and accessory proteins including MCM10. The CMG helicase plays a critical role in DNA replication by unwinding the double helix and enabling access of polymerases to single-stranded DNA, and thus helicase proteins are active in any proliferating cell. Replication stress, DNA damage, and cell cycle arrest are among the cellular phenotypes attributed to loss of function variants in CMG helicase proteins. Despite the ubiquitous function of the CMG helicase, NK cells have an apparent susceptibility to the deficiency of helicase proteins. This review will examine the role of the CMG helicase in inborn errors of immunity through the lens of NKD and further discuss why natural killer cells can be so strongly affected by helicase deficiency.
Collapse
Affiliation(s)
- Nicole C Guilz
- Vagelos College of Physicians and Surgeons, Department of Pediatrics, Columbia University Irving Medical Center, 630 W 168th St., New York, NY, 10032, USA
| | - Yong-Oon Ahn
- Vagelos College of Physicians and Surgeons, Department of Pediatrics, Columbia University Irving Medical Center, 630 W 168th St., New York, NY, 10032, USA
| | - Seungmae Seo
- Vagelos College of Physicians and Surgeons, Department of Pediatrics, Columbia University Irving Medical Center, 630 W 168th St., New York, NY, 10032, USA
| | - Emily M Mace
- Vagelos College of Physicians and Surgeons, Department of Pediatrics, Columbia University Irving Medical Center, 630 W 168th St., New York, NY, 10032, USA.
| |
Collapse
|
6
|
Zou Y, Pei J, Long H, Lan L, Dong K, Wang T, Li M, Zhao Z, Zhu L, Zhang G, Jin X, Wang Y, Wen Z, Wei M, Feng Y. H4S47 O-GlcNAcylation regulates the activation of mammalian replication origins. Nat Struct Mol Biol 2023:10.1038/s41594-023-00998-6. [PMID: 37202474 DOI: 10.1038/s41594-023-00998-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 04/12/2023] [Indexed: 05/20/2023]
Abstract
The transmission and maintenance of genetic information in eukaryotic cells relies on the faithful duplication of the entire genome. In each round of division, excessive replication origins are licensed, with only a fraction activated to give rise to bi-directional replication forks in the context of chromatin. However, it remains elusive how eukaryotic replication origins are selectively activated. Here we demonstrate that O-GlcNAc transferase (OGT) enhances replication initiation by catalyzing H4S47 O-GlcNAcylation. Mutation of H4S47 impairs DBF4-dependent protein kinase (DDK) recruitment on chromatin, causing reduced phosphorylation of the replicative helicase mini-chromosome maintenance (MCM) complex and compromised DNA unwinding. Our short nascent-strand sequencing results further confirm the importance of H4S47 O-GlcNAcylation in origin activation. We propose that H4S47 O-GlcNAcylation directs origin activation through facilitating MCM phosphorylation, and this may shed light on the control of replication efficiency by chromatin environment.
Collapse
Affiliation(s)
- Yingying Zou
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin, China
| | - Jiayao Pei
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin, China
| | - Haizhen Long
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Liting Lan
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kejian Dong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin, China
| | - Tingting Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin, China
| | - Ming Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin, China
| | - Zhexuan Zhao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin, China
| | - Lirun Zhu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin, China
| | - Gangxuan Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin, China
| | - Xin Jin
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin, China
| | - Yang Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin, China
| | - Zengqi Wen
- School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Min Wei
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin, China
| | - Yunpeng Feng
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, Jilin, China.
| |
Collapse
|
7
|
Williams KS, Secomb TW, El-Kareh AW. An autonomous mathematical model for the mammalian cell cycle. J Theor Biol 2023; 569:111533. [PMID: 37196820 DOI: 10.1016/j.jtbi.2023.111533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 04/04/2023] [Accepted: 05/10/2023] [Indexed: 05/19/2023]
Abstract
A mathematical model for the mammalian cell cycle is developed as a system of 13 coupled nonlinear ordinary differential equations. The variables and interactions included in the model are based on detailed consideration of available experimental data. A novel feature of the model is inclusion of cycle tasks such as origin licensing and initiation, nuclear envelope breakdown and kinetochore attachment, and their interactions with controllers (molecular complexes involved in cycle control). Other key features are that the model is autonomous, except for a dependence on external growth factors; the variables are continuous in time, without instantaneous resets at phase boundaries; mechanisms to prevent rereplication are included; and cycle progression is independent of cell size. Eight variables represent cell cycle controllers: the Cyclin D1-Cdk4/6 complex, APCCdh1, SCFβTrCP, Cdc25A, MPF, NuMA, the securin-separase complex, and separase. Five variables represent task completion, with four for the status of origins and one for kinetochore attachment. The model predicts distinct behaviors corresponding to the main phases of the cell cycle, showing that the principal features of the mammalian cell cycle, including restriction point behavior, can be accounted for in a quantitative mechanistic way based on known interactions among cycle controllers and their coupling to tasks. The model is robust to parameter changes, in that cycling is maintained over at least a five-fold range of each parameter when varied individually. The model is suitable for exploring how extracellular factors affect cell cycle progression, including responses to metabolic conditions and to anti-cancer therapies.
Collapse
Affiliation(s)
| | - Timothy W Secomb
- BIO5 Institute, University of Arizona, Tucson, AZ, USA; Department of Physiology, University of Arizona, Tucson, AZ, USA
| | | |
Collapse
|
8
|
Böhly N, Schmidt AK, Zhang X, Slusarenko BO, Hennecke M, Kschischo M, Bastians H. Increased replication origin firing links replication stress to whole chromosomal instability in human cancer. Cell Rep 2022; 41:111836. [PMID: 36516748 DOI: 10.1016/j.celrep.2022.111836] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 09/12/2022] [Accepted: 11/22/2022] [Indexed: 12/14/2022] Open
Abstract
Chromosomal instability (CIN) is a hallmark of cancer and comprises structural CIN (S-CIN) and numerical or whole chromosomal CIN (W-CIN). Recent work indicated that replication stress (RS), known to contribute to S-CIN, also affects mitotic chromosome segregation, possibly explaining the common co-existence of S-CIN and W-CIN in human cancer. Here, we show that RS-induced increased origin firing is sufficient to trigger W-CIN in human cancer cells. We discovered that overexpression of origin firing genes, including GINS1 and CDC45, correlates with W-CIN in human cancer specimens and causes W-CIN in otherwise chromosomally stable human cells. Furthermore, modulation of the ATR-CDK1-RIF1 axis increases the number of firing origins and leads to W-CIN. Importantly, chromosome missegregation upon additional origin firing is mediated by increased mitotic microtubule growth rates, a mitotic defect prevalent in chromosomally unstable cancer cells. Thus, our study identifies increased replication origin firing as a cancer-relevant trigger for chromosomal instability.
Collapse
Affiliation(s)
- Nicolas Böhly
- Georg August University Göttingen, University Medical Center Göttingen (UMG), Department of Molecular Oncology, Section for Cellular Oncology, 37077 Göttingen, Germany
| | - Ann-Kathrin Schmidt
- Georg August University Göttingen, University Medical Center Göttingen (UMG), Department of Molecular Oncology, Section for Cellular Oncology, 37077 Göttingen, Germany
| | - Xiaoxiao Zhang
- University of Applied Sciences Koblenz, Department of Mathematics and Technology, 53424 Remagen, Germany; Technical University of Munich, Department of Informatics, 81675 Munich, Germany
| | - Benjamin O Slusarenko
- Georg August University Göttingen, University Medical Center Göttingen (UMG), Department of Molecular Oncology, Section for Cellular Oncology, 37077 Göttingen, Germany
| | - Magdalena Hennecke
- Georg August University Göttingen, University Medical Center Göttingen (UMG), Department of Molecular Oncology, Section for Cellular Oncology, 37077 Göttingen, Germany
| | - Maik Kschischo
- University of Applied Sciences Koblenz, Department of Mathematics and Technology, 53424 Remagen, Germany
| | - Holger Bastians
- Georg August University Göttingen, University Medical Center Göttingen (UMG), Department of Molecular Oncology, Section for Cellular Oncology, 37077 Göttingen, Germany.
| |
Collapse
|
9
|
Lu Y, Chen X, Liu F, Yu H, Zhang Y, Du K, Nan Y, Huang Q. Systematic pan‑cancer analysis identifies CDC45 as having an oncogenic role in human cancers. Oncol Rep 2022; 48:185. [PMID: 36082823 PMCID: PMC9478988 DOI: 10.3892/or.2022.8400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/22/2022] [Indexed: 12/05/2022] Open
Abstract
Cell division cycle 45 (CDC45) is an essential protein required for the initiation of DNA replication. In the present study, the role of CDC45 across 33 cancers was systematically investigated. It was observed that the expression of CDC45 was significantly upregulated in most cancers, exhibiting a marked negative correlation with the overall survival. Next, there was no significant difference in prognosis between the genomically altered and unaltered groups with respect to clinical outcomes. A decreased level of CDC45 at the DNA promoter region was also identified in several cancers. Furthermore, CDC45 expression was associated with the levels of tumor-infiltrating immune cells in some specific cancer types. In addition, CDC45 was associated with m6A methylation, and CDC45 expression was primarily positively correlated with ‘writers’ and ‘readers’ in various cancers, particularly HNRNPC, RBM15 and YTHDC1. Gene enrichment analysis was also performed. In addition, the AUC of each cancer with respect to its 1-, 3-, and 5-year survival rates were explored. Finally, CCK-8 assays, EdU assays and cell cycle analysis were conducted. In conclusion, the present study demonstrated that CDC45 may be a potential biomarker and target for cancer treatment.
Collapse
Affiliation(s)
- Yalin Lu
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, P.R. China
| | - Xingjie Chen
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, P.R. China
| | - Fang Liu
- Institute of Mental Health, Tianjin Anding Hospital, Mental Health Center of Tianjin Medical University, Tianjin 300052, P.R. China
| | - Hao Yu
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, P.R. China
| | - Yu Zhang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, P.R. China
| | - Kangjie Du
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, P.R. China
| | - Yang Nan
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, P.R. China
| | - Qiang Huang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300052, P.R. China
| |
Collapse
|
10
|
Sudhahar V, Shi Y, Kaplan JH, Ushio-Fukai M, Fukai T. Whole-Transcriptome Sequencing Analyses of Nuclear Antixoxidant-1 in Endothelial Cells: Role in Inflammation and Atherosclerosis. Cells 2022; 11:2919. [PMID: 36139494 PMCID: PMC9496719 DOI: 10.3390/cells11182919] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/08/2022] [Accepted: 09/15/2022] [Indexed: 11/26/2022] Open
Abstract
Inflammation, oxidative stress, and copper (Cu) play an important role in cardiovascular disease, including atherosclerosis. We previously reported that cytosolic Cu chaperone antioxidant-1 (Atox1) translocates to the nucleus in response to inflammatory cytokines or exogenous Cu and that Atox1 is localized at the nucleus in the endothelium of inflamed atherosclerotic aorta. However, the roles of nuclear Atox1 and their function are poorly understood. Here we showed that Atox1 deficiency in ApoE-/- mice with a Western diet exhibited a significant reduction of atherosclerotic lesion formation. In vitro, adenovirus-mediated overexpression of nuclear-targeted Atox1 (Ad-Atox1-NLS) in cultured human endothelial cells (ECs) increased monocyte adhesion and reactive oxygen species (ROS) production compared to control cells (Ad-null). To address the underlying mechanisms, we performed genome-wide mapping of Atox1-regulated targets in ECs, using an unbiased systemic approach integrating sequencing data. Combination of ChIP-Seq and RNA-Seq analyses in ECs transfected with Ad-Atox1-NLS or Ad-null identified 1387 differentially expressed genes (DEG). Motif enrichment assay and KEGG pathway enrichment analysis revealed that 248 differentially expressed genes, including inflammatory and angiogenic genes, were regulated by Atox1-NLS, which was then confirmed by real-time qPCR. Among these genes, functional analysis of inflammatory responses identified CD137, CSF1, and IL5RA as new nuclear Atox1-targeted inflammatory genes, while CD137 is also a key regulator of Atox1-NLS-induced ROS production. These findings uncover new nuclear Atox1 downstream targets involved in inflammation and ROS production and provide insights into the nuclear Atox1 as a potential therapeutic target for the treatment of inflammatory diseases such as atherosclerosis.
Collapse
Affiliation(s)
- Varadarajan Sudhahar
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
- Charlie Norwood Veterans Affairs Medical Center, Augusta, GA 30901, USA
| | - Yang Shi
- Department of Population Health Science, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Jack H. Kaplan
- Department of Biochemistry and Molecular Genetics, University of Illinois College of Medicine, Chicago, IL 60607, USA
| | - Masuko Ushio-Fukai
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
- Department of Medicine (Cardiology), Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Tohru Fukai
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA
- Charlie Norwood Veterans Affairs Medical Center, Augusta, GA 30901, USA
| |
Collapse
|
11
|
Identification of Human Cell Cycle Phase Markers Based on Single-Cell RNA-Seq Data by Using Machine Learning Methods. BIOMED RESEARCH INTERNATIONAL 2022; 2022:2516653. [PMID: 36004205 PMCID: PMC9393965 DOI: 10.1155/2022/2516653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 07/25/2022] [Accepted: 07/29/2022] [Indexed: 12/17/2022]
Abstract
The cell cycle is composed of a series of ordered, highly regulated processes through which a cell grows and duplicates its genome and eventually divides into two daughter cells. According to the complex changes in cell structure and biosynthesis, the cell cycle is divided into four phases: gap 1 (G1), DNA synthesis (S), gap 2 (G2), and mitosis (M). Determining which cell cycle phases a cell is in is critical to the research of cancer development and pharmacy for targeting cell cycle. However, current detection methods have the following problems: (1) they are complicated and time consuming to perform, and (2) they cannot detect the cell cycle on a large scale. Rapid developments in single-cell technology have made dissecting cells on a large scale possible with unprecedented resolution. In the present research, we construct efficient classifiers and identify essential gene biomarkers based on single-cell RNA sequencing data through Boruta and three feature ranking algorithms (e.g., mRMR, MCFS, and SHAP by LightGBM) by utilizing four advanced classification algorithms. Meanwhile, we mine a series of classification rules that can distinguish different cell cycle phases. Collectively, we have provided a novel method for determining the cell cycle and identified new potential cell cycle-related genes, thereby contributing to the understanding of the processes that regulate the cell cycle.
Collapse
|
12
|
Fu Y, Lv Z, Kong D, Fan Y, Dong B. High abundance of CDC45 inhibits cell proliferation through elevation of HSPA6. Cell Prolif 2022; 55:e13257. [PMID: 35642733 PMCID: PMC9251052 DOI: 10.1111/cpr.13257] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 04/15/2022] [Accepted: 04/25/2022] [Indexed: 11/29/2022] Open
Abstract
OBJECTIVES CDC45 is the core component of CMG (CDC45-MCMs-GINS) complex that plays important role in the initial step of DNA replication in eukaryotic cells. The expression level of cdc45 is under the critical control for the accurate cell cycle progression. Loss-of-function of cdc45 has been demonstrated to inhibit cell proliferation and leads to cell death due to the inhibition of DNA replication and G1-phase arrest. An increasing of CDC45 inhibits cell proliferation as well. Nevertheless, a systematic analysis of the effect of high dose of CDC45 on cell physiology and behaviors is unclear. In the present study, we aimed to investigate the effects and mechanisms of high dose of CDC45 on cell behaviors. MATERIALS AND METHODS We overexpressed cdc45 in cultured cell lines, Ciona and Drosophila embryos, respectively. The cell cycle progression was examined by the BrdU incorporation experiment, flow cytometry and PH3 (phospho-Histone 3) staining. RNA-sequencing analysis and qRT-PCR were carried out to screen the affected genes in HeLa cells overexpressing cdc45. siRNA-mediated knockdown was performed to investigate gene functions in HeLa cells overexpressing cdc45. RESULTS We found that high level of cdc45 from different species (human, mammal, ascidian, and Drosophila) inhibited cell cycle in vitro and in vivo. High dose of CDC45 blocks cells entering into S phase. However, we failed to detect DNA damage and cell apoptosis. We identified hspa6 was the most upregulated gene in HeLa cells overexpressing cdc45 via RNA-seq analysis and qRT-PCR validation. Overexpression of Hs-hspa6 inhibited proliferation rate and DNA replication in HeLa cells, mimicking the phenotype of cdc45 overexpression. RNAi against hspa6 partially rescued the cell proliferation defect caused by high dose of CDC45. CONCLUSIONS Our study suggests that high abundance of CDC45 stops cell cycle. Instead of inducing apoptosis, excessive CDC45 prevents cell entering S phase probably due to promoting hspa6 expression.
Collapse
Affiliation(s)
- Yuanyuan Fu
- Sars‐Fang Centre, MoE Key Laboratory of Marine Genetics and BreedingCollege of Marine Life Sciences, Ocean University of ChinaQingdaoChina
| | - Zhiyi Lv
- Sars‐Fang Centre, MoE Key Laboratory of Marine Genetics and BreedingCollege of Marine Life Sciences, Ocean University of ChinaQingdaoChina
- Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
| | - Deqing Kong
- Department of BiologyPhilipps UniversityMarburgGermany
| | - Yuping Fan
- Sars‐Fang Centre, MoE Key Laboratory of Marine Genetics and BreedingCollege of Marine Life Sciences, Ocean University of ChinaQingdaoChina
| | - Bo Dong
- Sars‐Fang Centre, MoE Key Laboratory of Marine Genetics and BreedingCollege of Marine Life Sciences, Ocean University of ChinaQingdaoChina
- Institute of Evolution & Marine BiodiversityOcean University of ChinaQingdaoChina
- Laboratory for Marine Biology and BiotechnologyQingdao National Laboratory for Marine Science and TechnologyQingdaoChina
| |
Collapse
|
13
|
Wei C, Sun W, Liu C, Meng F, Sun L, Ding X. Hsa_circ_0062270 Promotes Tumorigenesis of Melanoma by Stabilizing the Linear Transcript Cell Division Cycle Protein 45. Front Genet 2022; 13:897440. [PMID: 35620458 PMCID: PMC9127359 DOI: 10.3389/fgene.2022.897440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/25/2022] [Indexed: 11/15/2022] Open
Abstract
Background: To elucidate the potential biological function of hsa_circ_0062270 in the malignant process of melanoma and its potential target. Methods: Quantitative real-time polymerase chain reaction (qRT-PCR) was conducted to examine relative level of hsa_circ_0062270 in melanoma tissues and normal skin tissues. The diagnostic and prognostic potentials of hsa_circ_0062270 in melanoma were evaluated. The regulatory effect of hsa_circ_0062270 on the expression of linear transcript Cell division cycle protein 45 (CDC45) was also examined. Results: Hsa_circ_0062270 was up-regulated in melanoma samples and cell lines, which displayed certain diagnostic and prognostic potentials in melanoma. Inhibition of hsa_circ_0062270 attenuated the proliferative, migratory and invasive functions. Hsa_circ_0062270 could stabilize the expression of linear transcript CDC45, and thus participated in the malignant process of melanoma. Conclusion: Hsa_circ_0062270 promotes proliferative, migratory and invasive functions of melanoma cells via stabilizing the linear transcript CDC45. Hsa_circ_0062270 can be used to diagnosis and treatment of melanoma.
Collapse
Affiliation(s)
- Cuie Wei
- Department of Plastic Surgery, The First People’s Hospital of Lianyungang, Lianyungang, China
| | - Wentao Sun
- Department of Plastic Surgery, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Changhai Liu
- Department of Plastic Surgery, The First People’s Hospital of Lianyungang, Lianyungang, China
| | - Fanjun Meng
- Department of Plastic Surgery, The First People’s Hospital of Lianyungang, Lianyungang, China
| | - Lele Sun
- Department of Plastic Surgery, The First People’s Hospital of Lianyungang, Lianyungang, China
| | - Xiangsheng Ding
- Department of Plastic Surgery, The First People’s Hospital of Lianyungang, Lianyungang, China
| |
Collapse
|
14
|
Pan Y, Yang Y, Huang R, Yang H, Huang Q, Ji Y, Dai J, Qiao K, Tang W, Xie L, Yin M, Ouyang J, Ning S, Su D. Ring finger protein 126 promotes breast cancer metastasis and serves as a potential target to improve the therapeutic sensitivity of ATR inhibitors. Breast Cancer Res 2022; 24:92. [PMID: 36539893 PMCID: PMC9764525 DOI: 10.1186/s13058-022-01586-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND/AIMS This study explores the relationship between the E3 ubiquitin ligase Ring finger protein 126 (RNF126) and early breast cancer metastasis and tests the hypothesis that RNF126 determines the efficacy of inhibitors targeting Ataxia telangiectasia mutated and Rad3-related kinase (ATR). METHODS Various metastasis-related genes were identified by univariable Cox proportional hazards regression analysis based on the GSE11121 dataset. The RNF126-related network modules were identified by WGCNA, whereas cell viability, invasion, and migration assays were performed to evaluate the biological characteristics of breast cancer cells with or without RNF126 knockdown. MTT, immunoblotting, immunofluorescence, and DNA fiber assays were conducted to determine the efficiency of ATR inhibitor in cells with or without RNF126 knockdown. RESULTS RNF126 was associated with early breast cancer metastasis. RNF126 promoted breast cancer cell proliferation, growth, migration, and invasion. ATR inhibitors were more effective at killing breast cancer cells with intact RNF126 due to replication stress compared with the corresponding cells with RNF126 knockdown. Cyclin-dependent kinase 2 (CDK2) was involved in regulating replication stress in breast cancer cells with intact RNF126. CONCLUSION A high level of expression of RNF126 in early breast cancer patients without lymph node metastases may indicate a high-risk type of metastatic disease, possibly due to RNF126, which may increase breast cancer cell proliferation and invasion. RNF126-expressing breast cancer cells exhibit CDK2-mediated replication stress that makes them potential targets for ATR inhibitors.
Collapse
Affiliation(s)
- You Pan
- grid.256607.00000 0004 1798 2653Department of Breast Surgery, Key Laboratory of Breast Cancer Diagnosis and Treatment Research of Guangxi Department of Education, Guangxi Medical University Cancer Hospital, Nanning, 530000 China
| | - Yuchao Yang
- grid.284723.80000 0000 8877 7471Guangdong Provincial Key Laboratory of Medical Biomechanics & Nation Key Discipline of Human Anatomy, School of Basic Medical Science, Southern Medical University, Guangzhou, 510515 China
| | - Rong Huang
- grid.256607.00000 0004 1798 2653Department of Breast Surgery, Key Laboratory of Breast Cancer Diagnosis and Treatment Research of Guangxi Department of Education, Guangxi Medical University Cancer Hospital, Nanning, 530000 China
| | - Huawei Yang
- grid.256607.00000 0004 1798 2653Department of Breast Surgery, Key Laboratory of Breast Cancer Diagnosis and Treatment Research of Guangxi Department of Education, Guangxi Medical University Cancer Hospital, Nanning, 530000 China
| | - Qinghua Huang
- grid.256607.00000 0004 1798 2653Department of Breast Surgery, Key Laboratory of Breast Cancer Diagnosis and Treatment Research of Guangxi Department of Education, Guangxi Medical University Cancer Hospital, Nanning, 530000 China
| | - Yinan Ji
- grid.256607.00000 0004 1798 2653Department of Breast Surgery, Key Laboratory of Breast Cancer Diagnosis and Treatment Research of Guangxi Department of Education, Guangxi Medical University Cancer Hospital, Nanning, 530000 China
| | - Jingxing Dai
- grid.284723.80000 0000 8877 7471Guangdong Provincial Key Laboratory of Medical Biomechanics & Nation Key Discipline of Human Anatomy, School of Basic Medical Science, Southern Medical University, Guangzhou, 510515 China
| | - Kun Qiao
- grid.412651.50000 0004 1808 3502Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, 150000 China
| | - Wei Tang
- grid.256607.00000 0004 1798 2653Department of Breast Surgery, Key Laboratory of Breast Cancer Diagnosis and Treatment Research of Guangxi Department of Education, Guangxi Medical University Cancer Hospital, Nanning, 530000 China
| | - Longgui Xie
- grid.256607.00000 0004 1798 2653Department of Breast Surgery, Key Laboratory of Breast Cancer Diagnosis and Treatment Research of Guangxi Department of Education, Guangxi Medical University Cancer Hospital, Nanning, 530000 China
| | - Ming Yin
- grid.284723.80000 0000 8877 7471Department of Imaging, Nanfang Hospital, Southern Medical University, Guangzhou, 510515 China
| | - Jun Ouyang
- grid.284723.80000 0000 8877 7471Guangdong Provincial Key Laboratory of Medical Biomechanics & Nation Key Discipline of Human Anatomy, School of Basic Medical Science, Southern Medical University, Guangzhou, 510515 China
| | - Shipeng Ning
- grid.256607.00000 0004 1798 2653Department of Breast Surgery, Key Laboratory of Breast Cancer Diagnosis and Treatment Research of Guangxi Department of Education, Guangxi Medical University Cancer Hospital, Nanning, 530000 China
| | - Danke Su
- grid.256607.00000 0004 1798 2653Department of Radiology, Guangxi Medical University Cancer Hospital, Nanning, 530000 China
| |
Collapse
|
15
|
Si N, Zhang Z, Huang X, Wang C, Guo P, Pan B, Jiang H. De novo 22q11.2 deletions and auricular findings in two Chinese patients with microtia. Mol Genet Genomic Med 2021; 10:e1862. [PMID: 34971493 PMCID: PMC8801138 DOI: 10.1002/mgg3.1862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 08/20/2021] [Accepted: 12/14/2021] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Congenital microtia is a common craniofacial malformation resulting from both environmental and genetic factors. Recurrent chromosomal imbalances were observed in patients with microtia. The 22q11.2 deletion is one of the most common microdeletions in human beings. The cell division cycle 45 gene (CDC45) embedded in the proximal 22q11.2 deleted region is involved in craniofacial development. However, only a few studies have focused on the 22q11.2 deletion as genetic etiology in microtia patients and studied its associated external ear deformity characteristics in detail. METHODS In this research, a total of 65 patients from north China with sporadic microtia were studied. Copy number variations of CDC45 were screened using AccuCopy assay. The 22q11.2 deletion harboring CDC45 was identified by whole-genome sequencing and targeted next-generation sequencing. A parental test was carried out to determine the origin of the deletion. RESULTS CDC45 copy number loss was identified in two patients with microtia. A set of qPCR assays demonstrated two patients carried a typical proximal 22q11.2 deletion between the low-copy repeats on chromosome 22q11.2 (LCR22A and LCR22D), encompassing CDC45. The 22q11.2 deletions were de novo in each patient. In-depth auricular phenotype assessment showed these two patients have a distinct concha-type ear malformation while other microtia patients have lobule-type microtia among the 65 microtia patient cohort in this study. CONCLUSION Here we present two additional Chinese microtia patients with de novo 22q11.2 proximal deletion harboring CDC45 and further report these patients' distinct ear malformation.
Collapse
Affiliation(s)
- Nuo Si
- Plastic Surgery Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing, China
| | - Zeya Zhang
- Plastic Surgery Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing, China
| | - Xin Huang
- Plastic Surgery Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing, China
| | - Chanchen Wang
- Plastic Surgery Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing, China
| | - Peipei Guo
- Plastic Surgery Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing, China
| | - Bo Pan
- Plastic Surgery Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing, China
| | - Haiyue Jiang
- Plastic Surgery Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing, China
| |
Collapse
|
16
|
Dual RNA-Seq Enables Full-Genome Assembly of Measles Virus and Characterization of Host-Pathogen Interactions. Microorganisms 2021; 9:microorganisms9071538. [PMID: 34361973 PMCID: PMC8303570 DOI: 10.3390/microorganisms9071538] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/12/2021] [Accepted: 07/14/2021] [Indexed: 11/24/2022] Open
Abstract
Measles virus (MeV) has a negative-sense 15 kb long RNA genome, which is generally conserved. Recent advances in high-throughput sequencing (HTS) and Dual RNA-seq allow the analysis of viral RNA genomes and the discovery of viral infection biomarkers, via the simultaneous characterization of the host transcriptome. However, these host–pathogen interactions remain largely unexplored in MeV infections. We performed untargeted Dual RNA-seq in 6 pharyngeal and 6 peripheral blood mononuclear cell (PBMCs) specimens from patients with MeV infection, as confirmed via routine real-time PCR testing. Following optimised DNase treatment of total nucleic acids, we used the pharyngeal samples to build poly-A-enriched NGS libraries. We reconstructed the viral genomes using the pharyngeal datasets and we further conducted differential expression, gene-ontology and pathways enrichment analysis to compare both the pharyngeal and the peripheral blood transcriptomes of the MeV-infected patients vs. control groups of healthy individuals. We obtained 6 MeV genotype-B3 full-genome sequences. We minutely analyzed the transcriptome of the MeV-infected pharyngeal epithelium, detecting all known viral infection biomarkers, but also revealing a functional cluster of local antiviral and inflammatory immune responses, which differ substantially from those observed in the PBMCs transcriptome. The application of Dual RNA-seq technologies in MeV-infected patients can potentially provide valuable information on the virus genome structure and the cellular innate immune responses and drive the discovery of new targets for antiviral therapy.
Collapse
|
17
|
Fan Y, Köberlin MS, Ratnayeke N, Liu C, Deshpande M, Gerhardt J, Meyer T. LRR1-mediated replisome disassembly promotes DNA replication by recycling replisome components. J Cell Biol 2021; 220:212186. [PMID: 34037657 PMCID: PMC8160578 DOI: 10.1083/jcb.202009147] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 03/30/2021] [Accepted: 05/04/2021] [Indexed: 11/22/2022] Open
Abstract
After two converging DNA replication forks meet, active replisomes are disassembled and unloaded from chromatin. A key process in replisome disassembly is the unloading of CMG helicases (CDC45–MCM–GINS), which is initiated in Caenorhabditis elegans and Xenopus laevis by the E3 ubiquitin ligase CRL2LRR1. Here, we show that human cells lacking LRR1 fail to unload CMG helicases and accumulate increasing amounts of chromatin-bound replisome components as cells progress through S phase. Markedly, we demonstrate that the failure to disassemble replisomes reduces the rate of DNA replication increasingly throughout S phase by sequestering rate-limiting replisome components on chromatin and blocking their recycling. Continued binding of CMG helicases to chromatin during G2 phase blocks mitosis by activating an ATR-mediated G2/M checkpoint. Finally, we provide evidence that LRR1 is an essential gene for human cell division, suggesting that CRL2LRR1 enzyme activity is required for the proliferation of cancer cells and is thus a potential target for cancer therapy.
Collapse
Affiliation(s)
- Yilin Fan
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA.,Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY
| | - Marielle S Köberlin
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA
| | - Nalin Ratnayeke
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA.,Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY
| | - Chad Liu
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA
| | - Madhura Deshpande
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY
| | - Jeannine Gerhardt
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY.,Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY
| | - Tobias Meyer
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA.,Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY
| |
Collapse
|
18
|
Branigan TB, Kozono D, Schade AE, Deraska P, Rivas HG, Sambel L, Reavis HD, Shapiro GI, D'Andrea AD, DeCaprio JA. MMB-FOXM1-driven premature mitosis is required for CHK1 inhibitor sensitivity. Cell Rep 2021; 34:108808. [PMID: 33657372 PMCID: PMC7970065 DOI: 10.1016/j.celrep.2021.108808] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 12/24/2020] [Accepted: 02/09/2021] [Indexed: 12/25/2022] Open
Abstract
To identify genes whose loss confers resistance to CHK1 inhibitors, we perform genome-wide CRISPR-Cas9 screens in non-small-cell lung cancer (NSCLC) cell lines treated with the CHK1 inhibitor prexasertib (CHK1i). Five of the top six hits of the screens, MYBL2 (B-MYB), LIN54, FOXM1, cyclin A2 (CCNA2), and CDC25B, are cell-cycle-regulated genes that contribute to entry into mitosis. Knockout of MMB-FOXM1 complex components LIN54 and FOXM1 reduce CHK1i-induced DNA replication stress markers and premature mitosis during Late S phase. Activation of a feedback loop between the MMB-FOXM1 complex and CDK1 is required for CHK1i-induced premature mitosis in Late S phase and subsequent replication catastrophe, indicating that dysregulation of the S to M transition is necessary for CHK1 inhibitor sensitivity. These findings provide mechanistic insights into small molecule inhibitors currently studied in clinical trials and provide rationale for combination therapies. Branigan et al., by using genome-wide CRISPR screens, identify the MMB-FOXM1 complex as being required for CHK1 inhibitor (CHK1i) sensitivity. Their study shows that CHK1i-induced premature activation of the G2/M transcriptional program by this complex triggers a breakdown in the separation of DNA synthesis and mitosis, leading to replication catastrophe.
Collapse
Affiliation(s)
- Timothy B Branigan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Program in Virology, Graduate School of Arts and Sciences, Harvard University, Cambridge, MA, USA
| | - David Kozono
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Amy E Schade
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Program in Virology, Graduate School of Arts and Sciences, Harvard University, Cambridge, MA, USA
| | - Peter Deraska
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Hembly G Rivas
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Program in Virology, Graduate School of Arts and Sciences, Harvard University, Cambridge, MA, USA
| | - Larissa Sambel
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Hunter D Reavis
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Geoffrey I Shapiro
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Alan D D'Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - James A DeCaprio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Program in Virology, Graduate School of Arts and Sciences, Harvard University, Cambridge, MA, USA; Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
19
|
Yang C, Xie S, Wu Y, Ru G, He X, Pan HY, Wang S, Tong X. Prognostic implications of cell division cycle protein 45 expression in hepatocellular carcinoma. PeerJ 2021; 9:e10824. [PMID: 33614286 PMCID: PMC7883691 DOI: 10.7717/peerj.10824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 01/03/2021] [Indexed: 12/24/2022] Open
Abstract
Background The overall prognosis of hepatocellular carcinoma (HCC) is poor and novel prognostic biomarkers might better monitor the progression of HCC. Cell division cycle protein 45 (CDC45) plays a key role in DNA replication and considered to be involved in tumorigenesis. This study investigated CDC45 expression in tumour tissues and defined its prognostic value in HCC patients. Methods We used immunohistochemistry (IHC) staining to examine the expression of CDC45 in tumour tissue specimens and compare them with adjacent normal tissue specimens using a constructed tissue microarray (TMA) and analyzed how clinical features are related to HCC prognosis. Functional enrichment analyses were used to describe significantly involved hallmark pathways of differentially expressed genes (DEGs, which were screened out according to the high or low expression of CDC45 in tumour tissues). Results Our findings showed that the proteome expression of CDC45 was evidently downregulated in HCC tissues compared with matched normal tissues (P < 0.0001). Although we did not find any differences in terms of vascular invasion, metastasis, lymphatic infiltration, or Edmondson grade between patients with high and low CDC45 expression, low CDC45 expression was significantly correlated with microvascular invasion (P = 0.046). Multivariate analysis indicated that CDC45 expression (P = 0.035) was an independent prognostic factor for the overall survival (OS) rate of HCC patients. Patients with CDC45 expression was positively correlated with OS rates among HCC patients (P < 0.05). Functional annotations indicated that CDC45 is involved in the most significant pathways, including the cell cycle, DNA replication, chemical carcinogenesis and drug metabolism–cytochrome P450 pathways. Discussion Our findings showed that low proteomic level of CDC45 was associated with a poor prognosis in HCC patients, indicating that CDC45 might be a novel prognostic marker.
Collapse
Affiliation(s)
- Chen Yang
- Department of Clinical Medicine, Qingdao University, Qingdao, China.,Molecular Diagnosis Laboratory, Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Shufang Xie
- Molecular Diagnosis Laboratory, Zhejiang Provincial People's Hospital, Hangzhou, China.,The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yi Wu
- Phase I Clinical Research Center, Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Guoqing Ru
- Department of Pathology, Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Xianglei He
- Department of Pathology, Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Hong-Yin Pan
- Department of Infectious Diseases, Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Shibing Wang
- Molecular Diagnosis Laboratory, Zhejiang Provincial People's Hospital, Hangzhou, China.,The Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital, Hangzhou, China
| | - Xiangmin Tong
- Molecular Diagnosis Laboratory, Zhejiang Provincial People's Hospital, Hangzhou, China.,The Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital, Hangzhou, China
| |
Collapse
|
20
|
Bostanabad SY, Noyan S, Dedeoglu BG, Gurdal H. Overexpression of β-Arrestins inhibits proliferation and motility in triple negative breast cancer cells. Sci Rep 2021; 11:1539. [PMID: 33452359 PMCID: PMC7810837 DOI: 10.1038/s41598-021-80974-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 12/31/2020] [Indexed: 01/29/2023] Open
Abstract
β-Arrestins (βArrs) are intracellular signal regulating proteins. Their expression level varies in some cancers and they have a significant impact on cancer cell function. In general, the significance of βArrs in cancer research comes from studies examining GPCR signalling. Given the diversity of different GPCR signals in cancer cell regulation, contradictory results are inevitable regarding the role of βArrs. Our approach examines the direct influence of βArrs on cellular function and gene expression profiles by changing their expression levels in breast cancer cells, MDA-MB-231 and MDA-MB-468. Reducing expression of βArr1 or βArr2 tended to increase cell proliferation and invasion whereas increasing their expression levels inhibited them. The overexpression of βArrs caused cell cycle S-phase arrest and differential expression of cell cycle genes, CDC45, BUB1, CCNB1, CCNB2, CDKN2C and reduced HER3, IGF-1R, and Snail. Regarding to the clinical relevance of our results, low expression levels of βArr1 were inversely correlated with CDC45, BUB1, CCNB1, and CCNB2 genes compared to normal tissue samples while positively correlated with poorer prognosis in breast tumours. These results indicate that βArr1 and βArr2 are significantly involved in cell cycle and anticancer signalling pathways through their influence on cell cycle genes and HER3, IGF-1R, and Snail in TNBC cells.
Collapse
Affiliation(s)
| | - Senem Noyan
- Biotechnology Institute of Ankara University, 06135, Ankara, Turkey
| | | | - Hakan Gurdal
- Department of Medical Pharmacology, Faculty of Medicine, University of Ankara, 06230, Ankara, Turkey.
| |
Collapse
|
21
|
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: 54] [Impact Index Per Article: 13.5] [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.
Collapse
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.
| |
Collapse
|
22
|
Qiu Z, Fa P, Liu T, Prasad CB, Ma S, Hong Z, Chan ER, Wang H, Li Z, He K, Wang QE, Williams TM, Yan C, Sizemore ST, Narla G, Zhang J. A Genome-Wide Pooled shRNA Screen Identifies PPP2R2A as a Predictive Biomarker for the Response to ATR and CHK1 Inhibitors. Cancer Res 2020; 80:3305-3318. [PMID: 32522823 PMCID: PMC7518641 DOI: 10.1158/0008-5472.can-20-0057] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 04/17/2020] [Accepted: 06/04/2020] [Indexed: 01/18/2023]
Abstract
There is currently a lack of precise predictive biomarkers for patient selection in clinical trials of inhibitors targeting replication stress (RS) response proteins ATR and CHK1. The objective of this study was to identify novel predictive biomarkers for the response to these agents in treating non-small cell lung cancer (NSCLC). A genome-wide loss-of-function screen revealed that tumor suppressor PPP2R2A, a B regulatory subunit of protein phosphatase 2 (PP2A), determines sensitivity to CHK1 inhibition. A synthetic lethal interaction between PPP2R2A deficiency and ATR or CHK1 inhibition was observed in NSCLC in vitro and in vivo and was independent of p53 status. ATR and CHK1 inhibition resulted in significantly increased levels of RS and altered replication dynamics, particularly in PPP2R2A-deficient NSCLC cells. Mechanistically, PPP2R2A negatively regulated translation of oncogene c-Myc protein. c-Myc activity was required for PPP2R2A deficiency-induced alterations of replication initiation/RS and sensitivity to ATR/CHK1 inhibitors. We conclude that PPP2R2A deficiency elevates RS by upregulating c-Myc activity, rendering cells reliant on the ATR/CHK1 axis for survival. Our studies show a novel synthetic lethal interaction and identify PPP2R2A as a potential new predictive biomarker for patient stratification in the clinical use of ATR and CHK1 inhibitors. SIGNIFICANCE: This study reveals new approaches to specifically target PPP2R2A-deficient lung cancer cells and provides a novel biomarker that will significantly improve treatment outcome with ATR and CHK1 inhibitors.
Collapse
MESH Headings
- Animals
- Ataxia Telangiectasia Mutated Proteins/antagonists & inhibitors
- Biomarkers, Tumor/deficiency
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Carcinoma, Non-Small-Cell Lung/chemistry
- Carcinoma, Non-Small-Cell Lung/drug therapy
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/metabolism
- Cell Line, Tumor
- Checkpoint Kinase 1/antagonists & inhibitors
- DNA Damage
- DNA Replication
- Drug Resistance, Neoplasm
- Female
- Gene Knockdown Techniques
- Genes, p53
- Genome-Wide Association Study
- Heterografts
- Humans
- Lung Neoplasms/chemistry
- Lung Neoplasms/drug therapy
- Lung Neoplasms/genetics
- Lung Neoplasms/metabolism
- Male
- Mice
- Mice, Nude
- Protein Phosphatase 2/deficiency
- Protein Phosphatase 2/genetics
- Protein Phosphatase 2/metabolism
- Proto-Oncogene Proteins c-myc/metabolism
- RNA, Small Interfering
Collapse
Affiliation(s)
- Zhaojun Qiu
- Department of Radiation Oncology, The Ohio State University James Comprehensive Cancer Center and College of Medicine, Ohio
| | - Pengyan Fa
- Department of Radiation Oncology, The Ohio State University James Comprehensive Cancer Center and College of Medicine, Ohio
| | - Tao Liu
- Department of Radiation Oncology, The Ohio State University James Comprehensive Cancer Center and College of Medicine, Ohio
| | - Chandra B Prasad
- Department of Radiation Oncology, The Ohio State University James Comprehensive Cancer Center and College of Medicine, Ohio
| | - Shanhuai Ma
- University of Rochester, Rochester, New York
| | - Zhipeng Hong
- Department of Radiation Oncology, The Ohio State University James Comprehensive Cancer Center and College of Medicine, Ohio
| | - Ernest R Chan
- Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio
| | - Hongbing Wang
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland
| | - Zaibo Li
- Department of Pathology, The Ohio State University James Comprehensive Cancer Center and College of Medicine, Ohio
| | - Kai He
- Department of Internal Medicine, The Ohio State University James Comprehensive Cancer Center and College of Medicine, Ohio
| | - Qi-En Wang
- Department of Radiation Oncology, The Ohio State University James Comprehensive Cancer Center and College of Medicine, Ohio
| | - Terence M Williams
- Department of Radiation Oncology, The Ohio State University James Comprehensive Cancer Center and College of Medicine, Ohio
| | - Chunhong Yan
- Georgia Cancer Center, Augusta University, Augusta, Georgia
| | - Steven T Sizemore
- Department of Radiation Oncology, The Ohio State University James Comprehensive Cancer Center and College of Medicine, Ohio
| | - Goutham Narla
- Department of Medicine, University of Michigan, Ann Arbor, Michigan
| | - Junran Zhang
- Department of Radiation Oncology, The Ohio State University James Comprehensive Cancer Center and College of Medicine, Ohio.
| |
Collapse
|
23
|
Pennycook BR, Vesela E, Peripolli S, Singh T, Barr AR, Bertoli C, de Bruin RAM. E2F-dependent transcription determines replication capacity and S phase length. Nat Commun 2020; 11:3503. [PMID: 32665547 PMCID: PMC7360579 DOI: 10.1038/s41467-020-17146-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 06/04/2020] [Indexed: 01/06/2023] Open
Abstract
DNA replication timing is tightly regulated during S-phase. S-phase length is determined by DNA synthesis rate, which depends on the number of active replication forks and their velocity. Here, we show that E2F-dependent transcription, through E2F6, determines the replication capacity of a cell, defined as the maximal amount of DNA a cell can synthesise per unit time during S-phase. Increasing or decreasing E2F-dependent transcription during S-phase increases or decreases replication capacity, and thereby replication rates, thus shortening or lengthening S-phase, respectively. The changes in replication rate occur mainly through changes in fork speed without affecting the number of active forks. An increase in fork speed does not induce replication stress directly, but increases DNA damage over time causing cell cycle arrest. Thus, E2F-dependent transcription determines the DNA replication capacity of a cell, which affects the replication rate, controlling the time it takes to duplicate the genome and complete S-phase.
Collapse
Affiliation(s)
- Betheney R Pennycook
- MRC Laboratory for Molecular Cell Biology, University College London, Gower street, London, WC1E 6BT, UK
- MRC London Institute of Medical Science Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Eva Vesela
- MRC Laboratory for Molecular Cell Biology, University College London, Gower street, London, WC1E 6BT, UK
| | - Silvia Peripolli
- MRC Laboratory for Molecular Cell Biology, University College London, Gower street, London, WC1E 6BT, UK
| | - Tanya Singh
- MRC Laboratory for Molecular Cell Biology, University College London, Gower street, London, WC1E 6BT, UK
| | - Alexis R Barr
- MRC London Institute of Medical Science Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
- Institute of Clinical Sciences, Imperial College London, London, W12 0NN, UK
| | - Cosetta Bertoli
- MRC Laboratory for Molecular Cell Biology, University College London, Gower street, London, WC1E 6BT, UK.
| | - Robertus A M de Bruin
- MRC Laboratory for Molecular Cell Biology, University College London, Gower street, London, WC1E 6BT, UK.
- UCL Cancer Institute, University College London, London, WC1E 6BT, UK.
| |
Collapse
|
24
|
A live-cell super-resolution technique demonstrated by imaging germinosomes in wild-type bacterial spores. Sci Rep 2020; 10:5312. [PMID: 32210351 PMCID: PMC7093444 DOI: 10.1038/s41598-020-62377-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 03/12/2020] [Indexed: 01/10/2023] Open
Abstract
Time-lapse fluorescence imaging of live cells at super-resolution remains a challenge, especially when the photon budget is limited. Current super-resolution techniques require either the use of special exogenous probes, high illumination doses or multiple image acquisitions with post-processing or combinations of the aforementioned. Here, we describe a new approach by combining annular illumination with rescan confocal microscopy. This optics-only technique generates images in a single scan, thereby avoiding any potential risks of reconstruction related artifacts. The lateral resolution is comparable to that of linear structured illumination microscopy and the axial resolution is similar to that of a standard confocal microscope. As a case study, we present super-resolution time-lapse imaging of wild-type Bacillus subtilis spores, which contain low numbers of germination receptor proteins in a focus (a germinosome) surrounded by an autofluorescent coat layer. Here, we give the first evidence for the existence of germinosomes in wild-type spores, show their spatio-temporal dynamics upon germinant addition and visualize spores coming to life.
Collapse
|
25
|
Warren NJH, Eastman A. Comparison of the different mechanisms of cytotoxicity induced by checkpoint kinase I inhibitors when used as single agents or in combination with DNA damage. Oncogene 2020; 39:1389-1401. [PMID: 31659257 PMCID: PMC7023985 DOI: 10.1038/s41388-019-1079-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 10/14/2019] [Accepted: 10/15/2019] [Indexed: 12/31/2022]
Abstract
Inhibition of the DNA damage response is an emerging strategy to treat cancer. Understanding how DNA damage response inhibitors cause cytotoxicity in cancer cells is crucial to their further clinical development. This review focuses on three different mechanisms of cell killing by checkpoint kinase I inhibitors (CHK1i). DNA damage induced by chemotherapy drugs, such as topoisomerase I inhibitors, results in S and G2 phase arrest. Addition of CHK1i promotes cell cycle progression before repair is completed resulting in mitotic catastrophe. Ribonucleotide reductase inhibitors such as gemcitabine also arrest cells in S phase by preventing dNTP synthesis. Addition of CHK1i re-activates the DNA helicase to unwind DNA, but in the absence of dNTPs, this leads to excessive single-strand DNA that exceeds the protective capacity of the single-strand-binding protein RPA. Unprotected DNA is subjected to nuclease cleavage, resulting in replication catastrophe. CHK1i alone also kills a subset of cell lines through MRE11 and MUS81-mediated DNA cleavage in S phase cells. The choice of mechanism depends on the activation state of CDK2. Low level activation of CDK2 mediates helicase activation, cell cycle progression, and both replication and mitotic catastrophe. In contrast, high CDK2 activity is required for sensitivity to CHK1i as monotherapy. This high CDK2 activity threshold usually occurs late in the cell cycle to prepare for mitosis, but in CHK1i-sensitive cells, high activity can be attained in early S phase, resulting in DNA cleavage and cell death. This sensitivity to CHK1i has previously been associated with endogenous replication stress, but the dependence on high CDK2 activity, as well as MRE11, contradicts this hypothesis. The major unresolved question is why some cell lines fail to restrain their high CDK2 activity and hence succumb to CHK1i in S phase. Resolving this question will facilitate stratification of patients for treatment with CHK1i as monotherapy.
Collapse
Affiliation(s)
- Nicholas J H Warren
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, 03756, USA
| | - Alan Eastman
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, 03756, USA.
- Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, 03756, USA.
| |
Collapse
|
26
|
Ruszkowska M, Sadowska A, Nynca A, Orlowska K, Swigonska S, Molcan T, Paukszto L, Jastrzebski JP, Ciereszko RE. The effects of 2,3,7,8-tetrachlorodibenzo- p-dioxin (TCDD) on the transcriptome of aryl hydrocarbon receptor (AhR) knock-down porcine granulosa cells. PeerJ 2020; 8:e8371. [PMID: 32002328 PMCID: PMC6982409 DOI: 10.7717/peerj.8371] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 12/09/2019] [Indexed: 12/18/2022] Open
Abstract
Background 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is a toxic man-made chemical, adversely affecting reproductive processes. The well-characterized canonical mechanism of TCDD action involves the activation of aryl hydrocarbon receptor (AhR) pathway, but AhR-independent mechanisms were also suggested. By applying RNA interference technology and Next Generation Sequencing (NGS) we aimed to identify genes involved in the mechanism of TCDD action in AhR knock-down porcine granulosa cells. Methods Porcine granulosa cells were transfected with small interfering RNAs targeting mRNA of AhR. After transfection, medium was exchanged and the AhR knock-down cells were treated with TCDD (100 nM) for 3, 12 or 24 h, total cellular RNA was isolated and designated for NGS. Following sequencing, differentially expressed genes (DEGs) were identified. To analyze functions and establish possible interactions of DEGs, the Gene Ontology (GO) database and the Search Tool for the Retrieval of Interacting Genes (STRING) database were used, respectively. Results The AhR gene expression level and protein abundance were significantly decreased after AhR-targeted siRNAs transfection of the cells. In TCDD-treated AhR knock-down cells we identified 360 differentially expressed genes (DEGs; P-adjusted < 0.05 and log2 fold change [log2FC] ≥ 1.0). The functional enrichment analysis of DEGs revealed that TCDD influenced the expression of genes involved, among other, in the metabolism of vitamin A, follicular development and oocyte maturation, proliferation and differentiation as well as inflammation, stress response, apoptosis and oncogenesis. The three-time point study demonstrated that TCDD-induced changes in the transcriptome of AhR knock-down porcine granulosa cells were especially pronounced during the early stages of the treatment (3 h). Conclusions TCDD affected the transcriptome of AhR knock-down porcine granulosa cells. The molecules involved in the AhR-independent action of TCDD were indicated in the study. The obtained data contribute to better understanding of molecular processes induced by xenobiotics in the ovary.
Collapse
Affiliation(s)
- Monika Ruszkowska
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Agnieszka Sadowska
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Anna Nynca
- Laboratory of Molecular Diagnostics, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Karina Orlowska
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Sylwia Swigonska
- Laboratory of Molecular Diagnostics, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Tomasz Molcan
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Lukasz Paukszto
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Jan P Jastrzebski
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Renata E Ciereszko
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland.,Laboratory of Molecular Diagnostics, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| |
Collapse
|
27
|
da Silva MS, Cayres-Silva GR, Vitarelli MO, Marin PA, Hiraiwa PM, Araújo CB, Scholl BB, Ávila AR, McCulloch R, Reis MS, Elias MC. Transcription activity contributes to the firing of non-constitutive origins in African trypanosomes helping to maintain robustness in S-phase duration. Sci Rep 2019; 9:18512. [PMID: 31811174 PMCID: PMC6898680 DOI: 10.1038/s41598-019-54366-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 11/04/2019] [Indexed: 12/31/2022] Open
Abstract
The co-synthesis of DNA and RNA potentially generates conflicts between replication and transcription, which can lead to genomic instability. In trypanosomatids, eukaryotic parasites that perform polycistronic transcription, this phenomenon and its consequences are still little studied. Here, we showed that the number of constitutive origins mapped in the Trypanosoma brucei genome is less than the minimum required to complete replication within S-phase duration. By the development of a mechanistic model of DNA replication considering replication-transcription conflicts and using immunofluorescence assays and DNA combing approaches, we demonstrated that the activation of non-constitutive (backup) origins are indispensable for replication to be completed within S-phase period. Together, our findings suggest that transcription activity during S phase generates R-loops, which contributes to the emergence of DNA lesions, leading to the firing of backup origins that help maintain robustness in S-phase duration. The usage of this increased pool of origins, contributing to the maintenance of DNA replication, seems to be of paramount importance for the survival of this parasite that affects million people around the world.
Collapse
Affiliation(s)
- Marcelo S da Silva
- Laboratório Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Gustavo R Cayres-Silva
- Laboratório Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Marcela O Vitarelli
- Laboratório Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Paula A Marin
- Laboratório Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Priscila M Hiraiwa
- Plataforma de citometria de fluxo, Instituto Carlos Chagas, FIOCRUZ, Paraná, Brazil
| | - Christiane B Araújo
- Laboratório Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Bruno B Scholl
- Laboratório Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil
| | - Andrea R Ávila
- Laboratório de Regulação da Expressão Gênica, Instituto Carlos Chagas, FIOCRUZ, Paraná, Brazil
| | - Richard McCulloch
- The Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Marcelo S Reis
- Laboratório Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil.
| | - Maria Carolina Elias
- Laboratório Especial de Ciclo Celular, Center of Toxins, Immune Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil.
| |
Collapse
|
28
|
Yao R, Chen X, Wang L, Wang Y, Chi S, Li N, Tian X, Li N, Liu J. Identification of key protein-coding genes in lung adenocarcinomas based on bioinformatic analysis. Transl Cancer Res 2019; 8:2829-2840. [PMID: 35117040 PMCID: PMC8799172 DOI: 10.21037/tcr.2019.10.45] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 10/11/2019] [Indexed: 11/06/2022]
Abstract
Background Lung cancer is one of the most common cancers and the primary cause of cancer-related deaths in the world. The 5-year survival of lung cancer patients is lower than 15%. As a common subtype of lung cancer, lung adenocarcinoma still has a high morbidity and mortality, although many strategies have been made, such as surgical operation, chemotherapy, targeted therapy. The use of gene expression microarray has provided a feasible and effective approach for the study on lung cancer. However, the biomarkers and potential therapeutic targets of lung adenocarcinomas are still not completely identified. Our study is aimed to find biomarkers and therapeutic targets of lung adenocarcinomas by identifying the key protein-coding gene in lung adenocarcinomas by bioinformatical approaches. Methods We selected and obtained messenger RNA microarray datasets from Gene Expression Omnibus database to identify differentially expressed genes between lung adenocarcinomas and normal lung tissue. The differentially expressed genes were clarified by Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, the protein-protein interaction (PPI) network and statistical analyses. Subsequently, quantitative real-time PCR was used to verify the results of bioinformatic analysis. Results We obtained 1,264, 896 and 408 differentially expressed genes from GSE32863, GSE43458 and GSE63459, respectively. The 242 common differentially expressed genes in three datasets were related to cell adhesion molecules, ECM-receptor interaction, leukocyte transendothelial migration according to KEGG analysis. GO analysis showed that these common differentially expressed genes were enriched in tumor-related functions. ASPM, CCNB2, CDC20, CDC45, MELK, TOP2A and UBE2T and KIAA0101 have the strongest protein-protein interaction relationships based on protein-protein interaction networks. Survival analysis showed that these nine genes were closely related to the survival of lung adenocarcinomas. The further qRT-PCR assays indicated that seven key genes (ASPM, CCNB2, CDC20, CDC45, MELK, TOP2A and UBE2T) display differential profile between clinical lung adenocarcinoma specimens and their matched normal tissues. Conclusions ASPM, CCNB2, CDC20, CDC45, MELK, TOP2A and UBE2T may be key protein coding genes in lung adenocarcinoma, and deserve further study to verify their feasibility and effectiveness as biomarkers and therapeutic targets for lung adenocarcinomas.
Collapse
Affiliation(s)
- Ruixue Yao
- Department of Pharmacology, School of Pharmacy, Qingdao University, Qingdao 266000, China
| | - Xiaoming Chen
- The Third Department of Cadre's Ward, Navy 971 Hospital, Qingdao 266071, China
| | - Luyao Wang
- Department of Pharmacology, School of Pharmacy, Qingdao University, Qingdao 266000, China
| | - Yuanyong Wang
- Department of Thoracic Surgery, Affiliated Hospital of Qingdao University, Qingdao 266000, China
| | - Shaoli Chi
- The Third Department of Cadre's Ward, Navy 971 Hospital, Qingdao 266071, China
| | - Na Li
- The Department of Nuclear Medicine, Navy 971 Hospital, Qingdao 266071, China
| | - Xuejun Tian
- Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, Institute of Materia Medica, Zhejiang Academy of Medical Sciences, Hangzhou 310013, China
| | - Nan Li
- The Third Department of Cadre's Ward, Navy 971 Hospital, Qingdao 266071, China
| | - Jia Liu
- Department of Pharmacology, School of Pharmacy, Qingdao University, Qingdao 266000, China
| |
Collapse
|
29
|
Liu B, Großhans J. The role of dNTP metabolites in control of the embryonic cell cycle. Cell Cycle 2019; 18:2817-2827. [PMID: 31544596 PMCID: PMC6791698 DOI: 10.1080/15384101.2019.1665948] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 09/03/2019] [Accepted: 09/06/2019] [Indexed: 01/06/2023] Open
Abstract
Deoxyribonucleotide metabolites (dNTPs) are the substrates for DNA synthesis. It has been proposed that their availability influences the progression of the cell cycle during development and pathological situations such as tumor growth. The mechanism has remained unclear for the link between cell cycle and dNTP levels beyond their role as substrates. Here, we review recent studies concerned with the dynamics of dNTP levels in early embryos and the role of DNA replication checkpoint as a sensor of dNTP levels.
Collapse
Affiliation(s)
- Boyang Liu
- Institut für Entwicklungsbiochemie, Universitätsmedizin, Georg-August-Universität, Göttingen, Germany
| | - Jörg Großhans
- Institut für Entwicklungsbiochemie, Universitätsmedizin, Georg-August-Universität, Göttingen, Germany
- Entwicklungsgenetik, Fachbereich Biologie, Philipps-Universität, Marburg, Germany
| |
Collapse
|
30
|
Lynch KL, Alvino GM, Kwan EX, Brewer BJ, Raghuraman MK. The effects of manipulating levels of replication initiation factors on origin firing efficiency in yeast. PLoS Genet 2019; 15:e1008430. [PMID: 31584938 PMCID: PMC6795477 DOI: 10.1371/journal.pgen.1008430] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 10/16/2019] [Accepted: 09/17/2019] [Indexed: 12/22/2022] Open
Abstract
Chromosome replication in Saccharomyces cerevisiae is initiated from ~300 origins that are regulated by DNA sequence and by the limited abundance of six trans-acting initiation proteins (Sld2, Sld3, Dpb11, Dbf4, Sld7 and Cdc45). We set out to determine how the levels of individual factors contribute to time of origin activation and/or origin efficiency using induced depletion of single factors and overexpression of sets of multiple factors. Depletion of Sld2 or Sld3 slows growth and S phase progression, decreases origin efficiency across the genome and impairs viability as a result of incomplete replication of the rDNA. We find that the most efficient early origins are relatively unaffected by depletion of either Sld2 or Sld3. However, Sld3 levels, and to a lesser extent Sld2 levels, are critical for firing of the less efficient early origins. Overexpression of Sld3 simultaneously with Sld2, Dpb11 and Dbf4 preserves the relative efficiency of origins. Only when Cdc45 and Sld7 are also overexpressed is origin efficiency equalized between early- and late-firing origins. Our data support a model in which Sld3 together with Cdc45 (and/or Sld7) is responsible for the differential efficiencies of origins across the yeast genome. Eukaryotic chromosome duplication begins at sites called origins of replication along the chromosomal DNA. A conserved property of eukaryotic origins is that they vary in efficiency—the proportion of cells in a population in which they “fire”—and in the average time of activation within S phase, but the molecular details underlying this variation are not well understood. Previous work has shown that limiting concentrations of a set of conserved replication initiation proteins referred to as “SSDDCS” (Sld2, Sld3, Dbf4, Dpb11, Cdc45, and Sld7) are rate limiting for origin activation in budding yeast and other eukaryotes; combined overexpression of these proteins increases and/or advances origin firing. However, it remained possible that different factors affect different aspects of origin activation (e.g., timing vs. efficiency). Here, by depleting individual factors or by overexpressing sets of factors in budding yeast, we demonstrate that it is levels of Sld3, Cdc45 and/or Sld7 levels are primarily responsible for modulating the differences in relative origin efficiency and timing. This work gives further insights into what shapes the landscape of genome duplication.
Collapse
Affiliation(s)
- Kelsey L. Lynch
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Gina M. Alvino
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Elizabeth X. Kwan
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Bonita J. Brewer
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - M. K. Raghuraman
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- * E-mail:
| |
Collapse
|
31
|
Shin G, Jeong D, Kim H, Im JS, Lee JK. RecQL4 tethering on the pre-replicative complex induces unscheduled origin activation and replication stress in human cells. J Biol Chem 2019; 294:16255-16265. [PMID: 31519754 DOI: 10.1074/jbc.ra119.009996] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 09/09/2019] [Indexed: 12/15/2022] Open
Abstract
Sequential activation of DNA replication origins is precisely programmed and critical to maintaining genome stability. RecQL4, a member of the conserved RecQ family of helicases, plays an essential role in the initiation of DNA replication in mammalian cells. Here, we showed that RecQL4 protein tethered on the pre-replicative complex (pre-RC) induces early activation of late replicating origins during S phase. Tethering of RecQL4 or its N terminus on pre-RCs via fusion with Orc4 protein resulted in the recruitment of essential initiation factors, such as Mcm10, And-1, Cdc45, and GINS, increasing nascent DNA synthesis in late replicating origins during early S phase. In this origin activation process, tethered RecQL4 was able to recruit Cdc45 even in the absence of cyclin-dependent kinase (CDK) activity, whereas CDK phosphorylation of RecQL4 N terminus was required for interaction with and origin recruitment of And-1 and GINS. In addition, forced activation of replication origins by RecQL4 tethering resulted in increased replication stress and the accumulation of ssDNAs, which can be recovered by transcription inhibition. Collectively, these results suggest that recruitment of RecQL4 to replication origins is an important step for temporal activation of replication origins during S phase. Further, perturbation of replication timing control by unscheduled origin activation significantly induces replication stress, which is mostly caused by transcription-replication conflicts.
Collapse
Affiliation(s)
- Gwangsu Shin
- Interdisciplinary Graduate Program in Genetic Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dongsoo Jeong
- Interdisciplinary Graduate Program in Genetic Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyunsup Kim
- Interdisciplinary Graduate Program in Genetic Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jun-Sub Im
- Department of Biology Education, Seoul National University, Seoul, 08826, Republic of Korea
| | - Joon-Kyu Lee
- Interdisciplinary Graduate Program in Genetic Engineering, Seoul National University, Seoul, 08826, Republic of Korea .,Department of Biology Education, Seoul National University, Seoul, 08826, Republic of Korea
| |
Collapse
|
32
|
Sugimoto N, Maehara K, Yoshida K, Ohkawa Y, Fujita M. Genome-wide analysis of the spatiotemporal regulation of firing and dormant replication origins in human cells. Nucleic Acids Res 2019; 46:6683-6696. [PMID: 29893900 PMCID: PMC6061783 DOI: 10.1093/nar/gky476] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 05/16/2018] [Indexed: 12/25/2022] Open
Abstract
In metazoan cells, only a limited number of mini chromosome maintenance (MCM) complexes are fired during S phase, while the majority remain dormant. Several methods have been used to map replication origins, but such methods cannot identify dormant origins. Herein, we determined MCM7-binding sites in human cells using ChIP-Seq, classified them into firing and dormant origins using origin data and analysed their association with various chromatin signatures. Firing origins, but not dormant origins, were well correlated with open chromatin regions and were enriched upstream of transcription start sites (TSSs) of transcribed genes. Aggregation plots of MCM7 signals revealed minimal difference in the efficacy of MCM loading between firing and dormant origins. We also analysed common fragile sites (CFSs) and found a low density of origins at these sites. Nevertheless, firing origins were enriched upstream of the TSSs. Based on the results, we propose a model in which excessive MCMs are actively loaded in a genome-wide manner, irrespective of chromatin status, but only a fraction are passively fired in chromatin areas with an accessible open structure, such as regions upstream of TSSs of transcribed genes. This plasticity in the specification of replication origins may minimize collisions between replication and transcription.
Collapse
Affiliation(s)
- Nozomi Sugimoto
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashiku, Fukuoka 812-8582, Japan
| | - Kazumitsu Maehara
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashiku, Fukuoka 812-8582, Japan
| | - Kazumasa Yoshida
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashiku, Fukuoka 812-8582, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashiku, Fukuoka 812-8582, Japan
| | - Masatoshi Fujita
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashiku, Fukuoka 812-8582, Japan
| |
Collapse
|
33
|
González Besteiro MA, Calzetta NL, Loureiro SM, Habif M, Bétous R, Pillaire MJ, Maffia A, Sabbioneda S, Hoffmann JS, Gottifredi V. Chk1 loss creates replication barriers that compromise cell survival independently of excess origin firing. EMBO J 2019; 38:e101284. [PMID: 31294866 DOI: 10.15252/embj.2018101284] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 06/11/2019] [Accepted: 06/19/2019] [Indexed: 01/18/2023] Open
Abstract
The effectiveness of checkpoint kinase 1 (Chk1) inhibitors at killing cancer cells is considered to be fully dependent on their effect on DNA replication initiation. Chk1 inhibition boosts origin firing, presumably limiting the availability of nucleotides and in turn provoking the slowdown and subsequent collapse of forks, thus decreasing cell viability. Here we show that slow fork progression in Chk1-inhibited cells is not an indirect effect of excess new origin firing. Instead, fork slowdown results from the accumulation of replication barriers, whose bypass is impeded by CDK-dependent phosphorylation of the specialized DNA polymerase eta (Polη). Also in contrast to the linear model, the accumulation of DNA damage in Chk1-deficient cells depends on origin density but is largely independent of fork speed. Notwithstanding this, origin dysregulation contributes only mildly to the poor proliferation rates of Chk1-depleted cells. Moreover, elimination of replication barriers by downregulation of helicase components, but not their bypass by Polη, improves cell survival. Our results thus shed light on the molecular basis of the sensitivity of tumors to Chk1 inhibition.
Collapse
Affiliation(s)
- Marina A González Besteiro
- Fundación Instituto Leloir - Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Nicolás L Calzetta
- Fundación Instituto Leloir - Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Sofía M Loureiro
- Fundación Instituto Leloir - Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Martín Habif
- Fundación Instituto Leloir - Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Rémy Bétous
- Equipe «Labellisée LA LIGUE CONTRE LE CANCER», Laboratoire d'Excellence Toulouse Cancer LABEX TOUCAN - Cancer Research Center of Toulouse, Inserm U1037, CNRS ERL5294, University Paul Sabatier, Toulouse, France
| | - Marie-Jeanne Pillaire
- Equipe «Labellisée LA LIGUE CONTRE LE CANCER», Laboratoire d'Excellence Toulouse Cancer LABEX TOUCAN - Cancer Research Center of Toulouse, Inserm U1037, CNRS ERL5294, University Paul Sabatier, Toulouse, France
| | - Antonio Maffia
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza" - CNR, Pavia, Italy
| | - Simone Sabbioneda
- Istituto di Genetica Molecolare "Luigi Luca Cavalli-Sforza" - CNR, Pavia, Italy
| | - Jean-Sébastien Hoffmann
- Equipe «Labellisée LA LIGUE CONTRE LE CANCER», Laboratoire d'Excellence Toulouse Cancer LABEX TOUCAN - Cancer Research Center of Toulouse, Inserm U1037, CNRS ERL5294, University Paul Sabatier, Toulouse, France
| | - Vanesa Gottifredi
- Fundación Instituto Leloir - Instituto de Investigaciones Bioquímicas de Buenos Aires, Consejo de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| |
Collapse
|
34
|
Motahari Z, Moody SA, Maynard TM, LaMantia AS. In the line-up: deleted genes associated with DiGeorge/22q11.2 deletion syndrome: are they all suspects? J Neurodev Disord 2019; 11:7. [PMID: 31174463 PMCID: PMC6554986 DOI: 10.1186/s11689-019-9267-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 04/21/2019] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND 22q11.2 deletion syndrome (22q11DS), a copy number variation (CNV) disorder, occurs in approximately 1:4000 live births due to a heterozygous microdeletion at position 11.2 (proximal) on the q arm of human chromosome 22 (hChr22) (McDonald-McGinn and Sullivan, Medicine 90:1-18, 2011). This disorder was known as DiGeorge syndrome, Velo-cardio-facial syndrome (VCFS) or conotruncal anomaly face syndrome (CTAF) based upon diagnostic cardiovascular, pharyngeal, and craniofacial anomalies (McDonald-McGinn and Sullivan, Medicine 90:1-18, 2011; Burn et al., J Med Genet 30:822-4, 1993) before this phenotypic spectrum was associated with 22q11.2 CNVs. Subsequently, 22q11.2 deletion emerged as a major genomic lesion associated with vulnerability for several clinically defined behavioral deficits common to a number of neurodevelopmental disorders (Fernandez et al., Principles of Developmental Genetics, 2015; Robin and Shprintzen, J Pediatr 147:90-6, 2005; Schneider et al., Am J Psychiatry 171:627-39, 2014). RESULTS The mechanistic relationships between heterozygously deleted 22q11.2 genes and 22q11DS phenotypes are still unknown. We assembled a comprehensive "line-up" of the 36 protein coding loci in the 1.5 Mb minimal critical deleted region on hChr22q11.2, plus 20 protein coding loci in the distal 1.5 Mb that defines the 3 Mb typical 22q11DS deletion. We categorized candidates based upon apparent primary cell biological functions. We analyzed 41 of these genes that encode known proteins to determine whether haploinsufficiency of any single 22q11.2 gene-a one gene to one phenotype correspondence due to heterozygous deletion restricted to that locus-versus complex multigenic interactions can account for single or multiple 22q11DS phenotypes. CONCLUSIONS Our 22q11.2 functional genomic assessment does not support current theories of single gene haploinsufficiency for one or all 22q11DS phenotypes. Shared molecular functions, convergence on fundamental cell biological processes, and related consequences of individual 22q11.2 genes point to a matrix of multigenic interactions due to diminished 22q11.2 gene dosage. These interactions target fundamental cellular mechanisms essential for development, maturation, or homeostasis at subsets of 22q11DS phenotypic sites.
Collapse
Affiliation(s)
- Zahra Motahari
- The Institute for Neuroscience, and Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, Washington DC, 20037 USA
| | - Sally Ann Moody
- The Institute for Neuroscience, and Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, Washington DC, 20037 USA
| | - Thomas Michael Maynard
- The Institute for Neuroscience, and Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, Washington DC, 20037 USA
| | - Anthony-Samuel LaMantia
- The Institute for Neuroscience, and Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, Washington DC, 20037 USA
| |
Collapse
|
35
|
Warren NJH, Eastman A. Inhibition of checkpoint kinase 1 following gemcitabine-mediated S phase arrest results in CDC7- and CDK2-dependent replication catastrophe. J Biol Chem 2018; 294:1763-1778. [PMID: 30573684 DOI: 10.1074/jbc.ra118.005231] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 12/17/2018] [Indexed: 11/06/2022] Open
Abstract
Combining DNA-damaging drugs with DNA checkpoint inhibitors is an emerging strategy to manage cancer. Checkpoint kinase 1 inhibitors (CHK1is) sensitize most cancer cell lines to DNA-damaging drugs and also elicit single-agent cytotoxicity in 15% of cell lines. Consequently, combination therapy may be effective in a broader patient population. Here, we characterized the molecular mechanism of sensitization to gemcitabine by the CHK1i MK8776. Brief gemcitabine incubation irreversibly inhibited ribonucleotide reductase, depleting dNTPs, resulting in durable S phase arrest. Addition of CHK1i 18 h after gemcitabine elicited cell division cycle 7 (CDC7)- and cyclin-dependent kinase 2 (CDK2)-dependent reactivation of the replicative helicase, but did not reinitiate DNA synthesis due to continued lack of dNTPs. Helicase reactivation generated extensive single-strand (ss)DNA that exceeded the protective capacity of the ssDNA-binding protein, replication protein A. The subsequent cleavage of unprotected ssDNA has been termed replication catastrophe. This mechanism did not occur with concurrent CHK1i plus gemcitabine treatment, providing support for delayed administration of CHK1i in patients. Alternative mechanisms of CHK1i-mediated sensitization to gemcitabine have been proposed, but their role was ruled out; these mechanisms include premature mitosis, inhibition of homologous recombination, and activation of double-strand break repair nuclease (MRE11). In contrast, single-agent activity of CHK1i was MRE11-dependent and was prevented by lower concentrations of a CDK2 inhibitor. Hence, both pathways require CDK2 but appear to depend on different CDK2 substrates. We conclude that a small-molecule inhibitor of CHK1 can elicit at least two distinct, context-dependent mechanisms of cytotoxicity in cancer cells.
Collapse
Affiliation(s)
- Nicholas J H Warren
- From the Department of Molecular and Systems Biology, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire 03756
| | - Alan Eastman
- From the Department of Molecular and Systems Biology, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire 03756
| |
Collapse
|
36
|
Role of DHH superfamily proteins in nucleic acids metabolism and stress tolerance in prokaryotes and eukaryotes. Int J Biol Macromol 2018; 127:66-75. [PMID: 30578903 DOI: 10.1016/j.ijbiomac.2018.12.123] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 12/14/2018] [Indexed: 01/05/2023]
Abstract
DHH superfamily proteins play pivotal roles in various cellular processes like replication, recombination, repair and nucleic acids metabolism. These proteins are important for homeostasis maintenance and stress tolerance in prokaryotes and eukaryotes. The prominent members of DHH superfamily include single-strand specific exonuclease RecJ, nanoRNases, polyphosphatase PPX1, pyrophosphatase, prune phosphodiesterase and cell cycle protein Cdc45. The mutations of genes coding for DHH superfamily proteins lead to severe growth defects and in some cases, may be lethal. The members of superfamily have a wide substrate spectrum. The spectrum of substrate for DHH superfamily members ranges from smaller molecules like pyrophosphate and cyclic nucleotides to longer single-stranded DNA molecule. Several genetic, structural and biochemical studies have provided interesting insights about roles of DHH superfamily members. However, there are still various unexplored members in both prokaryotes and eukaryotes. Many aspects of this superfamily associated with homeostasis maintenance and stress tolerance are still not clearly understood. A comprehensive understanding is pre-requisite to decipher the physiological significance of members of DHH superfamily. This article provides the current understanding of DHH superfamily members and their significance in nucleic acids metabolism and stress tolerance across diverse forms of life.
Collapse
|
37
|
Moiseeva TN, Bakkenist CJ. Regulation of the initiation of DNA replication in human cells. DNA Repair (Amst) 2018; 72:99-106. [PMID: 30266203 DOI: 10.1016/j.dnarep.2018.09.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 09/07/2018] [Indexed: 12/31/2022]
Abstract
The origin of species would not have been possible without high fidelity DNA replication and complex genomes evolved with mechanisms that control the initiation of DNA replication at multiple origins on multiple chromosomes such that the genome is duplicated once and only once. The mechanisms that control the assembly and activation of the replicative helicase and the initiation of DNA replication in yeast and Xenopus egg extract systems have been identified and reviewed [1,2]. The goal of this review is to organize currently available data on the mechanisms that control the initiation of DNA replication in human cells.
Collapse
Affiliation(s)
- Tatiana N Moiseeva
- Department of Radiation Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Christopher J Bakkenist
- Department of Radiation Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| |
Collapse
|
38
|
Sokka M, Koalick D, Hemmerich P, Syväoja JE, Pospiech H. The ATR-Activation Domain of TopBP1 Is Required for the Suppression of Origin Firing during the S Phase. Int J Mol Sci 2018; 19:ijms19082376. [PMID: 30104465 PMCID: PMC6121618 DOI: 10.3390/ijms19082376] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 08/04/2018] [Accepted: 08/06/2018] [Indexed: 11/23/2022] Open
Abstract
The mammalian DNA replication program is controlled at two phases, the licensing of potential origins of DNA replication in early gap 1 (G1), and the selective firing of a subset of licenced origins in the synthesis (S) phase. Upon entry into the S phase, serine/threonine-protein kinase ATR (ATR) is required for successful completion of the DNA replication program by limiting unnecessary dormant origin activation. Equally important is its activator, DNA topoisomerase 2-binding protein 1 (TopBP1), which is also required for the initiation of DNA replication after a rise in S-phase kinase levels. However, it is unknown how the ATR activation domain of TopBP1 affects DNA replication dynamics. Using human cells conditionally expressing a TopBP1 mutant deficient for ATR activation, we show that functional TopBP1 is required in suppressing local dormant origin activation. Our results demonstrate a regulatory role for TopBP1 in the local balancing of replication fork firing within the S phase.
Collapse
Affiliation(s)
- Miiko Sokka
- Department of Biology, University of Eastern Finland, FI-80101 Joensuu, Finland.
- Institute of Biomedicine, University of Eastern Finland, FI-70211 Kuopio, Finland.
| | - Dennis Koalick
- Leibniz Institute on Aging-Fritz Lipmann Institute, DE-07745 Jena, Germany.
| | - Peter Hemmerich
- Leibniz Institute on Aging-Fritz Lipmann Institute, DE-07745 Jena, Germany.
| | - Juhani E Syväoja
- Institute of Biomedicine, University of Eastern Finland, FI-70211 Kuopio, Finland.
| | - Helmut Pospiech
- Leibniz Institute on Aging-Fritz Lipmann Institute, DE-07745 Jena, Germany.
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, FI-90014 Oulu, Finland.
| |
Collapse
|
39
|
Ali R, Ramadurai S, Barry F, Nasheuer HP. Optimizing fluorescent protein expression for quantitative fluorescence microscopy and spectroscopy using herpes simplex thymidine kinase promoter sequences. FEBS Open Bio 2018; 8:1043-1060. [PMID: 29928582 PMCID: PMC5985997 DOI: 10.1002/2211-5463.12432] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 03/19/2018] [Accepted: 04/10/2018] [Indexed: 12/22/2022] Open
Abstract
The modulation of expression levels of fluorescent fusion proteins (FFPs) is central for recombinant DNA technologies in modern biology as overexpression of proteins contributes to artifacts in biological experiments. In addition, some microscopy techniques such as fluorescence correlation spectroscopy (FCS) and single-molecule-based techniques are very sensitive to high expression levels of FFPs. To reduce the levels of recombinant protein expression in comparison with the commonly used, very strong CMV promoter, the herpes simplex virus thymidine kinase (TK) gene promoter, and mutants thereof were analyzed. Deletion mutants of the TK promoter were constructed and introduced into the Gateway® system for ectopic expression of enhanced green fluorescent protein (eGFP), monomeric cherry (mCherry), and FFPs containing these FPs. Two promoter constructs, TK2ST and TKTSC, were established, which have optimal low expression levels suitable for FCS studies in U2OS, HeLa CCL2, NIH 3T3, and BALB/c cells. Interestingly, when tested in these four cell lines, promoter constructs having a deletion within TK gene 5'-UTR showed significantly higher protein expression levels than the equivalent constructs lacking this deletion. This suggests that a negative regulatory element is localized within the TK gene 5'-UTR.
Collapse
Affiliation(s)
- Rizwan Ali
- Systems Biology IrelandNUI GalwayIreland
- BiochemistrySchool of Natural Sciences and Centre for Chromosome BiologyNational University of Ireland GalwayIreland
- Present address:
Medical Core Facility & Research PlatformsKing Abdullah International Medical Research CenterNational Guard Health AffairsP.O. Box 3660Riyadh11481 Mail Code 1515Saudi Arabia
| | - Sivaramakrishnan Ramadurai
- Systems Biology IrelandNUI GalwayIreland
- BiochemistrySchool of Natural Sciences and Centre for Chromosome BiologyNational University of Ireland GalwayIreland
- Present address:
School of Chemical SciencesDublin City UniversityDublin‐9Ireland
| | - Frank Barry
- Systems Biology IrelandNUI GalwayIreland
- Regenerative Medicine InstituteNational University of Ireland GalwayIreland
| | - Heinz Peter Nasheuer
- Systems Biology IrelandNUI GalwayIreland
- BiochemistrySchool of Natural Sciences and Centre for Chromosome BiologyNational University of Ireland GalwayIreland
| |
Collapse
|
40
|
Khan AQ, Travers JB, Kemp MG. Roles of UVA radiation and DNA damage responses in melanoma pathogenesis. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2018; 59:438-460. [PMID: 29466611 PMCID: PMC6031472 DOI: 10.1002/em.22176] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/18/2018] [Accepted: 01/22/2018] [Indexed: 05/10/2023]
Abstract
The growing incidence of melanoma is a serious public health issue that merits a thorough understanding of potential causative risk factors, which includes exposure to ultraviolet radiation (UVR). Though UVR has been classified as a complete carcinogen and has long been recognized for its ability to damage genomic DNA through both direct and indirect means, the precise mechanisms by which the UVA and UVB components of UVR contribute to the pathogenesis of melanoma have not been clearly defined. In this review, we therefore highlight recent studies that have addressed roles for UVA radiation in the generation of DNA damage and in modulating the subsequent cellular responses to DNA damage in melanocytes, which are the cell type that gives rise to melanoma. Recent research suggests that UVA not only contributes to the direct formation of DNA lesions but also impairs the removal of UV photoproducts from genomic DNA through oxidation and damage to DNA repair proteins. Moreover, the melanocyte microenvironment within the epidermis of the skin is also expected to impact melanomagenesis, and we therefore discuss several paracrine signaling pathways that have been shown to impact the DNA damage response in UV-irradiated melanocytes. Lastly, we examine how alterations to the immune microenvironment by UVA-associated DNA damage responses may contribute to melanoma development. Thus, there appear to be multiple avenues by which UVA may elevate the risk of melanoma. Protective strategies against excess exposure to UVA wavelengths of light therefore have the potential to decrease the incidence of melanoma. Environ. Mol. Mutagen. 59:438-460, 2018. © 2018 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Aiman Q Khan
- Department of Pharmacology and Toxicology, Wright State University Boonshoft School of Medicine, Dayton, Ohio
| | - Jeffrey B Travers
- Department of Pharmacology and Toxicology, Wright State University Boonshoft School of Medicine, Dayton, Ohio
- Dayton Veterans Affairs Medical Center, Dayton, Ohio
| | - Michael G Kemp
- Department of Pharmacology and Toxicology, Wright State University Boonshoft School of Medicine, Dayton, Ohio
| |
Collapse
|
41
|
范 俣, 刘 瑞, 丁 晓, 上官 信, 吴 新. [Deguelin inhibits proliferation and regulates the expression of MCM3-CDC45 in MCF-7 and H1299 cells in vitro]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2017; 37:1545-1550. [PMID: 29180339 PMCID: PMC6779631 DOI: 10.3969/j.issn.1673-4254.2017.11.20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Indexed: 06/07/2023]
Abstract
OBJECTIVE To observe the effects of deguelin on the proliferation of breast cancer MCF-7 cells and lung cancer H1299 cells in vitro and the expression of minichromosome maintenance protein 3 (MCM3) and CDC45 in the cells. METHODS MTT assay was used to evaluate the proliferation of MCF-7 and H1299 cells exposed to different concentrations of deguelin for 48, 72 or 96 h. The growth of the cells was observed microscopically and the changes of MCM3 and CDC45 expressions in MCF-7 and H1299 cells following deguelin treatment were detected with fluorescence quantitative PCR. RESULTS The proliferation of MCF-7 cells was significantly inhibited by exposure to 0.25, 0.5, 1, 5, 10, 30, and 50 µmol/L deguelin for 48, 72, and 96 h in a concentration- and time-dependent manner. In MCF-7 cells, the IC50 of deguelin at 48, 72, and 96 h was 9, 3, and 2 µmol/L, respectively. Deguelin treatments of H1299 cells at 0.5, 1, 5, 10, 30, 50, and 100 µmol/L also resulted in a concentration- and time-dependent inhibition of the cell growth with an IC50 at 96 h of 2 µmol/L. Optical microscopy of the cells revealed a decreased number of viable cells with obvious cell shrinkage following deguelin treatments. The expression of MCM3 and CDC45 were significantly reduced in the cells after deguelin treatments. CONCLUSION Deguelin can inhibit the proliferation of MCF-7 and H1299 cells in vitro and down-regulate the expression of MCM3 and CDC45 in the cells.
Collapse
Affiliation(s)
- 俣琳 范
- 南方医科大学研究生院,广东 广州 510515Graduate School of Southern Medical University, Guangzhou 510515, China
- 广州军区广州总医院药学部,广东 广州 510010Department of Pharmacy, General Hospital of Guangzhou Military Command, Guangzhou 510010, China
| | - 瑞瑾 刘
- 广州军区广州总医院药学部,广东 广州 510010Department of Pharmacy, General Hospital of Guangzhou Military Command, Guangzhou 510010, China
| | - 晓艳 丁
- 广州军区广州总医院药学部,广东 广州 510010Department of Pharmacy, General Hospital of Guangzhou Military Command, Guangzhou 510010, China
| | - 信一 上官
- 广州军区广州总医院药学部,广东 广州 510010Department of Pharmacy, General Hospital of Guangzhou Military Command, Guangzhou 510010, China
| | - 新荣 吴
- 南方医科大学研究生院,广东 广州 510515Graduate School of Southern Medical University, Guangzhou 510515, China
- 广州军区广州总医院药学部,广东 广州 510010Department of Pharmacy, General Hospital of Guangzhou Military Command, Guangzhou 510010, China
| |
Collapse
|
42
|
Abstract
Complete duplication of large metazoan chromosomes requires thousands of potential initiation sites, only a small fraction of which are selected in each cell cycle. Assembly of the replication machinery is highly conserved and tightly regulated during the cell cycle, but the sites of initiation are highly flexible, and their temporal order of firing is regulated at the level of large-scale multi-replicon domains. Importantly, the number of replication forks must be quickly adjusted in response to replication stress to prevent genome instability. Here we argue that large genomes are divided into domains for exactly this reason. Once established, domain structure abrogates the need for precise initiation sites and creates a scaffold for the evolution of other chromosome functions.
Collapse
Affiliation(s)
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA; Center for Genomics and Personalized Medicine, Florida State University, Tallahassee, FL 32306-4295, USA.
| |
Collapse
|
43
|
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]
|
44
|
The impact of replication stress on replication dynamics and DNA damage in vertebrate cells. Nat Rev Genet 2017; 18:535-550. [DOI: 10.1038/nrg.2017.46] [Citation(s) in RCA: 170] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
45
|
Combined inhibition of Wee1 and Chk1 gives synergistic DNA damage in S-phase due to distinct regulation of CDK activity and CDC45 loading. Oncotarget 2017; 8:10966-10979. [PMID: 28030798 PMCID: PMC5355238 DOI: 10.18632/oncotarget.14089] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 12/15/2016] [Indexed: 12/24/2022] Open
Abstract
Recent studies have shown synergistic cytotoxic effects of simultaneous Chk1- and Wee1-inhibition. However, the mechanisms behind this synergy are not known. Here, we present a flow cytometry-based screen for compounds that cause increased DNA damage in S-phase when combined with the Wee1-inhibitor MK1775. Strikingly, the Chk1-inhibitors AZD7762 and LY2603618 were among the top candidate hits of 1664 tested compounds, suggesting that the synergistic cytotoxic effects are due to increased S-phase DNA damage. Combined Wee1- and Chk1-inhibition caused a strong synergy in induction of S-phase DNA damage and reduction of clonogenic survival. To address the underlying mechanisms, we developed a novel assay measuring CDK-dependent phosphorylations in single S-phase cells. Surprisingly, while Wee1-inhibition alone induced less DNA damage compared to Chk1-inhibition, Wee1-inhibition caused a bigger increase in S-phase CDK-activity. However, the loading of replication initiation factor CDC45 was more increased after Chk1- than Wee1-inhibition and further increased by the combined treatment, and thus correlated well with DNA damage. Therefore, when Wee1 alone is inhibited, Chk1 suppresses CDC45 loading and thereby limits the extent of unscheduled replication initiation and subsequent S-phase DNA damage, despite very high CDK-activity. These results can explain why combined treatment with Wee1- and Chk1-inhibitors gives synergistic anti-cancer effects.
Collapse
|
46
|
Müller CA, Nieduszynski CA. DNA replication timing influences gene expression level. J Cell Biol 2017; 216:1907-1914. [PMID: 28539386 PMCID: PMC5496624 DOI: 10.1083/jcb.201701061] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 04/06/2017] [Accepted: 04/19/2017] [Indexed: 12/31/2022] Open
Abstract
Eukaryotic genomes are replicated in a reproducible temporal order whose physiological significance is poorly understood. Müller and Nieduszynski compare the temporal order of genome replication in phylogenetically diverse yeast species and identify genes for which conserved replication timing contributes to maximal expression. Eukaryotic genomes are replicated in a reproducible temporal order; however, the physiological significance is poorly understood. We compared replication timing in divergent yeast species and identified genomic features with conserved replication times. Histone genes were among the earliest replicating loci in all species. We specifically delayed the replication of HTA1-HTB1 and discovered that this halved the expression of these histone genes. Finally, we showed that histone and cell cycle genes in general are exempt from Rtt109-dependent dosage compensation, suggesting the existence of pathways excluding specific loci from dosage compensation mechanisms. Thus, we have uncovered one of the first physiological requirements for regulated replication time and demonstrated a direct link between replication timing and gene expression.
Collapse
Affiliation(s)
- Carolin A Müller
- Sir William Dunn School of Pathology, University of Oxford, Oxford, England, UK
| | | |
Collapse
|
47
|
Gambus A. Termination of Eukaryotic Replication Forks. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1042:163-187. [DOI: 10.1007/978-981-10-6955-0_8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
48
|
Kemp MG, Spandau DF, Simman R, Travers JB. Insulin-like Growth Factor 1 Receptor Signaling Is Required for Optimal ATR-CHK1 Kinase Signaling in Ultraviolet B (UVB)-irradiated Human Keratinocytes. J Biol Chem 2016; 292:1231-1239. [PMID: 27979966 DOI: 10.1074/jbc.m116.765883] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 12/08/2016] [Indexed: 01/16/2023] Open
Abstract
UVB wavelengths of light induce the formation of photoproducts in DNA that are potentially mutagenic if not properly removed by the nucleotide excision repair machinery. As an additional mechanism to minimize the risk of mutagenesis, UVB-irradiated cells also activate a checkpoint signaling cascade mediated by the ATM and Rad3-related (ATR) and checkpoint kinase 1 (CHK1) kinases to transiently suppress DNA synthesis and cell cycle progression. Given that keratinocytes in geriatric skin display reduced activation of the insulin-like growth factor 1 receptor (IGF-1R) and alterations in DNA repair rate, apoptosis, and senescence following UVB exposure, here we used cultured human keratinocytes in vitro and skin explants ex vivo to examine how IGF-1R activation status affects ATR-CHK1 kinase signaling and the inhibition of DNA replication following UVB irradiation. We find that disruption of IGF-1R signaling with small-molecule inhibitors or IGF-1 withdrawal partially abrogates both the phosphorylation and activation of CHK1 by ATR and the accompanying inhibition of chromosomal DNA synthesis in UVB-irradiated keratinocytes. A critical protein factor that mediates both ATR-CHK1 signaling and nucleotide excision repair is replication protein A, and we find that its accumulation on UVB-damaged chromatin is partially attenuated in cells with an inactive IGF-1R. These results indicate that mutagenesis and skin carcinogenesis in IGF-1-deficient geriatric skin may be caused by defects in multiple cellular responses to UVB-induced DNA damage, including through a failure to properly suppress DNA synthesis on UVB-damaged DNA templates.
Collapse
Affiliation(s)
- Michael G Kemp
- From the Department of Pharmacology and Toxicology, Wright State University Boonshoft School of Medicine, Dayton, Ohio 45435,
| | - Dan F Spandau
- the Departments of Dermatology and.,Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, and
| | - Richard Simman
- From the Department of Pharmacology and Toxicology, Wright State University Boonshoft School of Medicine, Dayton, Ohio 45435
| | - Jeffrey B Travers
- From the Department of Pharmacology and Toxicology, Wright State University Boonshoft School of Medicine, Dayton, Ohio 45435.,the Dayton Veterans Affairs Medical Center, Dayton, Ohio 45428
| |
Collapse
|
49
|
Affiliation(s)
- Christian Speck
- a DNA Replication Group, Institute of Clinical Sciences, Imperial College London , London , UK.,b bMRC Clinical Sciences Centre , Du Cane Road, London , UK
| |
Collapse
|