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Replication Stress, Genomic Instability, and Replication Timing: A Complex Relationship. Int J Mol Sci 2021; 22:ijms22094764. [PMID: 33946274 PMCID: PMC8125245 DOI: 10.3390/ijms22094764] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 12/29/2022] Open
Abstract
The replication-timing program constitutes a key element of the organization and coordination of numerous nuclear processes in eukaryotes. This program is established at a crucial moment in the cell cycle and occurs simultaneously with the organization of the genome, thus indicating the vital significance of this process. With recent technological achievements of high-throughput approaches, a very strong link has been confirmed between replication timing, transcriptional activity, the epigenetic and mutational landscape, and the 3D organization of the genome. There is also a clear relationship between replication stress, replication timing, and genomic instability, but the extent to which they are mutually linked to each other is unclear. Recent evidence has shown that replication timing is affected in cancer cells, although the cause and consequence of this effect remain unknown. However, in-depth studies remain to be performed to characterize the molecular mechanisms of replication-timing regulation and clearly identify different cis- and trans-acting factors. The results of these studies will potentially facilitate the discovery of new therapeutic pathways, particularly for personalized medicine, or new biomarkers. This review focuses on the complex relationship between replication timing, replication stress, and genomic instability.
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52
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Gotovac JR, Kader T, Milne JV, Fujihara KM, Lara-Gonzalez LE, Gorringe KL, Kalimuthu SN, Jayawardana MW, Duong CP, Phillips WA, Clemons NJ. Loss of SMAD4 Is Sufficient to Promote Tumorigenesis in a Model of Dysplastic Barrett's Esophagus. Cell Mol Gastroenterol Hepatol 2021; 12:689-713. [PMID: 33774196 PMCID: PMC8267443 DOI: 10.1016/j.jcmgh.2021.03.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 03/14/2021] [Accepted: 03/16/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS Esophageal adenocarcinoma (EAC) develops from its precursor Barrett's esophagus through intermediate stages of low- and high-grade dysplasia. However, knowledge of genetic drivers and molecular mechanisms implicated in disease progression is limited. Herein, we investigated the effect of Mothers against decapentaplegic homolog 4 (SMAD4) loss on transforming growth factor β (TGF-β) signaling functionality and in vivo tumorigenicity in high-grade dysplastic Barrett's cells. METHODS An in vivo xenograft model was used to test tumorigenicity of SMAD4 knockdown or knockout in CP-B high-grade dysplastic Barrett's cells. RT2 polymerase chain reaction arrays were used to analyze TGF-β signaling functionality, and low-coverage whole-genome sequencing was performed to detect copy number alterations upon SMAD4 loss. RESULTS We found that SMAD4 knockout significantly alters the TGF-β pathway target gene expression profile. SMAD4 knockout positively regulates potential oncogenes such as CRYAB, ACTA2, and CDC6, whereas the CDKN2A/B tumor-suppressor locus was regulated negatively. We verified that SMAD4 in combination with CDC6-CDKN2A/B or CRYAB genetic alterations in patient tumors have significant predictive value for poor prognosis. Importantly, we investigated the effect of SMAD4 inactivation in Barrett's tumorigenesis. We found that genetic knockdown or knockout of SMAD4 was sufficient to promote tumorigenesis in dysplastic Barrett's esophagus cells in vivo. Progression to invasive EAC was accompanied by distinctive and consistent copy number alterations in SMAD4 knockdown or knockout xenografts. CONCLUSIONS Altogether, up-regulation of oncogenes, down-regulation of tumor-suppressor genes, and chromosomal instability within the tumors after SMAD4 loss implicates SMAD4 as a protector of genome integrity in EAC development and progression. Foremost, SMAD4 loss promotes tumorigenesis from dysplastic Barrett's toward EAC.
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Affiliation(s)
- Jovana R Gotovac
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, Parkville, Victoria, Australia
| | - Tanjina Kader
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, Parkville, Victoria, Australia
| | - Julia V Milne
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, Parkville, Victoria, Australia
| | - Kenji M Fujihara
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, Parkville, Victoria, Australia
| | - Luis E Lara-Gonzalez
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, Parkville, Victoria, Australia
| | - Kylie L Gorringe
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, Parkville, Victoria, Australia
| | - Sangeetha N Kalimuthu
- Anatomical Pathology, Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada; Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Madawa W Jayawardana
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, Parkville, Victoria, Australia
| | - Cuong P Duong
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, Parkville, Victoria, Australia
| | - Wayne A Phillips
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, Parkville, Victoria, Australia; Department of Surgery, St Vincent's Hospital, The University of Melbourne, Parkville, Victoria, Australia
| | - Nicholas J Clemons
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, Parkville, Victoria, Australia.
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53
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Abstract
The recruitment of the minichromosome maintenance complex (MCM) on DNA replication origins is a critical process for faithful genome duplication termed licensing. Aberrant licensing has been associated with cancer and, recently, with neurodevelopmental diseases. Investigating MCM loading in complicated tissues, such as brain, remains challenging. Here, we describe an optimized approach for the qualitative and quantitative analysis of DNA-bound MCMs in the developing mouse cortex through direct imaging, offering an innovative insight into the research of origin licensing in vivo.
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54
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Yang C, Tian C, Hoffman TE, Jacobsen NK, Spencer SL. Melanoma subpopulations that rapidly escape MAPK pathway inhibition incur DNA damage and rely on stress signalling. Nat Commun 2021; 12:1747. [PMID: 33741929 PMCID: PMC7979728 DOI: 10.1038/s41467-021-21549-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 01/28/2021] [Indexed: 12/11/2022] Open
Abstract
Despite the increasing number of effective anti-cancer therapies, successful treatment is limited by the development of drug resistance. While the contribution of genetic factors to drug resistance is undeniable, little is known about how drug-sensitive cells first evade drug action to proliferate in drug. Here we track the responses of thousands of single melanoma cells to BRAF inhibitors and show that a subset of cells escapes drug via non-genetic mechanisms within the first three days of treatment. Cells that escape drug rely on ATF4 stress signalling to cycle periodically in drug, experience DNA replication defects leading to DNA damage, and yet out-proliferate other cells over extended treatment. Together, our work reveals just how rapidly melanoma cells can adapt to drug treatment, generating a mutagenesis-prone subpopulation that expands over time.
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Affiliation(s)
- Chen Yang
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.,BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA.,Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Chengzhe Tian
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.,BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
| | - Timothy E Hoffman
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.,BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
| | - Nicole K Jacobsen
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA.,BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
| | - Sabrina L Spencer
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA. .,BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA.
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55
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He Z, Houghton PJ, Williams TM, Shen C. Regulation of DNA duplication by the mTOR signaling pathway. Cell Cycle 2021; 20:742-751. [PMID: 33691584 DOI: 10.1080/15384101.2021.1897271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Accurate and complete DNA replication and separation are essential for genetic information inheritance and organism maintenance. Errors in DNA duplication are the main source of genetic instability. Understanding DNA duplication regulation is the key to elucidate the mechanisms and find treatment strategies for human genetic disorders, especially cancer. The mechanistic target of rapamycin (mTOR) is a central regulator of cell growth and proliferation by integrating and processing extracellular and intracellular signals to monitor the well-being of cell physiology. mTOR signaling dysregulation is associated with many human diseases including cancer and diabetes. Emerging evidence has demonstrated that mTOR signaling plays a key role in DNA duplication. We herein review the current knowledge of mTOR signaling in the regulation of DNA replication origin licensing, replication fork progression, and stabilization.
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Affiliation(s)
- Zhengfu He
- Department of Thoracic Surgery, Sir Run Run Shaw Hospital, College of Medicine Zhejiang University, Hangzhou, China
| | - Peter J Houghton
- The Greehey Children's Cancer Research Institute, the University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Terence M Williams
- Department of Radiation Oncology, Beckman Research Institute, City of Hope National Medical Center, Duarte, California, USA
| | - Changxian Shen
- Department of Radiation Oncology, Beckman Research Institute, City of Hope National Medical Center, Duarte, California, USA
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56
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Yang G, Guan W, Cao Z, Guo W, Xiong G, Zhao F, Feng M, Qiu J, Liu Y, Zhang MQ, You L, Zhang T, Zhao Y, Gu J. Integrative Genomic Analysis of Gemcitabine Resistance in Pancreatic Cancer by Patient-derived Xenograft Models. Clin Cancer Res 2021; 27:3383-3396. [PMID: 33674273 DOI: 10.1158/1078-0432.ccr-19-3975] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 12/21/2020] [Accepted: 03/02/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Gemcitabine is most commonly used for pancreatic cancer. However, the molecular features and mechanisms of the frequently occurring resistance remain unclear. This work aims at exploring the molecular features of gemcitabine resistance and identifying candidate biomarkers and combinatorial targets for the treatment. EXPERIMENTAL DESIGN In this study, we established 66 patient-derived xenografts (PDXs) on the basis of clinical pancreatic cancer specimens and treated them with gemcitabine. We generated multiomics data (including whole-exome sequencing, RNA sequencing, miRNA sequencing, and DNA methylation array) of 15 drug-sensitive and 13 -resistant PDXs before and after the gemcitabine treatment. We performed integrative computational analysis to identify the molecular networks related to gemcitabine intrinsic and acquired resistance. Then, short hairpin RNA-based high-content screening was implemented to validate the function of the deregulated genes. RESULTS The comprehensive multiomics analysis and functional experiment revealed that MRPS5 and GSPT1 had strong effects on cell proliferation, and CD55 and DHTKD1 contributed to gemcitabine resistance in pancreatic cancer cells. Moreover, we found miR-135a-5p was significantly associated with the prognosis of patients with pancreatic cancer and could be a candidate biomarker to predict gemcitabine response. Comparing the molecular features before and after the treatment, we found that PI3K-Akt, p53, and hypoxia-inducible factor-1 pathways were significantly altered in multiple patients, providing candidate target pathways for reducing the acquired resistance. CONCLUSIONS This integrative genomic study systematically investigated the predictive markers and molecular mechanisms of chemoresistance in pancreatic cancer and provides potential therapy targets for overcoming gemcitabine resistance.
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Affiliation(s)
- Gang Yang
- Department of General Surgery, State Key Laboratory of Complex Severe and, Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Wenfang Guan
- MOE Key Laboratory of Bioinformatics, Division of BNRist Bioinformatics, Department of Automation, Tsinghua University, Beijing, P.R. China
| | - Zhe Cao
- Department of General Surgery, State Key Laboratory of Complex Severe and, Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Wenbo Guo
- MOE Key Laboratory of Bioinformatics, Division of BNRist Bioinformatics, Department of Automation, Tsinghua University, Beijing, P.R. China
| | - Guangbing Xiong
- Department of General Surgery, State Key Laboratory of Complex Severe and, Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Fangyu Zhao
- Department of General Surgery, State Key Laboratory of Complex Severe and, Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Mengyu Feng
- Department of General Surgery, State Key Laboratory of Complex Severe and, Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Jiangdong Qiu
- Department of General Surgery, State Key Laboratory of Complex Severe and, Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Yueze Liu
- Department of General Surgery, State Key Laboratory of Complex Severe and, Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Michael Q Zhang
- MOE Key Laboratory of Bioinformatics, Division of BNRist Bioinformatics, Department of Automation, Tsinghua University, Beijing, P.R. China
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, P.R. China
- Department of Biological Sciences, Center for Systems Biology, the University of Texas at Dallas, Richardson, Texas
| | - Lei You
- Department of General Surgery, State Key Laboratory of Complex Severe and, Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China.
| | - Taiping Zhang
- Department of General Surgery, State Key Laboratory of Complex Severe and, Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China.
| | - Yupei Zhao
- Department of General Surgery, State Key Laboratory of Complex Severe and, Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China.
| | - Jin Gu
- MOE Key Laboratory of Bioinformatics, Division of BNRist Bioinformatics, Department of Automation, Tsinghua University, Beijing, P.R. China.
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57
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Rapsomaniki MA, Maxouri S, Nathanailidou P, Garrastacho MR, Giakoumakis NN, Taraviras S, Lygeros J, Lygerou Z. In silico analysis of DNA re-replication across a complete genome reveals cell-to-cell heterogeneity and genome plasticity. NAR Genom Bioinform 2021; 3:lqaa112. [PMID: 33554116 PMCID: PMC7846089 DOI: 10.1093/nargab/lqaa112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/15/2020] [Accepted: 01/20/2021] [Indexed: 01/06/2023] Open
Abstract
DNA replication is a complex and remarkably robust process: despite its inherent uncertainty, manifested through stochastic replication timing at a single-cell level, multiple control mechanisms ensure its accurate and timely completion across a population. Disruptions in these mechanisms lead to DNA re-replication, closely connected to genomic instability and oncogenesis. Here, we present a stochastic hybrid model of DNA re-replication that accurately portrays the interplay between discrete dynamics, continuous dynamics and uncertainty. Using experimental data on the fission yeast genome, model simulations show how different regions respond to re-replication and permit insight into the key mechanisms affecting re-replication dynamics. Simulated and experimental population-level profiles exhibit a good correlation along the genome, robust to model parameters, validating our approach. At a single-cell level, copy numbers of individual loci are affected by intrinsic properties of each locus, in cis effects from adjoining loci and in trans effects from distant loci. In silico analysis and single-cell imaging reveal that cell-to-cell heterogeneity is inherent in re-replication and can lead to genome plasticity and a plethora of genotypic variations.
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Affiliation(s)
- Maria Anna Rapsomaniki
- Department of Biology, School of Medicine, University of Patras, 26500 Rio Patras, Greece
| | - Stella Maxouri
- Department of Biology, School of Medicine, University of Patras, 26500 Rio Patras, Greece
| | - Patroula Nathanailidou
- Department of Biology, School of Medicine, University of Patras, 26500 Rio Patras, Greece
| | | | | | - Stavros Taraviras
- Department of Physiology, School of Medicine, University of Patras, 26500 Rio Patras, Greece
| | - John Lygeros
- Automatic Control Laboratory, ETH Zurich, 8092 Zurich, Switzerland
| | - Zoi Lygerou
- Department of Biology, School of Medicine, University of Patras, 26500 Rio Patras, Greece
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58
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Murayama T, Takeuchi Y, Yamawaki K, Natsume T, Li M, Marcela RCN, Nishimura T, Kogure Y, Nakata A, Tominaga K, Sasahara A, Yano M, Ishikawa S, Ohta T, Ikeda K, Horie-Inoue K, Inoue S, Seki M, Suzuki Y, Sugano S, Enomoto T, Tanabe M, Tada KI, Kanemaki MT, Okamoto K, Tojo A, Gotoh N. MCM10 compensates for Myc-induced DNA replication stress in breast cancer stem-like cells. Cancer Sci 2021; 112:1209-1224. [PMID: 33340428 PMCID: PMC7935783 DOI: 10.1111/cas.14776] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 11/16/2020] [Accepted: 12/14/2020] [Indexed: 12/15/2022] Open
Abstract
Cancer stem-like cells (CSCs) induce drug resistance and recurrence of tumors when they experience DNA replication stress. However, the mechanisms underlying DNA replication stress in CSCs and its compensation remain unclear. Here, we demonstrate that upregulated c-Myc expression induces stronger DNA replication stress in patient-derived breast CSCs than in differentiated cancer cells. Our results suggest critical roles for mini-chromosome maintenance protein 10 (MCM10), a firing (activating) factor of DNA replication origins, to compensate for DNA replication stress in CSCs. MCM10 expression is upregulated in CSCs and is maintained by c-Myc. c-Myc-dependent collisions between RNA transcription and DNA replication machinery may occur in nuclei, thereby causing DNA replication stress. MCM10 may activate dormant replication origins close to these collisions to ensure the progression of replication. Moreover, patient-derived breast CSCs were found to be dependent on MCM10 for their maintenance, even after enrichment for CSCs that were resistant to paclitaxel, the standard chemotherapeutic agent. Further, MCM10 depletion decreased the growth of cancer cells, but not of normal cells. Therefore, MCM10 may robustly compensate for DNA replication stress and facilitate genome duplication in cancer cells in the S-phase, which is more pronounced in CSCs. Overall, we provide a preclinical rationale to target the c-Myc-MCM10 axis for preventing drug resistance and recurrence of tumors.
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Affiliation(s)
- Takahiko Murayama
- Division of Molecular Therapy, Institute of Medical Science, The University of Tokyo, Minato-ku, Japan.,Division of Cancer Cell Biology, Cancer Research Institute, Kanazawa University, Kanazawa City, Japan
| | - Yasuto Takeuchi
- Division of Cancer Cell Biology, Cancer Research Institute, Kanazawa University, Kanazawa City, Japan
| | - Kaoru Yamawaki
- Division of Cancer Differentiation, National Cancer Center Research Institute, Chuo-ku, Japan.,Department of Obstetrics and Gynecology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Toyoaki Natsume
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima City, Japan.,Department of Genetics, SOKENDAI, Mishima City, Japan
| | - Mengjiao Li
- Division of Cancer Cell Biology, Cancer Research Institute, Kanazawa University, Kanazawa City, Japan
| | - Rojas-Chaverra N Marcela
- Division of Cancer Cell Biology, Cancer Research Institute, Kanazawa University, Kanazawa City, Japan
| | - Tatsunori Nishimura
- Division of Cancer Cell Biology, Cancer Research Institute, Kanazawa University, Kanazawa City, Japan
| | - Yuta Kogure
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Science, The University of Tokyo, Kashiwa City, Japan
| | - Asuka Nakata
- Division of Cancer Cell Biology, Cancer Research Institute, Kanazawa University, Kanazawa City, Japan.,Department of Pediatrics, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Kana Tominaga
- Division of Molecular Therapy, Institute of Medical Science, The University of Tokyo, Minato-ku, Japan.,Division of Cancer Cell Biology, Cancer Research Institute, Kanazawa University, Kanazawa City, Japan.,Division of Cancer Differentiation, National Cancer Center Research Institute, Chuo-ku, Japan
| | - Asako Sasahara
- Division of Molecular Therapy, Institute of Medical Science, The University of Tokyo, Minato-ku, Japan.,Department of Breast & Endocrine Surgery, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
| | - Masao Yano
- Department of Surgery, Minamimachida Hospital, Machida City, Japan
| | - Satoko Ishikawa
- Department of Gastroenterological Surgery, Kanazawa University, Kanazawa City, Japan
| | - Tetsuo Ohta
- Department of Gastroenterological Surgery, Kanazawa University, Kanazawa City, Japan
| | - Kazuhiro Ikeda
- Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Hidaka City, Japan
| | - Kuniko Horie-Inoue
- Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Hidaka City, Japan
| | - Satoshi Inoue
- Division of Gene Regulation and Signal Transduction, Research Center for Genomic Medicine, Saitama Medical University, Hidaka City, Japan
| | - Masahide Seki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa City, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa City, Japan
| | - Sumio Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa City, Japan
| | - Takayuki Enomoto
- Department of Obstetrics and Gynecology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Masahiko Tanabe
- Department of Breast & Endocrine Surgery, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
| | - Kei-Ichiro Tada
- Department of Pediatrics, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Masato T Kanemaki
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima City, Japan.,Department of Genetics, SOKENDAI, Mishima City, Japan
| | - Koji Okamoto
- Division of Cancer Differentiation, National Cancer Center Research Institute, Chuo-ku, Japan
| | - Arinobu Tojo
- Division of Molecular Therapy, Institute of Medical Science, The University of Tokyo, Minato-ku, Japan
| | - Noriko Gotoh
- Division of Molecular Therapy, Institute of Medical Science, The University of Tokyo, Minato-ku, Japan.,Division of Cancer Cell Biology, Cancer Research Institute, Kanazawa University, Kanazawa City, Japan
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59
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Beyond Kinases: Targeting Replication Stress Proteins in Cancer Therapy. Trends Cancer 2020; 7:430-446. [PMID: 33203609 DOI: 10.1016/j.trecan.2020.10.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/19/2020] [Accepted: 10/26/2020] [Indexed: 12/13/2022]
Abstract
DNA replication stress describes a state of impaired replication fork progress that triggers a cellular stress response to maintain genome stability and complete DNA synthesis. Replication stress is a common state that must be tolerated in many cancers. One promising therapeutic approach is targeting replication stress response factors such as the ataxia telangiectasia and rad 3-related kinase (ATR) or checkpoint kinase 1 (CHK1) kinases that some cancers depend upon to survive endogenous replication stress. However, research revealing the complexity of the replication stress response suggests new genetic interactions and candidate therapeutic targets. Many of these candidates regulate DNA transactions around reversed replication forks, including helicases, nucleases and alternative polymerases that promote fork stability and restart. Here we review emerging strategies to exploit replication stress for cancer therapy.
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60
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Abstract
Post-translational modifications of cellular substrates with ubiquitin and ubiquitin-like proteins (UBLs), including ubiquitin, SUMOs, and neural precursor cell-expressed developmentally downregulated protein 8, play a central role in regulating many aspects of cell biology. The UBL conjugation cascade is initiated by a family of ATP-dependent enzymes termed E1 activating enzymes and executed by the downstream E2-conjugating enzymes and E3 ligases. Despite their druggability and their key position at the apex of the cascade, pharmacologic modulation of E1s with potent and selective drugs has remained elusive until 2009. Among the eight E1 enzymes identified so far, those initiating ubiquitylation (UBA1), SUMOylation (SAE), and neddylation (NAE) are the most characterized and are implicated in various aspects of cancer biology. To date, over 40 inhibitors have been reported to target UBA1, SAE, and NAE, including the NAE inhibitor pevonedistat, evaluated in more than 30 clinical trials. In this Review, we discuss E1 enzymes, the rationale for their therapeutic targeting in cancer, and their different inhibitors, with emphasis on the pharmacologic properties of adenosine sulfamates and their unique mechanism of action, termed substrate-assisted inhibition. Moreover, we highlight other less-characterized E1s-UBA6, UBA7, UBA4, UBA5, and autophagy-related protein 7-and the opportunities for targeting these enzymes in cancer. SIGNIFICANCE STATEMENT: The clinical successes of proteasome inhibitors in cancer therapy and the emerging resistance to these agents have prompted the exploration of other signaling nodes in the ubiquitin-proteasome system including E1 enzymes. Therefore, it is crucial to understand the biology of different E1 enzymes, their roles in cancer, and how to translate this knowledge into novel therapeutic strategies with potential implications in cancer treatment.
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Affiliation(s)
- Samir H Barghout
- Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada (S.H.B., A.D.S.); Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada (S.H.B., A.D.S.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Tanta University, Tanta, Egypt (S.H.B.)
| | - Aaron D Schimmer
- Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada (S.H.B., A.D.S.); Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada (S.H.B., A.D.S.); and Department of Pharmacology and Toxicology, Faculty of Pharmacy, Tanta University, Tanta, Egypt (S.H.B.)
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61
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Hsu RYC, Giri S, Wang Y, Lin YC, Liu D, Wopat S, Chakraborty A, Prasanth KV, Prasanth SG. The E3 ligase RFWD3 stabilizes ORC in a p53-dependent manner. Cell Cycle 2020; 19:2927-2938. [PMID: 33044890 DOI: 10.1080/15384101.2020.1829823] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
RFWD3 is an E3 ubiquitin ligase that plays important roles in DNA damage response and DNA replication. We have previously demonstrated that the stabilization of RFWD3 by PCNA at the replication fork enables ubiquitination of the single-stranded binding protein, RPA and its subsequent degradation for replication progression. Here, we report that RFWD3 associates with the Origin Recognition Complex (ORC) and ORC-Associated (ORCA/LRWD1), components of the pre-replicative complex required for the initiation of DNA replication. Overexpression of ORC/ORCA leads to the stabilization of RFWD3. Interestingly, RFWD3 seems to stabilize ORC/ORCA in cells expressing wild type p53, as the depletion of RFWD3 reduces the levels of ORC/ORCA. Further, the catalytic activity of RFWD3 is required for the stabilization of ORC. Our results indicate that the RFWD3 promotes the stability of ORC, enabling efficient pre-RC assembly.
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Affiliation(s)
- Rosaline Y C Hsu
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign , Urbana, IL, USA
| | - Sumanprava Giri
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign , Urbana, IL, USA
| | - Yating Wang
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign , Urbana, IL, USA
| | - Yo-Chuen Lin
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign , Urbana, IL, USA
| | - Dazhen Liu
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign , Urbana, IL, USA
| | - Susan Wopat
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign , Urbana, IL, USA
| | - Arindam Chakraborty
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign , Urbana, IL, USA
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign , Urbana, IL, USA
| | - Supriya G Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign , Urbana, IL, USA
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62
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Origin of Genome Instability and Determinants of Mutational Landscape in Cancer Cells. Genes (Basel) 2020; 11:genes11091101. [PMID: 32967144 PMCID: PMC7563369 DOI: 10.3390/genes11091101] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 09/12/2020] [Accepted: 09/18/2020] [Indexed: 12/31/2022] Open
Abstract
Genome instability is a crucial and early event associated with an increased predisposition to tumor formation. In the absence of any exogenous agent, a single human cell is subjected to about 70,000 DNA lesions each day. It has now been shown that physiological cellular processes including DNA transactions during DNA replication and transcription contribute to DNA damage and induce DNA damage responses in the cell. These processes are also influenced by the three dimensional-chromatin architecture and epigenetic regulation which are altered during the malignant transformation of cells. In this review, we have discussed recent insights about how replication stress, oncogene activation, chromatin dynamics, and the illegitimate recombination of cell-free chromatin particles deregulate cellular processes in cancer cells and contribute to their evolution. The characterization of such endogenous sources of genome instability in cancer cells can be exploited for the development of new biomarkers and more effective therapies for cancer treatment.
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63
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Chromatin and Nuclear Architecture: Shaping DNA Replication in 3D. Trends Genet 2020; 36:967-980. [PMID: 32713597 DOI: 10.1016/j.tig.2020.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/26/2020] [Accepted: 07/02/2020] [Indexed: 12/13/2022]
Abstract
In eukaryotes, DNA replication progresses through a finely orchestrated temporal and spatial program. The 3D genome structure and nuclear architecture have recently emerged as fundamental determinants of the replication program. Factors with established roles in replication have been recognized as genome organization regulators. Exploiting paradigms from yeasts and mammals, we discuss how DNA replication is regulated in time and space through DNA-associated trans-acting factors, diffusible limiting replication initiation factors, higher-order chromatin folding, dynamic origin localization, and specific nuclear microenvironments. We present an integrated model for the regulation of DNA replication in 3D and highlight the importance of accurate spatio-temporal regulation of DNA replication in physiology and disease.
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64
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Panagopoulos A, Taraviras S, Nishitani H, Lygerou Z. CRL4Cdt2: Coupling Genome Stability to Ubiquitination. Trends Cell Biol 2020; 30:290-302. [DOI: 10.1016/j.tcb.2020.01.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/12/2020] [Accepted: 01/14/2020] [Indexed: 12/20/2022]
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Champeris Tsaniras S, Delinasios GJ, Petropoulos M, Panagopoulos A, Anagnostopoulos AK, Villiou M, Vlachakis D, Bravou V, Stathopoulos GT, Taraviras S. DNA Replication Inhibitor Geminin and Retinoic Acid Signaling Participate in Complex Interactions Associated With Pluripotency. Cancer Genomics Proteomics 2019; 16:593-601. [PMID: 31659113 PMCID: PMC6885373 DOI: 10.21873/cgp.20162] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 09/23/2019] [Accepted: 10/10/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND/AIM Several links between DNA replication, pluripotency and development have been recently identified. The involvement of miRNA in the regulation of cell cycle events and pluripotency factors has also gained attention. MATERIALS AND METHODS In the present study, we used the g:Profiler platform to analyze transcription factor binding sites, miRNA networks and protein-protein interactions to identify novel links among the aforementioned processes. RESULTS AND CONCLUSION A complex circuitry between retinoic acid signaling, SWI/SNF components, pluripotency factors including Oct4, Sox2 and Nanog and cell cycle regulators was identified. It is suggested that the DNA replication inhibitor geminin plays a central role in this circuitry.
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Affiliation(s)
- Spyridon Champeris Tsaniras
- Department of Physiology, Medical School, University of Patras, Patras, Greece
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, U.S.A
| | | | | | | | - Athanasios K Anagnostopoulos
- International Institute of Anticancer Research, Kapandriti, Greece
- Proteomics Research Unit, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Maria Villiou
- Department of Physiology, Medical School, University of Patras, Patras, Greece
| | - Dimitrios Vlachakis
- Bioinformatics & Medical Informatics Laboratory, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Vasiliki Bravou
- Department of Anatomy-Histology-Embryology, Faculty of Medicine, University of Patras, Patras, Greece
| | - Georgios T Stathopoulos
- Laboratory for Molecular Respiratory Carcinogenesis, Department of Physiology, Faculty of Medicine, University of Patras, Patras, Greece
| | - Stavros Taraviras
- Department of Physiology, Medical School, University of Patras, Patras, Greece
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