1
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Prasad CB, Oo A, Liu Y, Qiu Z, Zhong Y, Li N, Singh D, Xin X, Cho YJ, Li Z, Zhang X, Yan C, Zheng Q, Wang QE, Guo D, Kim B, Zhang J. The thioredoxin system determines CHK1 inhibitor sensitivity via redox-mediated regulation of ribonucleotide reductase activity. Nat Commun 2024; 15:4667. [PMID: 38821952 PMCID: PMC11143221 DOI: 10.1038/s41467-024-48076-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 04/19/2024] [Indexed: 06/02/2024] Open
Abstract
Checkpoint kinase 1 (CHK1) is critical for cell survival under replication stress (RS). CHK1 inhibitors (CHK1i's) in combination with chemotherapy have shown promising results in preclinical studies but have displayed minimal efficacy with substantial toxicity in clinical trials. To explore combinatorial strategies that can overcome these limitations, we perform an unbiased high-throughput screen in a non-small cell lung cancer (NSCLC) cell line and identify thioredoxin1 (Trx1), a major component of the mammalian antioxidant-system, as a determinant of CHK1i sensitivity. We establish a role for redox recycling of RRM1, the larger subunit of ribonucleotide reductase (RNR), and a depletion of the deoxynucleotide pool in this Trx1-mediated CHK1i sensitivity. Further, the TrxR inhibitor auranofin, an approved anti-rheumatoid arthritis drug, shows a synergistic interaction with CHK1i via interruption of the deoxynucleotide pool. Together, we show a pharmacological combination to treat NSCLC that relies on a redox regulatory link between the Trx system and mammalian RNR activity.
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Affiliation(s)
- Chandra Bhushan Prasad
- Department of Radiation Oncology, James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Adrian Oo
- Center for ViroScience and Cure, Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Yujie Liu
- Department of Radiation Oncology, James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Zhaojun Qiu
- Department of Radiation Oncology, James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Yaogang Zhong
- Department of Radiation Oncology, James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH, 43210, USA
- The Comprehensive Cancer Center, Center for Cancer Metabolism, The Ohio State University, Columbus, OH, 43210, USA
| | - Na Li
- Department of Radiation Oncology, James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Deepika Singh
- Department of Radiation Oncology, James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Xiwen Xin
- The Ohio State University, Columbus, OH, 43210, USA
| | - Young-Jae Cho
- Center for ViroScience and Cure, Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Zaibo Li
- Department of Pathology, The Ohio State University Wexner Medical Center, College of Medicine, Columbus, OH, 43210, USA
| | - Xiaoli Zhang
- Department of Biomedical Informatics, Wexner Medical Center, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Chunhong Yan
- Georgia Cancer Center, Augusta University, Augusta, GA, 30912, USA
| | - Qingfei Zheng
- Department of Radiation Oncology, James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH, 43210, USA
- The Comprehensive Cancer Center, Center for Cancer Metabolism, The Ohio State University, Columbus, OH, 43210, USA
| | - Qi-En Wang
- Department of Radiation Oncology, James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Deliang Guo
- Department of Radiation Oncology, James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH, 43210, USA
- The Comprehensive Cancer Center, Center for Cancer Metabolism, The Ohio State University, Columbus, OH, 43210, USA
| | - Baek Kim
- Center for ViroScience and Cure, Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Junran Zhang
- Department of Radiation Oncology, James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH, 43210, USA.
- The Comprehensive Cancer Center, Center for Cancer Metabolism, The Ohio State University, Columbus, OH, 43210, USA.
- The Comprehensive Cancer Center, Pelotonia Institute for Immuno-Oncology, The Ohio State University, Columbus, OH, 43210, USA.
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2
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Kulagin KA, Starodubova ES, Osipova PJ, Lipatova AV, Cherdantsev IA, Poddubko SV, Karpov VL, Karpov DS. Synergistic Effect of a Combination of Proteasome and Ribonucleotide Reductase Inhibitors in a Biochemical Model of the Yeast Saccharomyces cerevisiae and a Glioblastoma Cell Line. Int J Mol Sci 2024; 25:3977. [PMID: 38612788 PMCID: PMC11011839 DOI: 10.3390/ijms25073977] [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: 03/08/2024] [Revised: 03/31/2024] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
Proteasome inhibitors are used in the therapy of several cancers, and clinical trials are underway for their use in the treatment of glioblastoma (GBM). However, GBM becomes resistant to chemotherapy relatively rapidly. Recently, the overexpression of ribonucleotide reductase (RNR) genes was found to mediate therapy resistance in GBM. The use of combinations of chemotherapeutic agents is considered a promising direction in cancer therapy. The present work aimed to evaluate the efficacy of the combination of proteasome and RNR inhibitors in yeast and GBM cell models. We have shown that impaired proteasome function results in increased levels of RNR subunits and increased enzyme activity in yeast. Co-administration of the proteasome inhibitor bortezomib and the RNR inhibitor hydroxyurea was found to significantly reduce the growth rate of S. cerevisiae yeast. Accordingly, the combination of bortezomib and another RNR inhibitor gemcitabine reduced the survival of DBTRG-05MG compared to the HEK293 cell line. Thus, yeast can be used as a simple model to evaluate the efficacy of combinations of proteasome and RNR inhibitors.
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Affiliation(s)
- Kirill A. Kulagin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (K.A.K.); (E.S.S.); (P.J.O.); (A.V.L.); (I.A.C.)
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Elizaveta S. Starodubova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (K.A.K.); (E.S.S.); (P.J.O.); (A.V.L.); (I.A.C.)
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Pamila J. Osipova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (K.A.K.); (E.S.S.); (P.J.O.); (A.V.L.); (I.A.C.)
- Institute of Biomedical Problems of Russian Academy of Sciences, 123007 Moscow, Russia;
| | - Anastasia V. Lipatova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (K.A.K.); (E.S.S.); (P.J.O.); (A.V.L.); (I.A.C.)
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Igor A. Cherdantsev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (K.A.K.); (E.S.S.); (P.J.O.); (A.V.L.); (I.A.C.)
| | - Svetlana V. Poddubko
- Institute of Biomedical Problems of Russian Academy of Sciences, 123007 Moscow, Russia;
| | - Vadim L. Karpov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Dmitry S. Karpov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (K.A.K.); (E.S.S.); (P.J.O.); (A.V.L.); (I.A.C.)
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
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3
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Dombi E, Marinaki T, Spingardi P, Millar V, Hadjichristou N, Carver J, Johnston IG, Fratter C, Poulton J. Nucleoside supplements as treatments for mitochondrial DNA depletion syndrome. Front Cell Dev Biol 2024; 12:1260496. [PMID: 38665433 PMCID: PMC11043827 DOI: 10.3389/fcell.2024.1260496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 03/11/2024] [Indexed: 04/28/2024] Open
Abstract
Introduction: In mitochondrial DNA (mtDNA) depletion syndrome (MDS), patients cannot maintain sufficient mtDNA for their energy needs. MDS presentations range from infantile encephalopathy with hepatopathy (Alpers syndrome) to adult chronic progressive external ophthalmoplegia. Most are caused by nucleotide imbalance or by defects in the mtDNA replisome. There is currently no curative treatment available. Nucleoside therapy is a promising experimental treatment for TK2 deficiency, where patients are supplemented with exogenous deoxypyrimidines. We aimed to explore the benefits of nucleoside supplementation in POLG and TWNK deficient fibroblasts. Methods: We used high-content fluorescence microscopy with software-based image analysis to assay mtDNA content and membrane potential quantitatively, using vital dyes PicoGreen and MitoTracker Red CMXRos respectively. We tested the effect of 15 combinations (A, T, G, C, AT, AC, AG, CT, CG, GT, ATC, ATG, AGC, TGC, ATGC) of deoxynucleoside supplements on mtDNA content of fibroblasts derived from four patients with MDS (POLG1, POLG2, DGUOK, TWNK) in both a replicating (10% dialysed FCS) and quiescent (0.1% dialysed FCS) state. We used qPCR to measure mtDNA content of supplemented and non-supplemented fibroblasts following mtDNA depletion using 20 µM ddC and after 14- and 21-day recovery in a quiescent state. Results: Nucleoside treatments at 200 µM that significantly increased mtDNA content also significantly reduced the number of cells remaining in culture after 7 days of treatment, as well as mitochondrial membrane potential. These toxic effects were abolished by reducing the concentration of nucleosides to 50 µM. In POLG1 and TWNK cells the combination of ATGC treatment increased mtDNA content the most after 7 days in non-replicating cells. ATGC nucleoside combination significantly increased the rate of mtDNA recovery in quiescent POLG1 cells following mtDNA depletion by ddC. Conclusion: High-content imaging enabled us to link mtDNA copy number with key read-outs linked to patient wellbeing. Elevated G increased mtDNA copy number but severely impaired fibroblast growth, potentially by inhibiting purine synthesis and/or causing replication stress. Combinations of nucleosides ATGC, T, or TC, benefited growth of cells harbouring POLG mutations. These combinations, one of which reflects a commercially available preparation, could be explored further for treatment of POLG patients.
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Affiliation(s)
- Eszter Dombi
- Nuffield Department of Women’s and Reproductive Health, University of Oxford, Oxford, United Kingdom
| | - Tony Marinaki
- Purine Research Laboratory, Department of Biochemical Sciences, Guy’s and St Thomas’ Hospitals, London, United Kingdom
| | - Paolo Spingardi
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Val Millar
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Janet Carver
- Nuffield Department of Women’s and Reproductive Health, University of Oxford, Oxford, United Kingdom
| | - Iain G. Johnston
- Department of Mathematics, University of Bergen, Bergen, Norway
- Computational Biology Unit, University of Bergen, Bergen, Norway
| | - Carl Fratter
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Joanna Poulton
- Nuffield Department of Women’s and Reproductive Health, University of Oxford, Oxford, United Kingdom
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4
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McCown C, Yu CH, Ivanov DN. Allosteric substrate activation of SAMHD1 shapes deoxynucleotide triphosphate imbalances by interconnecting the depletion and biosynthesis of different dNTPs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.14.567083. [PMID: 38014186 PMCID: PMC10680743 DOI: 10.1101/2023.11.14.567083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
SAMHD1 is a dNTPase that impedes replication of HIV-1 in myeloid cells and resting T lymphocytes. Here we elucidate the substrate activation mechanism of SAMHD1 that depends on dNTP binding at allosteric sites and the concomitant tetramerization of the enzyme. The study reveals that SAMHD1 activation involves an inactive tetrameric intermediate with partial occupancy of the allosteric sites. The equilibrium between the inactive and active tetrameric states, which is coupled to cooperative binding/dissociation of at least two allosteric dNTP ligands, controls the dNTPase activity of the enzyme, which, in addition, depends on the identity of the dNTPs occupying the four allosteric sites of the active tetramer. We show how such allosteric regulation determines deoxynucleotide triphosphate levels established in the dynamic equilibria between dNTP production and SAMHD1-catalyzed depletion. Notably, the mechanism enables a distinctive functionality of SAMHD1, which we call facilitated dNTP depletion, whereby elevated biosynthesis of some dNTPs results in more efficient depletion of others. The regulatory relationship between the biosynthesis and depletion of different dNTPs sheds light on the emerging role of SAMHD1 in the biology of dNTP homeostasis with implications for HIV/AIDS, innate antiviral immunity, T cell disorders, telomere maintenance and therapeutic efficacy of nucleoside analogs.
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5
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Ponnienselvan K, Liu P, Nyalile T, Oikemus S, Joynt AT, Kelly K, Guo D, Chen Z, Lee JM, Schiffer CA, Emerson CP, Lawson ND, Watts JK, Sontheimer EJ, Luban J, Wolfe SA. Addressing the dNTP bottleneck restricting prime editing activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.21.563443. [PMID: 37904991 PMCID: PMC10614944 DOI: 10.1101/2023.10.21.563443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Prime editing efficiency is modest in cells that are quiescent or slowly proliferating where intracellular dNTP levels are tightly regulated. MMLV-reverse transcriptase - the prime editor polymerase subunit - requires high intracellular dNTPs levels for efficient polymerization. We report that prime editing efficiency in primary cells and in vivo is increased by mutations that enhance the enzymatic properties of MMLV-reverse transcriptase and can be further complemented by targeting SAMHD1 for degradation.
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6
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Harada Y, Mizote Y, Suzuki T, Hirayama A, Ikeda S, Nishida M, Hiratsuka T, Ueda A, Imagawa Y, Maeda K, Ohkawa Y, Murai J, Freeze HH, Miyoshi E, Higashiyama S, Udono H, Dohmae N, Tahara H, Taniguchi N. Metabolic clogging of mannose triggers dNTP loss and genomic instability in human cancer cells. eLife 2023; 12:e83870. [PMID: 37461317 DOI: 10.7554/elife.83870] [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: 09/30/2022] [Accepted: 06/12/2023] [Indexed: 07/20/2023] Open
Abstract
Mannose has anticancer activity that inhibits cell proliferation and enhances the efficacy of chemotherapy. How mannose exerts its anticancer activity, however, remains poorly understood. Here, using genetically engineered human cancer cells that permit the precise control of mannose metabolic flux, we demonstrate that the large influx of mannose exceeding its metabolic capacity induced metabolic remodeling, leading to the generation of slow-cycling cells with limited deoxyribonucleoside triphosphates (dNTPs). This metabolic remodeling impaired dormant origin firing required to rescue stalled forks by cisplatin, thus exacerbating replication stress. Importantly, pharmacological inhibition of de novo dNTP biosynthesis was sufficient to retard cell cycle progression, sensitize cells to cisplatin, and inhibit dormant origin firing, suggesting dNTP loss-induced genomic instability as a central mechanism for the anticancer activity of mannose.
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Affiliation(s)
- Yoichiro Harada
- Department of Glyco-Oncology and Medical Biochemistry, Research Institute, Osaka International Cancer Institute, Osaka, Japan
| | - Yu Mizote
- Department of Cancer Drug Discovery and Development, Research Institute, Osaka International Cancer Institute, Osaka, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Saitama, Japan
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, Yamagata, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Kanagawa, Japan
| | - Satsuki Ikeda
- Institute for Advanced Biosciences, Keio University, Yamagata, Japan
| | - Mikako Nishida
- Department of Immunology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Toru Hiratsuka
- Department of Oncogenesis and Growth Regulation, Research Institute, Osaka International Cancer Institute, Osaka, Japan
| | - Ayaka Ueda
- Department of Molecular Biochemistry and Clinical Investigation, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yusuke Imagawa
- Department of Oncogenesis and Growth Regulation, Research Institute, Osaka International Cancer Institute, Osaka, Japan
| | - Kento Maeda
- Department of Glyco-Oncology and Medical Biochemistry, Research Institute, Osaka International Cancer Institute, Osaka, Japan
| | - Yuki Ohkawa
- Department of Glyco-Oncology and Medical Biochemistry, Research Institute, Osaka International Cancer Institute, Osaka, Japan
| | - Junko Murai
- Institute for Advanced Biosciences, Keio University, Yamagata, Japan
- Division of Cell Growth and Tumor Regulation, Proteo-Science Center, Ehime University, Ehime, Japan
- Department of Biochemistry and Molecular Genetics, Graduate School of Medicine, Ehime University, Ehime, Japan
| | - Hudson H Freeze
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, United States
| | - Eiji Miyoshi
- Department of Molecular Biochemistry and Clinical Investigation, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Shigeki Higashiyama
- Department of Oncogenesis and Growth Regulation, Research Institute, Osaka International Cancer Institute, Osaka, Japan
- Division of Cell Growth and Tumor Regulation, Proteo-Science Center, Ehime University, Ehime, Japan
- Department of Biochemistry and Molecular Genetics, Graduate School of Medicine, Ehime University, Ehime, Japan
| | - Heiichiro Udono
- Department of Immunology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Saitama, Japan
| | - Hideaki Tahara
- Department of Cancer Drug Discovery and Development, Research Institute, Osaka International Cancer Institute, Osaka, Japan
- Project Division of Cancer Biomolecular Therapy, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Naoyuki Taniguchi
- Department of Glyco-Oncology and Medical Biochemistry, Research Institute, Osaka International Cancer Institute, Osaka, Japan
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7
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Saez-Ayala M, Hoffer L, Abel S, Ben Yaala K, Sicard B, Andrieu GP, Latiri M, Davison EK, Ciufolini MA, Brémond P, Rebuffet E, Roche P, Derviaux C, Voisset E, Montersino C, Castellano R, Collette Y, Asnafi V, Betzi S, Dubreuil P, Combes S, Morelli X. From a drug repositioning to a structure-based drug design approach to tackle acute lymphoblastic leukemia. Nat Commun 2023; 14:3079. [PMID: 37248212 DOI: 10.1038/s41467-023-38668-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 05/11/2023] [Indexed: 05/31/2023] Open
Abstract
Cancer cells utilize the main de novo pathway and the alternative salvage pathway for deoxyribonucleotide biosynthesis to achieve adequate nucleotide pools. Deoxycytidine kinase is the rate-limiting enzyme of the salvage pathway and it has recently emerged as a target for anti-proliferative therapies for cancers where it is essential. Here, we present the development of a potent inhibitor applying an iterative multidisciplinary approach, which relies on computational design coupled with experimental evaluations. This strategy allows an acceleration of the hit-to-lead process by gradually implementing key chemical modifications to increase affinity and activity. Our lead compound, OR0642, is more than 1000 times more potent than its initial parent compound, masitinib, previously identified from a drug repositioning approach. OR0642 in combination with a physiological inhibitor of the de novo pathway doubled the survival rate in a human T-cell acute lymphoblastic leukemia patient-derived xenograft mouse model, demonstrating the proof-of-concept of this drug design strategy.
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Affiliation(s)
- Magali Saez-Ayala
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France.
| | - Laurent Hoffer
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France
- Drug Discovery Program, Ontario Institute for Cancer Research (OICR), Toronto, ON, Canada
| | - Sébastien Abel
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France
| | - Khaoula Ben Yaala
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France
| | - Benoit Sicard
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France
| | - Guillaume P Andrieu
- Institut Necker Enfants Malades (INEM), INSERM, Hôpital Necker Enfants-Malades, Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Université de Paris, Paris, France
| | - Mehdi Latiri
- Institut Necker Enfants Malades (INEM), INSERM, Hôpital Necker Enfants-Malades, Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Université de Paris, Paris, France
| | - Emma K Davison
- Department of Chemistry, Faculty of Science, University of British Columbia, Vancouver, BC, Canada
- Department of Chemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Marco A Ciufolini
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France
- Department of Chemistry, Faculty of Science, University of British Columbia, Vancouver, BC, Canada
| | - Paul Brémond
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France
| | - Etienne Rebuffet
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France
| | - Philippe Roche
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France
| | - Carine Derviaux
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France
| | - Edwige Voisset
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France
| | - Camille Montersino
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France
| | - Remy Castellano
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France
| | - Yves Collette
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France
| | - Vahid Asnafi
- Institut Necker Enfants Malades (INEM), INSERM, Hôpital Necker Enfants-Malades, Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Université de Paris, Paris, France
| | - Stéphane Betzi
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France
| | - Patrice Dubreuil
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France.
| | - Sébastien Combes
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France.
| | - Xavier Morelli
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France.
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8
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Sharma S, Kong Z, Jia S, Tran P, Nilsson AK, Chabes A. Quantitative Analysis of Nucleoside Triphosphate Pools in Mouse Muscle Using Hydrophilic Interaction Liquid Chromatography Coupled with Tandem Mass Spectrometry Detection. Methods Mol Biol 2023; 2615:267-280. [PMID: 36807798 DOI: 10.1007/978-1-0716-2922-2_19] [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] [Indexed: 02/23/2023]
Abstract
Defects in deoxyribonucleoside triphosphate (dNTP) metabolism are associated with a number of mitochondrial DNA (mtDNA) depletion syndromes (MDS). These disorders affect the muscles, liver, and brain, and the concentrations of dNTPs in these tissues are already normally low and are, therefore, difficult to measure. Thus, information about the concentrations of dNTPs in tissues of healthy animals and animals with MDS are important for mechanistic studies of mtDNA replication, analysis of disease progression, and the development of therapeutic interventions. Here, we present a sensitive method for the simultaneous analysis of all four dNTPs as well as all four ribonucleoside triphosphates (NTPs) in mouse muscles using hydrophilic interaction liquid chromatography coupled with triple quadrupole mass spectrometry. The simultaneous detection of NTPs allows them to be used as internal standards for the normalization of dNTP concentrations. The method can be applied for measuring dNTP and NTP pools in other tissues and organisms.
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Affiliation(s)
- Sushma Sharma
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Ziqing Kong
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Shaodong Jia
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Phong Tran
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Anna Karin Nilsson
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden.
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9
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dNTP concentrations do not increase in mammalian cells in response to DNA damage. Cell Metab 2022; 34:1895-1896. [PMID: 36476929 DOI: 10.1016/j.cmet.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A recent publication reported a uniform ∼5- to 6-fold increase in dNTP pools 30 min after exposure to ionizing radiation. Das et al. were not able to reproduce these results. Their data instead agree with earlier publications reporting no increase in dNTP pools in mammalian cells in response to DNA damage.
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10
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Babai R, Izrael R, Vértessy BG. Characterization of the dynamics of Plasmodium falciparum deoxynucleotide-triphosphate pool in a stage-specific manner. Sci Rep 2022; 12:19926. [PMID: 36402851 PMCID: PMC9675800 DOI: 10.1038/s41598-022-23807-4] [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: 06/13/2022] [Accepted: 11/06/2022] [Indexed: 11/21/2022] Open
Abstract
Understanding and characterizing the molecular background of the maintenance of genomic integrity might be a major factor in comprehending the exceptional ability of the malaria parasite, Plasmodium falciparum to adapt at a fast pace to antimalarials. A balanced nucleotide pool is an essential factor for high-fidelity replication. The lack of detailed studies on deoxynucleotide-triphosphate (dNTP) pools in various intraerythrocytic stages of Plasmodium falciparum motivated our present study. Here, we focused on the building blocks of DNA and utilized an EvaGreen-based dNTP incorporation assay to successfully measure the temporal dynamics of dNTPs in every intraerythrocytic stage and in drug-treated trophozoites. Our findings show that the ratio of dNTPs in the ring-stage parasites significantly differs from the more mature trophozoite and schizont stages. We were also able to detect dGTP levels that have never been shown before and found it to be the least abundant dNTP in all stages. Treatment with WR99210, a TS-DHFR inhibitor drug, affected not only dTTP, but also dGTP levels, despite its presumed selective action on pyrimidine biosynthesis. Results from our studies might assist in a better understanding of genome integrity mechanisms and may potentially lead to novel drug related aspects involving purine and pyrimidine metabolic targets.
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Affiliation(s)
- Réka Babai
- grid.425578.90000 0004 0512 3755Malaria Research Laboratory, Institute of Enzymology, Research Centre for Natural Sciences, Budapest, 1117 Hungary ,grid.6759.d0000 0001 2180 0451George A. Olah Doctoral School of Chemistry and Chemical Technology, BME Budapest University of Technology and Economics, Budapest, 1111 Hungary ,grid.6759.d0000 0001 2180 0451Department of Applied Biotechnology and Food Sciences, BME Budapest University of Technology and Economics, Budapest, 1111 Hungary
| | - Richard Izrael
- grid.425578.90000 0004 0512 3755Malaria Research Laboratory, Institute of Enzymology, Research Centre for Natural Sciences, Budapest, 1117 Hungary ,grid.9008.10000 0001 1016 9625Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, Szeged, 6720 Hungary
| | - Beáta G. Vértessy
- grid.425578.90000 0004 0512 3755Malaria Research Laboratory, Institute of Enzymology, Research Centre for Natural Sciences, Budapest, 1117 Hungary ,grid.6759.d0000 0001 2180 0451Department of Applied Biotechnology and Food Sciences, BME Budapest University of Technology and Economics, Budapest, 1111 Hungary
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11
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Jung KW, Kwon S, Jung JH, Bahn YS. Essential Roles of Ribonucleotide Reductases under DNA Damage and Replication Stresses in Cryptococcus neoformans. Microbiol Spectr 2022; 10:e0104422. [PMID: 35736239 PMCID: PMC9431586 DOI: 10.1128/spectrum.01044-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/30/2022] [Indexed: 12/03/2022] Open
Abstract
A balance in the deoxyribonucleotide (dNTPs) intracellular concentration is critical for the DNA replication and repair processes. In the model yeast Saccharomyces cerevisiae, the Mec1-Rad53-Dun1 kinase cascade mainly regulates the ribonucleotide reductase (RNR) gene expression during DNA replication and DNA damage stress. However, the RNR regulatory mechanisms in basidiomycete fungi during DNA replication and damage stress remain elusive. Here, we observed that in C. neoformans, RNR1 (large RNR subunit) and RNR21 (one small RNR subunit) were required for cell viability, but not RNR22 (another small RNR subunit). RNR22 overexpression compensated for the lethality of RNR21 suppression. In contrast to the regulatory mechanisms of RNRs in S. cerevisiae, Rad53 and Chk1 kinases cooperatively or divergently controlled RNR1 and RNR21 expression under DNA damage and DNA replication stress. In particular, this study revealed that Chk1 mainly regulated RNR1 expression during DNA replication stress, whereas Rad53, rather than Chk1, played a significant role in controlling the expression of RNR21 during DNA damage stress. Furthermore, the expression of RNR22, not but RNR1 and RNR21, was suppressed by the Ssn6-Tup1 complex during DNA replication stress. Notably, we observed that RNR1 expression was mainly regulated by Mbs1, whereas RNR21 expression was cooperatively controlled by Mbs1 and Bdr1 as downstream factors of Rad53 and Chk1 during DNA replication and damage stress. Collectively, the regulation of RNRs in C. neoformans has both evolutionarily conserved and divergent features in DNA replication and DNA damage stress, compared with other yeasts. IMPORTANCE Upon DNA replication or damage stresses, it is critical to provide proper levels of deoxynucleotide triphosphates (dNTPs) and activate DNA repair machinery. Ribonucleotide reductases (RNRs), which are composed of large and small subunits, are required for synthesizing dNTP. An imbalance in the intracellular concentration of dNTPs caused by the perturbation of RNR results in a reduction in DNA repair fidelity. Despite the importance of their roles, functions and regulations of RNR have not been elucidated in the basidiomycete fungi. In this study, we found that the roles of RNR1, RNR21, and RNR22 genes encoding RNR subunits in the viability of C. neoformans. Furthermore, their expression levels are divergently regulated by the Rad53-Chk1 pathway and the Ssn6-Tup1 complex in response to DNA replication and damage stresses. Therefore, this study provides insight into the regulatory mechanisms of RNR genes to DNA replication and damage stresses in basidiomycete fungi.
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Affiliation(s)
- Kwang-Woo Jung
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Sunhak Kwon
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Jong-Hyun Jung
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
- Department of Radiation Science and Technology, University of Science and Technology, Daejeon, Republic of Korea
| | - Yong-Sun Bahn
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
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12
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Chen WJ, Lin IH, Lee CW, Yoshioka K, Ono Y, Yan YT, Yen Y, Chen YF. Ribonucleotide reductase M2B in the myofibers modulates stem cell fate in skeletal muscle. NPJ Regen Med 2022; 7:37. [PMID: 35906243 PMCID: PMC9338274 DOI: 10.1038/s41536-022-00231-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 07/06/2022] [Indexed: 11/17/2022] Open
Abstract
The balance among quiescence, differentiation, and self-renewal of skeletal muscle stem cells (MuSCs) is tightly regulated by their intrinsic and extrinsic properties from the niche. How the niche controls MuSC fate remains unclear. Ribonucleotide reductase M2B (Rrm2b) modulates MuSC quiescence/differentiation in muscle in response to injury. Rrm2b knockout in myofibers, but not in MuSCs, led to weakness of muscles, such as a loss of muscle mass and strength. After muscle injury, damaged myofibers were more efficiently repaired in the Rrm2b myofiber-specific knockout mice than the control mice, but these myofibers were thinner and showed weak functioning. Rrm2b-deleted myofibers released several myokines, which trigger MuSCs to differentiate but not re-enter the quiescent stage to replenish the stem cell pool. Overall, Rrm2b in the myofibers plays a critical role in modulating the MuSC fate by modifying the microenvironment, and it may lead to a possible strategy to treat muscle disorders.
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Affiliation(s)
- Wan-Jing Chen
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei, 11529, Taiwan
| | - I-Hsuan Lin
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, 11031, Taipei, Taiwan
| | - Chien-Wei Lee
- Center for Translational Genomics Research, China Medical University Hospital, Taichung, 404327, Taiwan
| | - Kiyoshi Yoshioka
- Department of Muscle Development and Regeneration, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Yusuke Ono
- Department of Muscle Development and Regeneration, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Yu-Ting Yan
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei, 11529, Taiwan.,Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Yun Yen
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, 11031, Taipei, Taiwan. .,Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, 11031, Taipei, Taiwan. .,Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, 11031, Taipei, Taiwan. .,Cancer Center, Taipei Municipal WanFang Hospital, 116081, Taipei, Taiwan. .,Center for Cancer Translational Research, Tzu Chi University, Hualien, Taiwan.
| | - Yi-Fan Chen
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei, 11529, Taiwan. .,Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, 11031, Taipei, Taiwan. .,International Ph.D. Program for Translational Science, College of Medical Science and Technology, Taipei Medical University, 11031, Taipei, Taiwan. .,Master Program in Clinical Genomics and Proteomics, School of Pharmacy, Taipei Medical University, Taipei, 11031, Taiwan.
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13
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Disruption of dNTP homeostasis by ribonucleotide reductase hyperactivation overcomes AML differentiation blockade. Blood 2022; 139:3752-3770. [PMID: 35439288 PMCID: PMC9247363 DOI: 10.1182/blood.2021015108] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 04/07/2022] [Indexed: 01/09/2023] Open
Abstract
Differentiation blockade is a hallmark of acute myeloid leukemia (AML). A strategy to overcome such a blockade is a promising approach against the disease. The lack of understanding of the underlying mechanisms hampers development of such strategies. Dysregulated ribonucleotide reductase (RNR) is considered a druggable target in proliferative cancers susceptible to deoxynucleoside triphosphate (dNTP) depletion. Herein, we report an unanticipated discovery that hyperactivating RNR enables differentiation and decreases leukemia cell growth. We integrate pharmacogenomics and metabolomics analyses to identify that pharmacologically (eg, nelarabine) or genetically upregulating RNR subunit M2 (RRM2) creates a dNTP pool imbalance and overcomes differentiation arrest. Moreover, R-loop-mediated DNA replication stress signaling is responsible for RRM2 activation by nelarabine treatment. Further aggravating dNTP imbalance by depleting the dNTP hydrolase SAM domain and HD domain-containing protein 1 (SAMHD1) enhances ablation of leukemia stem cells by RRM2 hyperactivation. Mechanistically, excessive activation of extracellular signal-regulated kinase (ERK) signaling downstream of the imbalance contributes to cellular outcomes of RNR hyperactivation. A CRISPR screen identifies a synthetic lethal interaction between loss of DUSP6, an ERK-negative regulator, and nelarabine treatment. These data demonstrate that dNTP homeostasis governs leukemia maintenance, and a combination of DUSP inhibition and nelarabine represents a therapeutic strategy.
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14
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Preclinical validation and phase I trial of 4-hydroxysalicylanilide, targeting ribonucleotide reductase mediated dNTP synthesis in multiple myeloma. J Biomed Sci 2022; 29:32. [PMID: 35546402 PMCID: PMC9097096 DOI: 10.1186/s12929-022-00813-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 04/29/2022] [Indexed: 11/25/2022] Open
Abstract
Background Aberrant DNA repair pathways contribute to malignant transformation or disease progression and the acquisition of drug resistance in multiple myeloma (MM); therefore, these pathways could be therapeutically exploited. Ribonucleotide reductase (RNR) is the rate-limiting enzyme for the biosynthesis of deoxyribonucleotides (dNTPs), which are essential for DNA replication and DNA damage repair. In this study, we explored the efficacy of the novel RNR inhibitor, 4-hydroxysalicylanilide (HDS), in myeloma cells and xenograft model. In addition, we assessed the clinical activity and safety of HDS in patients with MM. Methods We applied bioinformatic, genetic, and pharmacological approaches to demonstrate that HDS was an RNR inhibitor that directly bound to RNR subunit M2 (RRM2). The activity of HDS alone or in synergy with standard treatments was evaluated in vitro and in vivo. We also initiated a phase I clinical trial of single-agent HDS in MM patients (ClinicalTrials.gov: NCT03670173) to assess safety and efficacy. Results HDS inhibited the activity of RNR by directly targeting RRM2. HDS decreased the RNR-mediated dNTP synthesis and concomitantly inhibited DNA damage repair, resulting in the accumulation of endogenous unrepaired DNA double-strand breaks (DSBs), thus inhibiting MM cell proliferation and inducing apoptosis. Moreover, HDS overcame the protective effects of IL-6, IGF-1 and bone marrow stromal cells (BMSCs) on MM cells. HDS prolonged survival in a MM xenograft model and induced synergistic anti-myeloma activity in combination with melphalan and bortezomib. HDS also showed a favorable safety profile and demonstrated clinical activity against MM. Conclusions Our study provides a rationale for the clinical evaluation of HDS as an anti-myeloma agent, either alone or in combination with standard treatments for MM. Trial registration: ClinicalTrials.gov, NCT03670173, Registered 12 September 2018. Supplementary information The online version contains supplementary material available at 10.1186/s12929-022-00813-2.
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15
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Abstract
Significance: The small, multicopy mitochondrial genome (mitochondrial DNA [mtDNA]) is essential for efficient energy production, as alterations in its coding information or a decrease in its copy number disrupt mitochondrial ATP synthesis. However, the mitochondrial replication machinery encounters numerous challenges that may limit its ability to duplicate this important genome and that jeopardize mtDNA stability, including various lesions in the DNA template, topological stress, and an insufficient nucleotide supply. Recent Advances: An ever-growing array of DNA repair or maintenance factors are being reported to localize to the mitochondria. We review current knowledge regarding the mitochondrial factors that may contribute to the tolerance or repair of various types of changes in the mitochondrial genome, such as base damage, incorporated ribonucleotides, and strand breaks. We also discuss the newly discovered link between mtDNA instability and activation of the innate immune response. Critical Issues: By which mechanisms do mitochondria respond to challenges that threaten mtDNA maintenance? What types of mtDNA damage are repaired, and when are the affected molecules degraded instead? And, finally, which forms of mtDNA instability trigger an immune response, and how? Future Directions: Further work is required to understand the contribution of the DNA repair and damage-tolerance factors present in the mitochondrial compartment, as well as the balance between mtDNA repair and degradation. Finally, efforts to understand the events underlying mtDNA release into the cytosol are warranted. Pursuing these and many related avenues can improve our understanding of what goes wrong in mitochondrial disease. Antioxid. Redox Signal. 36, 885-905.
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Affiliation(s)
- Gustavo Carvalho
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Bruno Marçal Repolês
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Isabela Mendes
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Paulina H Wanrooij
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
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Long MJC, Ly P, Aye Y. Still no Rest for the Reductases: Ribonucleotide Reductase (RNR) Structure and Function: An Update. Subcell Biochem 2022; 99:155-197. [PMID: 36151376 DOI: 10.1007/978-3-031-00793-4_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Herein we present a multidisciplinary discussion of ribonucleotide reductase (RNR), the essential enzyme uniquely responsible for conversion of ribonucleotides to deoxyribonucleotides. This chapter primarily presents an overview of this multifaceted and complex enzyme, covering RNR's role in enzymology, biochemistry, medicinal chemistry, and cell biology. It further focuses on RNR from mammals, whose interesting and often conflicting roles in health and disease are coming more into focus. We present pitfalls that we think have not always been dealt with by researchers in each area and further seek to unite some of the field-specific observations surrounding this enzyme. Our work is thus not intended to cover any one topic in extreme detail, but rather give what we consider to be the necessary broad grounding to understand this critical enzyme holistically. Although this is an approach we have advocated in many different areas of scientific research, there is arguably no other single enzyme that embodies the need for such broad study than RNR. Thus, we submit that RNR itself is a paradigm of interdisciplinary research that is of interest from the perspective of the generalist and the specialist alike. We hope that the discussions herein will thus be helpful to not only those wanting to tackle RNR-specific problems, but also those working on similar interdisciplinary projects centering around other enzymes.
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Affiliation(s)
- Marcus J C Long
- University of Lausanne (UNIL), Lausanne, Switzerland
- Department of Biochemistry, UNIL, Epalinges, Switzerland
| | - Phillippe Ly
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
- EPFL SB ISIC LEAGO, Lausanne, Switzerland
| | - Yimon Aye
- Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
- EPFL SB ISIC LEAGO, Lausanne, Switzerland.
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17
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Ozturk M, Metin M, Altay V, De Filippis L, Ünal BT, Khursheed A, Gul A, Hasanuzzaman M, Nahar K, Kawano T, Caparrós PG. Molecular Biology of Cadmium Toxicity in Saccharomyces cerevisiae. Biol Trace Elem Res 2021; 199:4832-4846. [PMID: 33462792 DOI: 10.1007/s12011-021-02584-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/08/2021] [Indexed: 02/08/2023]
Abstract
Cadmium (Cd) is a toxic heavy metal mainly originating from industrial activities and causes environmental pollution. To better understand its toxicity and pollution remediation, we must understand the effects of Cd on living beings. Saccharomyces cerevisiae (budding yeast) is an eukaryotic unicellular model organism. It has provided much scientific knowledge about cellular and molecular biology in addition to its economic benefits. Effects associated with copper and zinc, sulfur and selenium metabolism, calcium (Ca2+) balance/signaling, and structure of phospholipids as a result of exposure to cadmium have been evaluated. In yeast as a result of cadmium stress, "mitogen-activated protein kinase," "high osmolarity glycerol," and "cell wall integrity" pathways have been reported to activate different signaling pathways. In addition, abnormalities and changes in protein structure, ribosomes, cell cycle disruption, and reactive oxygen species (ROS) following cadmium cytotoxicity have also been detailed. Moreover, the key OLE1 gene that encodes for delta-9 FA desaturase in relation to cadmium toxicity has been discussed in more detail. Keeping all these studies in mind, an attempt has been made to evaluate published cellular and molecular toxicity data related to Cd stress, and specifically published on S. cerevisiae.
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Affiliation(s)
- Munir Ozturk
- Department of Botany and Centre for Environmental Studies, Ege University, Izmir, Turkey.
| | - Mert Metin
- Graduate School of Environmental Engineering, The University of Kitakyushu, 1-1 Hibikino, Wakamatsu-ku, Kitakyushu, Fukuoka, 808-0135, Japan
| | - Volkan Altay
- Department of Biology, Faculty of Science and Arts, Hatay Mustafa Kemal University, Antakya, Hatay, Turkey
| | - Luigi De Filippis
- School of Life Sciences, University of Technology Sydney, Sydney, 123, Australia
| | - Bengu Turkyilmaz Ünal
- Faculty of Science and Arts, Department of Biotechnology, Nigde Omer Halisdemir University, Nigde, Turkey
| | - Anum Khursheed
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, Pakistan
| | - Alvina Gul
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences & Technology, Islamabad, Pakistan
| | - Mirza Hasanuzzaman
- Department of Agronomy, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Dhaka, Bangladesh
| | - Kamuran Nahar
- Department of Agricultural Botany, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Dhaka, Bangladesh
| | - Tomonori Kawano
- Graduate School of Environmental Engineering, The University of Kitakyushu, 1-1 Hibikino, Wakamatsu-ku, Kitakyushu, Fukuoka, 808-0135, Japan
| | - Pedro García Caparrós
- Agronomy Department of Superior School Engineering, University of Almería, Ctra. Sacramento s/n, La Cañadade San Urbano, 04120, Almería, Spain
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Li Y, Luo W, Zhang H, Wang C, Yu C, Jiang Z, Zhang W. Antitumor Mechanism of Hydroxycamptothecin via the Metabolic Perturbation of Ribonucleotide and Deoxyribonucleotide in Human Colorectal Carcinoma Cells. Molecules 2021; 26:4902. [PMID: 34443490 PMCID: PMC8398164 DOI: 10.3390/molecules26164902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 12/12/2022] Open
Abstract
Hydroxycamptothecin (SN38) is a natural plant extract isolated from Camptotheca acuminate. It has a broad spectrum of anticancer activity through inhibition of DNA topoisomerase I, which could affect DNA synthesis and lead to DNA damage. Thus, the action of SN38 against cancers could inevitably affect endogenous levels of ribonucleotide (RNs) and deoxyribonucleotide (dRNs) that play critical roles in many biological processes, especially in DNA synthesis and repair. However, the exact impact of SN38 on RNs and dRNs is yet to be fully elucidated. In this study, we evaluated the anticancer effect and associated mechanism of SN38 in human colorectal carcinoma HCT 116 cells. As a result, SN38 could decrease the cell viability and induce DNA damage in a concentration-dependent manner. Furthermore, cell cycle arrest and intracellular nucleotide metabolism were perturbed due to DNA damage response, of which ATP, UTP, dATP, and TTP may be the critical metabolites during the whole process. Combined with the expression of deoxyribonucleoside triphosphates synthesis enzymes, our results demonstrated that the alteration and imbalance of deoxyribonucleoside triphosphates caused by SN38 was mainly due to the de novo nucleotide synthesis at 24 h, and subsequently the salvage pathways at 48 h. The unique features of SN38 suggested that it might be recommended as an effective supplementary drug with an anticancer effect.
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Affiliation(s)
- Yan Li
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau 999078, China; (Y.L.); (W.L.); (H.Z.); (C.W.)
| | - Wendi Luo
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau 999078, China; (Y.L.); (W.L.); (H.Z.); (C.W.)
| | - Huixia Zhang
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau 999078, China; (Y.L.); (W.L.); (H.Z.); (C.W.)
| | - Caiyun Wang
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau 999078, China; (Y.L.); (W.L.); (H.Z.); (C.W.)
| | - Caiyuan Yu
- Faculty of Agroforestry and Medicine, The Open University of China, Beijing 100039, China;
| | - Zhihong Jiang
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau 999078, China; (Y.L.); (W.L.); (H.Z.); (C.W.)
| | - Wei Zhang
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau 999078, China; (Y.L.); (W.L.); (H.Z.); (C.W.)
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19
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Hydroxyurea-The Good, the Bad and the Ugly. Genes (Basel) 2021; 12:genes12071096. [PMID: 34356112 PMCID: PMC8304116 DOI: 10.3390/genes12071096] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/13/2021] [Accepted: 07/16/2021] [Indexed: 01/23/2023] Open
Abstract
Hydroxyurea (HU) is mostly referred to as an inhibitor of ribonucleotide reductase (RNR) and as the agent that is commonly used to arrest cells in the S-phase of the cycle by inducing replication stress. It is a well-known and widely used drug, one which has proved to be effective in treating chronic myeloproliferative disorders and which is considered a staple agent in sickle anemia therapy and—recently—a promising factor in preventing cognitive decline in Alzheimer’s disease. The reversibility of HU-induced replication inhibition also makes it a common laboratory ingredient used to synchronize cell cycles. On the other hand, prolonged treatment or higher dosage of hydroxyurea causes cell death due to accumulation of DNA damage and oxidative stress. Hydroxyurea treatments are also still far from perfect and it has been suggested that it facilitates skin cancer progression. Also, recent studies have shown that hydroxyurea may affect a larger number of enzymes due to its less specific interaction mechanism, which may contribute to further as-yet unspecified factors affecting cell response. In this review, we examine the actual state of knowledge about hydroxyurea and the mechanisms behind its cytotoxic effects. The practical applications of the recent findings may prove to enhance the already existing use of the drug in new and promising ways.
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20
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De novo deoxyribonucleotide biosynthesis regulates cell growth and tumor progression in small-cell lung carcinoma. Sci Rep 2021; 11:13474. [PMID: 34188151 PMCID: PMC8242079 DOI: 10.1038/s41598-021-92948-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 06/07/2021] [Indexed: 11/09/2022] Open
Abstract
Deoxyribonucleotide biosynthesis from ribonucleotides supports the growth of active cancer cells by producing building blocks for DNA. Although ribonucleotide reductase (RNR) is known to catalyze the rate-limiting step of de novo deoxyribonucleotide triphosphate (dNTP) synthesis, the biological function of the RNR large subunit (RRM1) in small-cell lung carcinoma (SCLC) remains unclear. In this study, we established siRNA-transfected SCLC cell lines to investigate the anticancer effect of silencing RRM1 gene expression. We found that RRM1 is required for the full growth of SCLC cells both in vitro and in vivo. In particular, the deletion of RRM1 induced a DNA damage response in SCLC cells and decreased the number of cells with S phase cell cycle arrest. We also elucidated the overall changes in the metabolic profile of SCLC cells caused by RRM1 deletion. Together, our findings reveal a relationship between the deoxyribonucleotide biosynthesis axis and key metabolic changes in SCLC, which may indicate a possible link between tumor growth and the regulation of deoxyribonucleotide metabolism in SCLC.
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21
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Lamb NA, Bard JE, Buck MJ, Surtees JA. A selection-based next generation sequencing approach to develop robust, genotype-specific mutation profiles in Saccharomyces cerevisiae. G3 GENES|GENOMES|GENETICS 2021; 11:6204636. [PMID: 33784385 PMCID: PMC8495734 DOI: 10.1093/g3journal/jkab099] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/11/2021] [Indexed: 11/13/2022]
Abstract
Distinct mutation signatures arise from environmental exposures and/or from defects in metabolic pathways that promote genome stability. The presence of a particular mutation signature can therefore predict the underlying mechanism of mutagenesis. These insults to the genome often alter dNTP pools, which itself impacts replication fidelity. Therefore, the impact of altered dNTP pools should be considered when making mechanistic predictions based on mutation signatures. We developed a targeted deep-sequencing approach on the CAN1 gene in Saccharomyces cerevisiae to define information-rich mutational profiles associated with distinct rnr1 backgrounds. Mutations in the activity and selectivity sites of rnr1 lead to elevated and/or unbalanced dNTP levels, which compromises replication fidelity and increases mutation rates. The mutation spectra of rnr1Y285F and rnr1Y285A alleles were characterized previously; our analysis was consistent with this prior work but the sequencing depth achieved in our study allowed a significantly more robust and nuanced computational analysis of the variants observed, generating profiles that integrated information about mutation spectra, position effects, and sequence context. This approach revealed previously unidentified, genotype-specific mutation profiles in the presence of even modest changes in dNTP pools. Furthermore, we identified broader sequence contexts and nucleotide motifs that influenced variant profiles in different rnr1 backgrounds, which allowed specific mechanistic predictions about the impact of altered dNTP pools on replication fidelity.
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Affiliation(s)
- Natalie A Lamb
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo (SUNY), Buffalo, NY 14203, USA
| | - Jonathan E Bard
- University at Buffalo Genomics and Bioinformatics Core, Buffalo, NY 14203, USA
- Genetics, Genomics and Bioinformatics Graduate Program, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo (SUNY), Buffalo, NY 14203, USA
| | - Michael J Buck
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo (SUNY), Buffalo, NY 14203, USA
- Genetics, Genomics and Bioinformatics Graduate Program, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo (SUNY), Buffalo, NY 14203, USA
| | - Jennifer A Surtees
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo (SUNY), Buffalo, NY 14203, USA
- Genetics, Genomics and Bioinformatics Graduate Program, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo (SUNY), Buffalo, NY 14203, USA
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22
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Dual roles of SAMHD1 in tumor development and chemoresistance to anticancer drugs. Oncol Lett 2021; 21:451. [PMID: 33907561 PMCID: PMC8063254 DOI: 10.3892/ol.2021.12712] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 03/10/2021] [Indexed: 11/05/2022] Open
Abstract
Human sterile alpha motif and HD-domain-containing protein 1 (SAMHD1) has been identified as a GTP or dGTP-dependent deoxynucleotide triphosphohydrolase (dNTPase) and acts as an antiviral factor against certain retroviruses and DNA viruses. Genetic mutation in SAMHD1 causes the inflammatory Aicardi-Goutières Syndrome and abnormal intracellular deoxyribonucleoside triphosphates (dNTPs) pool. At present, the role of SAMHD1 in numerous types of cancer, such as chronic lymphocytic leukemia, lung cancer and colorectal cancer, is highly studied. Furthermore, it has been found that methylation, acetylation and phosphorylation are involved in the regulation of SAMHD1 expression, and that genetic mutations can cause changes in its activities, including dNTPase activity, long interspersed element type 1 (LINE-1) suppression and DNA damage repair, which could lead to uncontrolled cell cycle progression and cancer development. In addition, SAMHD1 has been reported to have a negative regulatory role in the chemosensitivity to anticancer drugs through its dNTPase activity. The present review aimed to summarize the regulation of SAMHD1 expression in cancer and its function in tumor growth and chemotherapy sensitivity, and discussed controversial points and future directions.
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23
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Purhonen J, Banerjee R, McDonald AE, Fellman V, Kallijärvi J. A sensitive assay for dNTPs based on long synthetic oligonucleotides, EvaGreen dye and inhibitor-resistant high-fidelity DNA polymerase. Nucleic Acids Res 2020; 48:e87. [PMID: 32573728 PMCID: PMC7470940 DOI: 10.1093/nar/gkaa516] [Citation(s) in RCA: 282] [Impact Index Per Article: 70.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/03/2020] [Accepted: 06/05/2020] [Indexed: 12/15/2022] Open
Abstract
Deoxyribonucleoside triphosphates (dNTPs) are vital for the biosynthesis and repair of DNA. Their cellular concentration peaks during the S phase of the cell cycle. In non-proliferating cells, dNTP concentrations are low, making their reliable quantification from tissue samples of heterogeneous cellular composition challenging. Partly because of this, the current knowledge related to the regulation of and disturbances in cellular dNTP concentrations derive mostly from cell culture experiments with little corroboration at the tissue or organismal level. Here, we fill the methodological gap by presenting a simple non-radioactive microplate assay for the quantification of dNTPs with a minimum requirement of 4-12 mg of biopsy material. In contrast to published assays, this assay is based on long synthetic single-stranded DNA templates (50-200 nucleotides), an inhibitor-resistant high-fidelity DNA polymerase, and the double-stranded-DNA-binding EvaGreen dye. The assay quantified reliably less than 50 fmol of each of the four dNTPs and discriminated well against ribonucleotides. Additionally, thermostable RNAse HII-mediated nicking of the reaction products and a subsequent shift in their melting temperature allowed near-complete elimination of the interfering ribonucleotide signal, if present. Importantly, the assay allowed measurement of minute dNTP concentrations in mouse liver, heart and skeletal muscle.
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Affiliation(s)
- Janne Purhonen
- Folkhälsan Research Center, Helsinki, Finland.,Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Finland
| | - Rishi Banerjee
- Folkhälsan Research Center, Helsinki, Finland.,Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Finland
| | | | - Vineta Fellman
- Folkhälsan Research Center, Helsinki, Finland.,Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Finland.,Department of Clinical Sciences, Lund, Pediatrics, Lund University, Sweden.,Children's Hospital, Helsinki University Hospital, Finland
| | - Jukka Kallijärvi
- Folkhälsan Research Center, Helsinki, Finland.,Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Finland
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24
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Tseng YT, Li SW, HuangFu WC, Yen Y, Liu IH. The single nucleotide variant at c.662A>G in human RRM2B is a loss-of-function mutation. Mol Genet Genomic Med 2020; 8:e1497. [PMID: 32931159 PMCID: PMC7667293 DOI: 10.1002/mgg3.1497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 08/14/2020] [Accepted: 08/21/2020] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Mitochondrial DNA maintenance defects (MDMDs) is one of the critical pediatric dysfunction. One of the recent report indicated that a severe patient of MDMDs carries the NP_056528.2:p.Asn221Ser (N221S) variation in the RRM2B gene (NM_015713.5). However, there is no direct evidence demonstrating the nature of the N221S variation. MATERIALS AND METHODS This study aimed to utilize zebrafish and morpholino oligomer (MO) knockdown technique to provide direct evidence for the nature of the N221S variation in the RRM2B. RESULTS The results showed that two distinct MOs were both able to perturb the expression of rrm2b in zebrafish and dose-dependently induced morphological defects. Furthermore, co-injection of human wild-type RRM2B mRNA with MO-e4i4 successfully rescued the developmental defects, whereas co-injection of RRM2B/N221S mRNA with MO-e4i4 did not rescue the developmental defects. CONCLUSION In conclusion, the functional assay in this study provided the direct evidence proving that the N221S variation is a loss-of-function mutation and plausibly related to the pathogenic developmental defects found in the infants of previous clinical reports.
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Affiliation(s)
- Yen-Tzu Tseng
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Shang-Wei Li
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.,Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Wei-Chun HuangFu
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.,Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Yun Yen
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.,Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.,TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, Taiwan.,Cancer Center, Taipei Municipal WanFang Hospital, Taipei, Taiwan
| | - I-Hsuan Liu
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan.,Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan.,School of Veterinary Medicine, National Taiwan University, Taipei, Taiwan
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25
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Li Y, Guo J, Zhang H, Lam CW, Luo W, Zhou H, Zhang W. Protective Effect of Thymidine on DNA Damage Induced by Hydrogen Peroxide in Human Hepatocellular Cancer Cells. ACS OMEGA 2020; 5:21796-21804. [PMID: 32905386 PMCID: PMC7469367 DOI: 10.1021/acsomega.0c02843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 08/04/2020] [Indexed: 06/11/2023]
Abstract
Intracellular ribonucleotide (RN) and deoxyribonucleotide (dRN) pool sizes are critical for the fidelity of DNA synthesis. They are likely to be severely perturbed by many factors which disrupt the integrity and stability of DNA, leading to DNA damage. Exogenously supplied nucleosides are able to increase the deoxynucleoside triphosphate pools, then reverse the DNA damage, and decrease the oncogene-induced transformation dramatically. In this study, the impact of thymidine on the hydrogen peroxide (H2O2)-induced DNA damage was investigated in HepG2 liver cancer cells. From the result of the comet assay, the tail length of cells in the thymidine 600 μM + H2O2 1.0 mM group was dramatically decreased from 42.1 ± 10.8 to 21.9 ± 2.4 μm compared to that exposed with 1.0 mM H2O2 (p < 0.05), suggesting that pretreatment of thymidine reduced the DNA damage of HepG2 cells. Although the RN and dRN contents decreased in the damage group, most of them presented increasing tendency when pretreated with thymidine, especially the key metabolites dCTP, which was mainly related with the decline in the rate of DNA synthesis. The restoration also showed a significant G0/G1 phase arrest of cell cycle progression from 44.6 ± 2.2 to 56.6 ± 0.4% after pretreated with thymidine (p < 0.05). In conclusion, our data demonstrated that the pretreatment with thymidine had a potential protective ability against oxidative damage for DNA in HepG2 cells through the perturbation of RN and dRN pools as well as cell cycle arrest, which should provide new insights into the molecular basis of preventing H2O2-induced oxidative DNA damage in mammalian cells.
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26
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Abstract
The clinical, molecular, and genetic heterogeneity of uterine cervix cancers makes the discovery of effective therapies a challenge. Optimal evaluation of effective radiotherapy-agent combinations requires sophisticated trial strategies from the United States National Cancer Institute and its pharmaceutical collaborators. One strategy involves the phase 0 trial, which falls under the United States Food and Drug Administration Exploratory Investigational New Drug Guidance, or xIND. As currently envisioned for radiotherapy-based trials, the phase 0 trial provides a platform for study of pharmacodynamic effects linked to pharmacokinetic exposures, designed to screen a new experimental agent's dose or schedule, in combination with standard radiotherapy regimens, in a very small number (10-15) of subjects. In the phase 0 trial, radiotherapy-agent combinations are intended to be biologically active, but a new experimental agent's low dose or infrequent schedule is considered nontoxic and nonbeneficial. The phase 0 trial primary endpoint is an individual subject's pharmacodynamic response. Regimens move on from phase 0 trial development if and when a predetermined all-subject pharmacodynamic response rate is crossed. An initial safety experience during and after the radiotherapy-agent combination determines future feasibility. For this article, the clinical example of women with abdominopelvic lymph node-positive uterine cervix cancer is used to elaborate the phase 0 trial approach to the discovery of novel radiosensitizing oncological agents. It is expected that phase 0 radiotherapy-agent trials will become more prevalent in near-term clinical development.
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27
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Song Y, Shvartsman SY. Chemical Embryology Redux: Metabolic Control of Development. Trends Genet 2020; 36:577-586. [PMID: 32532533 PMCID: PMC10947471 DOI: 10.1016/j.tig.2020.05.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/14/2020] [Accepted: 05/18/2020] [Indexed: 11/16/2022]
Abstract
New studies of metabolic reactions and networks in embryos are making important additions to regulatory models of development, so far dominated by genes and signals. Metabolic control of development is not a new idea and can be traced back to Joseph Needham's 'Chemical Embryology', published in the 1930s. Even though Needham's ideas fell by the wayside with the advent of genetic studies of embryogenesis, they demonstrated that embryos provide convenient models for addressing fundamental questions in biochemistry and are now experiencing a comeback, enabled by the powerful merger of detailed mechanistic studies and systems-level techniques. Here we review recent results from studies that quantified the energy budget of embryogenesis in Drosophila and started to untangle the intricate connections between core anabolic processes and developmental transitions. Dynamic coordination of metabolic, genetic, and signaling networks appears to be essential for seamless progression of development.
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Affiliation(s)
- Yonghyun Song
- Computational Sciences Department, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
| | - Stanislav Y Shvartsman
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA; Center for Computational Biology, Flatiron Institute - Simons Foundation, New York, NY 10010, USA.
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28
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Cell-cycle-dependent phosphorylation of RRM1 ensures efficient DNA replication and regulates cancer vulnerability to ATR inhibition. Oncogene 2020; 39:5721-5733. [PMID: 32712628 DOI: 10.1038/s41388-020-01403-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 07/14/2020] [Accepted: 07/20/2020] [Indexed: 11/08/2022]
Abstract
Ribonucleotide reductase (RNR) catalyzes the rate-limiting step of de novo synthesis of deoxyribonucleotide triphosphates (dNTPs) building blocks for DNA synthesis, and is a well-recognized target for cancer therapy. RNR is a heterotetramer consisting of two large RRM1 subunits and two small RRM2 subunits. RNR activity is greatly stimulated by transcriptional activation of RRM2 during S/G2 phase to ensure adequate dNTP supply for DNA replication. However, little is known about the cell-cycle-dependent regulation of RNR activity through RRM1. Here, we report that RRM1 is phosphorylated at Ser 559 by CDK2/cyclin A during S/G2 phase. And this S559 phosphorylation of RRM1enhances RNR enzymatic activity and is required for maintaining sufficient dNTPs during normal DNA replication. Defective RRM1 S559 phosphorylation causes DNA replication stress, double-strand break, and genomic instability. Moreover, combined targeting of RRM1 S559 phosphorylation and ATR triggers lethal replication stress and profound antitumor effects. Thus, this posttranslational phosphorylation of RRM1 provides an alternative mechanism to finely regulating RNR and therapeutic opportunities for cancer treatment.
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29
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DNA Damage Response and Metabolic Reprogramming in Health and Disease. Trends Genet 2020; 36:777-791. [PMID: 32684438 DOI: 10.1016/j.tig.2020.06.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 01/08/2023]
Abstract
Nuclear DNA damage contributes to cellular malfunction and the premature onset of age-related diseases, including cancer. Until recently, the canonical DNA damage response (DDR) was thought to represent a collection of nuclear processes that detect, signal and repair damaged DNA. However, recent evidence suggests that beyond nuclear events, the DDR rewires an intricate network of metabolic circuits, fine-tunes protein synthesis, trafficking, and secretion as well as balances growth with defense strategies in response to genotoxic insults. In this review, we discuss how the active DDR signaling mobilizes extranuclear and systemic responses to promote cellular homeostasis and organismal survival in health and disease.
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30
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Wang L, Sun R, Eriksson S. Basic biochemical characterization of cytosolic enzymes in thymidine nucleotide synthesis in adult rat tissues: implications for tissue specific mitochondrial DNA depletion and deoxynucleoside-based therapy for TK2-deficiency. BMC Mol Cell Biol 2020; 21:33. [PMID: 32345222 PMCID: PMC7189545 DOI: 10.1186/s12860-020-00272-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/31/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Deficiency in thymidine kinase 2 (TK2) or p53 inducible ribonucleotide reductase small subunit (p53R2) is associated with tissue specific mitochondrial DNA (mtDNA) depletion. To understand the mechanisms of the tissue specific mtDNA depletion we systematically studied key enzymes in dTMP synthesis in mitochondrial and cytosolic extracts prepared from adult rat tissues. RESULTS In addition to mitochondrial TK2 a cytosolic isoform of TK2 was characterized, which showed similar substrate specificity to the mitochondrial TK2. Total TK activity was highest in spleen and lowest in skeletal muscle. Thymidylate synthase (TS) was detected in cytosols and its activity was high in spleen but low in other tissues. TS protein levels were high in heart, brain and skeletal muscle, which deviated from TS activity levels. The p53R2 proteins were at similar levels in all tissues except liver where it was ~ 6-fold lower. Our results strongly indicate that mitochondria in most tissues are capable of producing enough dTTP for mtDNA replication via mitochondrial TK2, but skeletal muscle mitochondria do not and are most likely dependent on both the salvage and de novo synthesis pathways. CONCLUSION These results provide important information concerning mechanisms for the tissue dependent variation of dTTP synthesis and explained why deficiency in TK2 or p53R2 leads to skeletal muscle dysfunctions. Furthermore, the presence of a putative cytosolic TK2-like enzyme may provide basic knowledge for the understanding of deoxynucleoside-based therapy for mitochondrial disorders.
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Affiliation(s)
- Liya Wang
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden.
| | - Ren Sun
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
| | - Staffan Eriksson
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
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31
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Forey R, Poveda A, Sharma S, Barthe A, Padioleau I, Renard C, Lambert R, Skrzypczak M, Ginalski K, Lengronne A, Chabes A, Pardo B, Pasero P. Mec1 Is Activated at the Onset of Normal S Phase by Low-dNTP Pools Impeding DNA Replication. Mol Cell 2020; 78:396-410.e4. [PMID: 32169162 DOI: 10.1016/j.molcel.2020.02.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 01/09/2020] [Accepted: 02/24/2020] [Indexed: 10/24/2022]
Abstract
The Mec1 and Rad53 kinases play a central role during acute replication stress in budding yeast. They are also essential for viability in normal growth conditions, but the signal that activates the Mec1-Rad53 pathway in the absence of exogenous insults is currently unknown. Here, we show that this pathway is active at the onset of normal S phase because deoxyribonucleotide triphosphate (dNTP) levels present in G1 phase may not be sufficient to support processive DNA synthesis and impede DNA replication. This activation can be suppressed experimentally by increasing dNTP levels in G1 phase. Moreover, we show that unchallenged cells entering S phase in the absence of Rad53 undergo irreversible fork collapse and mitotic catastrophe. Together, these data indicate that cells use suboptimal dNTP pools to detect the onset of DNA replication and activate the Mec1-Rad53 pathway, which in turn maintains functional forks and triggers dNTP synthesis, allowing the completion of DNA replication.
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Affiliation(s)
- Romain Forey
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | - Ana Poveda
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France; Instituto de Investigación en Salud Pública y Zoonosis, Facultad de Ciencias Químicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Sushma Sharma
- Department of Medical Biochemistry and Biophysics and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Antoine Barthe
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | - Ismael Padioleau
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | - Claire Renard
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | - Robin Lambert
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | - Magdalena Skrzypczak
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Armelle Lengronne
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics and Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Benjamin Pardo
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France.
| | - Philippe Pasero
- Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier, France.
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32
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Sommerville EW, Dalla Rosa I, Rosenberg MM, Bruni F, Thompson K, Rocha M, Blakely EL, He L, Falkous G, Schaefer AM, Yu‐Wai‐Man P, Chinnery PF, Hedstrom L, Spinazzola A, Taylor RW, Gorman GS. Identification of a novel heterozygous guanosine monophosphate reductase (GMPR) variant in a patient with a late-onset disorder of mitochondrial DNA maintenance. Clin Genet 2020; 97:276-286. [PMID: 31600844 PMCID: PMC7004030 DOI: 10.1111/cge.13652] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/18/2019] [Accepted: 09/27/2019] [Indexed: 12/18/2022]
Abstract
Autosomal dominant progressive external ophthalmoplegia (adPEO) is a late-onset, Mendelian mitochondrial disorder characterised by paresis of the extraocular muscles, ptosis, and skeletal-muscle restricted multiple mitochondrial DNA (mtDNA) deletions. Although dominantly inherited, pathogenic variants in POLG, TWNK and RRM2B are among the most common genetic defects of adPEO, identification of novel candidate genes and the underlying pathomechanisms remains challenging. We report the clinical, genetic and molecular investigations of a patient who presented in the seventh decade of life with PEO. Oxidative histochemistry revealed cytochrome c oxidase-deficient fibres and occasional ragged red fibres showing subsarcolemmal mitochondrial accumulation in skeletal muscle, while molecular studies identified the presence of multiple mtDNA deletions. Negative candidate screening of known nuclear genes associated with PEO prompted diagnostic exome sequencing, leading to the prioritisation of a novel heterozygous c.547G>C variant in GMPR (NM_006877.3) encoding guanosine monophosphate reductase, a cytosolic enzyme required for maintaining the cellular balance of adenine and guanine nucleotides. We show that the novel c.547G>C variant causes aberrant splicing, decreased GMPR protein levels in patient skeletal muscle, proliferating and quiescent cells, and is associated with subtle changes in nucleotide homeostasis protein levels and evidence of disturbed mtDNA maintenance in skeletal muscle. Despite confirmation of GMPR deficiency, demonstrating marked defects of mtDNA replication or nucleotide homeostasis in patient cells proved challenging. Our study proposes that GMPR is the 19th locus for PEO and highlights the complexities of uncovering disease mechanisms in late-onset PEO phenotypes.
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Affiliation(s)
- Ewen W. Sommerville
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Ilaria Dalla Rosa
- Department of Clinical and Movement Neurosciences, UCL Queens Square Institute of Neurology, Royal Free CampusUniversity College LondonLondonUK
| | | | - Francesco Bruni
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of Bari “ldo Moro”BariItaly
| | - Kyle Thompson
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Mariana Rocha
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Emma L. Blakely
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Langping He
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Gavin Falkous
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Andrew M. Schaefer
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Patrick Yu‐Wai‐Man
- NIHR Biomedical Research Centre at Moorfields Eye Hospital and UCL Institute of OphthalmologyLondonUK
- MRC Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
- Cambridge Centre for Brain Repair, Department of Clinical NeurosciencesUniversity of CambridgeCambridgeUK
| | - Patrick F. Chinnery
- Department of Clinical Neuroscience & Medical Research Council Mitochondrial Biology UnitSchool of Clinical Medicine, University of CambridgeCambridgeUK
| | - Lizbeth Hedstrom
- Department of BiologyBrandeis UniversityWalthamMA
- Department of ChemistryBrandeis University, 415 South St.WalthamMA
| | - Antonella Spinazzola
- Department of Clinical and Movement Neurosciences, UCL Queens Square Institute of Neurology, Royal Free CampusUniversity College LondonLondonUK
- MRC Centre for Neuromuscular DiseasesUCL Institute of Neurology and National Hospital for Neurology and NeurosurgeryLondonUK
| | - Robert W. Taylor
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Gráinne S. Gorman
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
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33
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Zhang T, Wallis M, Petrovic V, Challis J, Kalitsis P, Hudson DF. Loss of TOP3B leads to increased R-loop formation and genome instability. Open Biol 2019; 9:190222. [PMID: 31795919 PMCID: PMC6936252 DOI: 10.1098/rsob.190222] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 11/01/2019] [Indexed: 12/19/2022] Open
Abstract
Topoisomerase III beta (TOP3B) is one of the least understood members of the topoisomerase family of proteins and remains enigmatic. Our recent data shed light on the function and relevance of TOP3B to disease. A homozygous deletion for the TOP3B gene was identified in a patient with bilateral renal cancer. Analyses in both patient and modelled human cells show the disruption of TOP3B causes genome instability with a rise in DNA damage and chromosome bridging (mis-segregation). The primary molecular defect underlying this pathology is a significant increase in R-loop formation. Our data show that TOP3B is necessary to prevent the accumulation of excessive R-loops and identify TOP3B as a putative cancer gene, and support recent data showing that R-loops are involved in cancer aetiology.
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Affiliation(s)
- Tao Zhang
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria 3052, Australia
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, Victoria 3052, Australia
| | - Mathew Wallis
- Tasmanian Clinical Genetics Services, Royal Hobart Hospital, Hobart, Tasmania 7001, Australia
- School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Vida Petrovic
- Cytogenetics Department, Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria 3052, Australia
| | - Jackie Challis
- Cytogenetics Department, Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria 3052, Australia
| | - Paul Kalitsis
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria 3052, Australia
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, Victoria 3052, Australia
- Cytogenetics Department, Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria 3052, Australia
| | - Damien F. Hudson
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria 3052, Australia
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, Victoria 3052, Australia
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34
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Long MJC, Van Hall-Beauvais A, Aye Y. The more the merrier: how homo-oligomerization alters the interactome and function of ribonucleotide reductase. Curr Opin Chem Biol 2019; 54:10-18. [PMID: 31734537 DOI: 10.1016/j.cbpa.2019.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/03/2019] [Accepted: 09/19/2019] [Indexed: 02/05/2023]
Abstract
Stereotyped as a nexus of dNTP synthesis, the dual-subunit enzyme - ribonucleotide reductase (RNR) - is coming into view as a paradigm of oligomerization and moonlighting behavior. In the present issue of 'omics', we discuss what makes the larger subunit of this enzyme (RNR-α) so interesting, highlighting its emerging cellular interactome based on its unique oligomeric dynamism that dictates its compartment-specific occupations. Linking the history of the field with the multivariable nature of this exceedingly sophisticated enzyme, we further discuss implications of new data pertaining to DNA-damage response, S-phase checkpoints, and ultimately tumor suppression. We hereby hope to provide ideas for those interested in these fields and exemplify conceptual frameworks and tools that are useful to study RNR's broader roles in biology.
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Affiliation(s)
| | - Alexandra Van Hall-Beauvais
- Swiss Federal Institute of Technology Lausanne (EPFL), Institute of Chemical Sciences and Engineering, 1015, Lausanne, Switzerland
| | - Yimon Aye
- Swiss Federal Institute of Technology Lausanne (EPFL), Institute of Chemical Sciences and Engineering, 1015, Lausanne, Switzerland.
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35
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Okonska A, Bühler S, Rao V, Ronner M, Blijlevens M, van der Meulen-Muileman IH, de Menezes RX, Wipplinger M, Oehl K, Smit EF, Weder W, Stahel RA, Penengo L, van Beusechem VW, Felley-Bosco E. Functional Genomic Screen in Mesothelioma Reveals that Loss of Function of BRCA1-Associated Protein 1 Induces Chemoresistance to Ribonucleotide Reductase Inhibition. Mol Cancer Ther 2019; 19:552-563. [PMID: 31619462 DOI: 10.1158/1535-7163.mct-19-0356] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 09/06/2019] [Accepted: 10/10/2019] [Indexed: 11/16/2022]
Abstract
Loss of function of BRCA1-associated protein 1 (BAP1) is observed in about 50% of malignant pleural mesothelioma (MPM) cases. The aim of this study was to investigate whether this aspect could be exploited for targeted therapy. A genetically engineered model was established expressing either functional or nonfunctional BAP1, and whole-genome siRNA synthetic lethality screens were performed assessing differentially impaired survival between the two cell lines. The whole-genome siRNA screen unexpectedly revealed 11 hits (FDR < 0.05) that were more cytotoxic to BAP1-proficient cells. Two actionable targets, ribonucleotide reductase (RNR) catalytic subunit M1 (RRM1) and RNR regulatory subunit M2 (RRM2), were validated. In line with the screen results, primary mesothelioma (BAP1 +/-) overexpressing BAP1 C91A (catalytically dead mutant) was more resistant to RNR inhibition, while BAP1 knockdown in the BAP1-proficient cell lines rescued the cells from their vulnerability to RNR depletion. Gemcitabine and hydroxyurea were more cytotoxic in BAP1-proficient cell line-derived spheroids compared with BAP1 deficient. Upregulation of RRM2 upon gemcitabine and hydroxyurea treatment was more profound in BAP1 mut/del cell lines. Increased lethality mediated by RNR inhibition was observed in NCI-H2452 cells reconstituted with BAP1-WT but not with BAP1 C91A. Upregulation of RRM2 in NCI-H2452-BAP1 WT spheroids was modest compared with control or C91A mutant. Together, we found that BAP1 is involved in the regulation of RNR levels during replication stress. Our observations reveal a potential clinical application where BAP1 status could serve as predictive or stratification biomarker for RNR inhibition-based therapy in MPM.
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Affiliation(s)
- Agata Okonska
- Laboratory of Molecular Oncology, Lungen- und Thoraxonkologie Zentrum, University Hospital Zürich, Zürich, Switzerland
| | - Saskja Bühler
- Laboratory of Molecular Oncology, Lungen- und Thoraxonkologie Zentrum, University Hospital Zürich, Zürich, Switzerland
| | - Vasundhara Rao
- Laboratory of Molecular Oncology, Lungen- und Thoraxonkologie Zentrum, University Hospital Zürich, Zürich, Switzerland
| | - Manuel Ronner
- Laboratory of Molecular Oncology, Lungen- und Thoraxonkologie Zentrum, University Hospital Zürich, Zürich, Switzerland
| | - Maxime Blijlevens
- Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | | | - Renee X de Menezes
- Amsterdam UMC, Vrije Universiteit Amsterdam, Epidemiology and Biostatistics, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Martin Wipplinger
- Laboratory of Molecular Oncology, Lungen- und Thoraxonkologie Zentrum, University Hospital Zürich, Zürich, Switzerland
| | - Kathrin Oehl
- Institute of Pathology and Molecular Pathology, University Hospital Zürich, Zürich, Switzerland
| | - Egbert F Smit
- Department of Thoracic Surgery, NKI, Amsterdam, the Netherlands
| | - Walter Weder
- Department of Thoracic Surgery, University Hospital Zürich, Zürich, Switzerland
| | - Rolf A Stahel
- Lungen- und Thoraxonkologie Zentrum, University Hospital Zürich, 8091 Zürich, Switzerland
| | - Lorenza Penengo
- Institute of Molecular Cancer Research, University of Zürich, Zürich, Switzerland
| | - Victor W van Beusechem
- Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Emanuela Felley-Bosco
- Laboratory of Molecular Oncology, Lungen- und Thoraxonkologie Zentrum, University Hospital Zürich, Zürich, Switzerland.
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36
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Kunos CA, Andrews SJ, Moore KN, Chon HS, Ivy SP. Randomized Phase II Trial of Triapine-Cisplatin-Radiotherapy for Locally Advanced Stage Uterine Cervix or Vaginal Cancers. Front Oncol 2019; 9:1067. [PMID: 31681600 PMCID: PMC6803528 DOI: 10.3389/fonc.2019.01067] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 09/30/2019] [Indexed: 11/13/2022] Open
Abstract
Uterine cervix or vaginal cancers have inherent overactivity of ribonucleotide reductase (RNR), making these cancers rational targets for therapy based on interruption of cisplatin-radiotherapy-induced DNA damage repair. We conducted a pilot, open-label randomized phase II trial to evaluate the efficacy and safety of cisplatin-radiotherapy with or without triapine, a small molecule with RNR-inhibitory activity, in patients with advanced-stage uterine cervix or vaginal cancers (NCT01835171), as a lead in to a randomized phase III study (NCT02466971). A total of 26 women were randomly assigned to receive 6 weeks of daily radiotherapy followed by brachytherapy (80 Gy) and once-weekly cisplatin (40 mg m−2)—with or without three-times weekly intravenous triapine (25 mg m−2)—in one 56-days cycle. Primary end points were metabolic complete response by positron emission tomography and safety. Additional end points included the rate of clinical response, rate of methemoglobinemia, and progression-free survival. The addition of triapine to cisplatin-radiotherapy improved the rate of metabolic complete response from 69 to 92% (P = 0.32) and raised the 3-year progression-free survival estimate from 77 to 92% (hazard ratio for progression, 0.30; P = 0.27). The most frequent grade 3 or 4 adverse events in either treatment group included reversible leukopenia, neutropenia, fatigue, or electrolyte abnormalities. No significant differences were seen between the two groups in the rate of adverse events. Symptomatic methemoglobinemia was not encountered after triapine infusion. In conclusion, the addition of triapine to cisplatin-radiotherapy improved the rate of metabolic complete response in patients with advanced-stage uterine cervix or vaginal cancers without significant toxicity. A phase III trial adequately powered to evaluate progression-free and overall survival is underway (NCT02466971).
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Affiliation(s)
- Charles A Kunos
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD, United States
| | | | - Kathleen N Moore
- University of Oklahoma Stephenson Cancer Center, Oklahoma City, OK, United States
| | - Hye Sook Chon
- H. Lee Moffitt Cancer & Research Institute, Tampa, FL, United States
| | - S Percy Ivy
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD, United States
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37
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Kong Z, Jia S, Chabes AL, Appelblad P, Lundmark R, Moritz T, Chabes A. Simultaneous determination of ribonucleoside and deoxyribonucleoside triphosphates in biological samples by hydrophilic interaction liquid chromatography coupled with tandem mass spectrometry. Nucleic Acids Res 2019; 46:e66. [PMID: 29554314 PMCID: PMC6009580 DOI: 10.1093/nar/gky203] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 03/08/2018] [Indexed: 11/13/2022] Open
Abstract
Information about the intracellular concentration of dNTPs and NTPs is important for studies of the mechanisms of DNA replication and repair, but the low concentration of dNTPs and their chemical similarity to NTPs present a challenge for their measurement. Here, we describe a new rapid and sensitive method utilizing hydrophilic interaction liquid chromatography coupled with tandem mass spectrometry for the simultaneous determination of dNTPs and NTPs in biological samples. The developed method showed linearity (R2 > 0.99) in wide concentration ranges and could accurately quantify dNTPs and NTPs at low pmol levels. The intra-day and inter-day precision were below 13%, and the relative recovery was between 92% and 108%. In comparison with other chromatographic methods, the current method has shorter analysis times and simpler sample pre-treatment steps, and it utilizes an ion-pair-free mobile phase that enhances mass-spectrometric detection. Using this method, we determined dNTP and NTP concentrations in actively dividing and quiescent mouse fibroblasts.
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Affiliation(s)
- Ziqing Kong
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden
| | - Shaodong Jia
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden
| | - Anna Lena Chabes
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden
| | - Patrik Appelblad
- Department of Pharmacology and Clinical Neuroscience, Umeå University, SE-901 87, Umeå, Sweden.,Merck Chemicals and Life Science AB, SE 169-03 Solna, Sweden
| | - Richard Lundmark
- Dept. of Integrative Medical Biology, Umeå University, SE-901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87 Umeå, Sweden
| | - Thomas Moritz
- Umeå Plant Science Centre (UPSC), Dept. of Forest Genetics and Plant Physiology, SLU, SE-901 87 Umeå, Sweden
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87 Umeå, Sweden
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38
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Cohen R, Milo S, Sharma S, Savidor A, Covo S. Ribonucleotide reductase from Fusarium oxysporum does not Respond to DNA replication stress. DNA Repair (Amst) 2019; 83:102674. [PMID: 31375409 DOI: 10.1016/j.dnarep.2019.102674] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 07/22/2019] [Accepted: 07/22/2019] [Indexed: 12/14/2022]
Abstract
Ribonucleotide reductase (RNR) catalyzes the rate limiting step in dNTP biosynthesis and is tightly regulated at the transcription and activity levels. One of the best characterized responses of yeast to DNA damage is up-regulation of RNR transcription and activity and consequently, elevation of the dNTP pools. Hydroxyurea is a universal inhibitor of RNR that causes S phase arrest. It is used in the clinic to treat certain types of cancers. Here we studied the response of the fungal plant pathogen Fusarium oxysporum to hydroxyurea in order to generate hypotheses that can be used in the future in development of a new class of pesticides. F. oxysporum causes severe damage to more than 100 agricultural crops and specifically threatens banana cultivation world-wide. Although the recovery of F. oxysporum from transient hydroxyurea exposure was similar to the one of Saccharomyces cerevisiae, colony formation was strongly inhibited in F. oxysporum in comparison with S. cerevisiae. As expected, genomic and phosphoproteomic analyses of F. oxysporum conidia (spores) exposed to hydroxyurea showed hallmarks of DNA replication perturbation and activation of recombination. Unexpectedly and strikingly, RNR was not induced by either hydroxyurea or the DNA-damaging agent methyl methanesulfonate as determined at the RNA and protein levels. Consequently, dNTP concentrations were significantly reduced, even in response to a low dose of hydroxyurea. Methyl methanesulfonate treatment did not induce dNTP pools in F. oxysporum, in contrast to the response of RNR and dNTP pools to DNA damage and hydroxyurea in several tested organisms. Our results are important because the lack of a feedback mechanism to increase RNR expression in F. oxysporum is expected to sensitize the pathogen to a fungal-specific ribonucleotide inhibitor. The potential impact of our observations on F. oxysporum genome stability and genome evolution is discussed.
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Affiliation(s)
- Rotem Cohen
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University, Rehovot, 76100, Israel
| | - Shira Milo
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University, Rehovot, 76100, Israel
| | - Sushma Sharma
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Alon Savidor
- de Botton Institute for Protein Profiling, the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Shay Covo
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University, Rehovot, 76100, Israel.
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39
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Tran P, Wanrooij PH, Lorenzon P, Sharma S, Thelander L, Nilsson AK, Olofsson AK, Medini P, von Hofsten J, Stål P, Chabes A. De novo dNTP production is essential for normal postnatal murine heart development. J Biol Chem 2019; 294:15889-15897. [PMID: 31300555 DOI: 10.1074/jbc.ra119.009492] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 06/26/2019] [Indexed: 11/06/2022] Open
Abstract
The building blocks of DNA, dNTPs, can be produced de novo or can be salvaged from deoxyribonucleosides. However, to what extent the absence of de novo dNTP production can be compensated for by the salvage pathway is unknown. Here, we eliminated de novo dNTP synthesis in the mouse heart and skeletal muscle by inactivating ribonucleotide reductase (RNR), a key enzyme for the de novo production of dNTPs, at embryonic day 13. All other tissues had normal de novo dNTP synthesis and theoretically could supply heart and skeletal muscle with deoxyribonucleosides needed for dNTP production by salvage. We observed that the dNTP and NTP pools in WT postnatal hearts are unexpectedly asymmetric, with unusually high dGTP and GTP levels compared with those in whole mouse embryos or murine cell cultures. We found that RNR inactivation in heart led to strongly decreased dGTP and increased dCTP, dTTP, and dATP pools; aberrant DNA replication; defective expression of muscle-specific proteins; progressive heart abnormalities; disturbance of the cardiac conduction system; and lethality between the second and fourth weeks after birth. We conclude that dNTP salvage cannot substitute for de novo dNTP synthesis in the heart and that cardiomyocytes and myocytes initiate DNA replication despite an inadequate dNTP supply. We discuss the possible reasons for the observed asymmetry in dNTP and NTP pools in WT hearts.
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Affiliation(s)
- Phong Tran
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden
| | - Paulina H Wanrooij
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden
| | - Paolo Lorenzon
- Department of Integrative Medical Biology (IMB), Umeå University, 901 87 Umeå, Sweden
| | - Sushma Sharma
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden
| | - Lars Thelander
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden
| | - Anna Karin Nilsson
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden
| | - Anna-Karin Olofsson
- Department of Integrative Medical Biology (IMB), Umeå University, 901 87 Umeå, Sweden
| | - Paolo Medini
- Department of Integrative Medical Biology (IMB), Umeå University, 901 87 Umeå, Sweden
| | - Jonas von Hofsten
- Department of Integrative Medical Biology (IMB), Umeå University, 901 87 Umeå, Sweden.,Umeå Centre for Molecular Medicine (UCMM), Umeå University, 901 87 Umeå, Sweden
| | - Per Stål
- Department of Integrative Medical Biology (IMB), Umeå University, 901 87 Umeå, Sweden
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics, Umeå University, 901 87 Umeå, Sweden .,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 901 87 Umeå, Sweden
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40
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The missing link: allostery and catalysis in the anti-viral protein SAMHD1. Biochem Soc Trans 2019; 47:1013-1027. [PMID: 31296733 PMCID: PMC7045340 DOI: 10.1042/bst20180348] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/04/2019] [Accepted: 06/05/2019] [Indexed: 12/11/2022]
Abstract
Vertebrate protein SAMHD1 (sterile-α-motif and HD domain containing protein 1) regulates the cellular dNTP (2′-deoxynucleoside-5′-triphosphate) pool by catalysing the hydrolysis of dNTP into 2′-deoxynucleoside and triphosphate products. As an important regulator of cell proliferation and a key player in dNTP homeostasis, mutations to SAMHD1 are implicated in hypermutated cancers, and germline mutations are associated with Chronic Lymphocytic Leukaemia and the inflammatory disorder Aicardi–Goutières Syndrome. By limiting the supply of dNTPs for viral DNA synthesis, SAMHD1 also restricts the replication of several retroviruses, such as HIV-1, and some DNA viruses in dendritic and myeloid lineage cells and resting T-cells. SAMHD1 activity is regulated throughout the cell cycle, both at the level of protein expression and post-translationally, through phosphorylation. In addition, allosteric regulation further fine-tunes the catalytic activity of SAMHD1, with a nucleotide-activated homotetramer as the catalytically active form of the protein. In cells, GTP and dATP are the likely physiological activators of two adjacent allosteric sites, AL1 (GTP) and AL2 (dATP), that bridge monomer–monomer interfaces to stabilise the protein homotetramer. This review summarises the extensive X-ray crystallographic, biophysical and molecular dynamics experiments that have elucidated important features of allosteric regulation in SAMHD1. We present a comprehensive mechanism detailing the structural and protein dynamics components of the allosteric coupling between nucleotide-induced tetramerization and the catalysis of dNTP hydrolysis by SAMHD1.
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41
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Sengupta R, Coppo L, Mishra P, Holmgren A. Glutathione-glutaredoxin is an efficient electron donor system for mammalian p53R2-R1-dependent ribonucleotide reductase. J Biol Chem 2019; 294:12708-12716. [PMID: 31266802 DOI: 10.1074/jbc.ra119.008752] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 06/28/2019] [Indexed: 01/09/2023] Open
Abstract
Deoxyribonucleotides are DNA building blocks and are produced de novo by reduction of ribose to deoxyribose. This reduction is catalyzed by ribonucleotide reductase (RNR), a heterodimeric tetramer enzyme in mammalian cells, having one of two free radical-containing subunits called R2 and p53R2. R2 is S-phase specific and used for DNA replication, whereas p53R2 functions in DNA repair and mitochondrial DNA synthesis. The larger RNR subunit, R1, has catalytically active cysteine thiols in its buried active site and a C-terminal swinging arm, with a Cys-Leu-Met-Cys sequence suggested to act as a shuttle dithiol/disulfide for electron transport. After each catalytic cycle the active site contains a disulfide, which has to be reduced for turnover. Thioredoxin (Trx) and glutaredoxin (Grx) systems have been implicated as electron donors for the RNR disulfide reduction via the swinging arm. Using mouse R1-R2 and R1-p53R2 complexes, we found here that the catalytic efficiency of the GSH-Grx system is 4-6 times higher than that of the Trx1 system. For both complexes, the V max values for Grx are strongly depended on GSH concentrations. The GSH disulfide resulting from the Grx reaction was reduced by NADPH and GSH reductase and this enzyme was essential because reaction with GSH alone yielded only little activity. These results indicate that C-terminal shuttle dithiols of mammalian R1 have a crucial catalytic role and that the GSH-Grx system favors the R1-p53R2 enzyme for DNA replication in hypoxic conditions, mitochondrial DNA synthesis, and in DNA repair outside the S-phase.
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Affiliation(s)
- Rajib Sengupta
- Department of Medical Biochemistry and Biophysics, Division of Biochemistry, Karolinska Institute, Stockholm SE-17177, Sweden
| | - Lucia Coppo
- Department of Medical Biochemistry and Biophysics, Division of Biochemistry, Karolinska Institute, Stockholm SE-17177, Sweden
| | - Pradeep Mishra
- Department of Medical Biochemistry and Biophysics, Division of Biochemistry, Karolinska Institute, Stockholm SE-17177, Sweden
| | - Arne Holmgren
- Department of Medical Biochemistry and Biophysics, Division of Biochemistry, Karolinska Institute, Stockholm SE-17177, Sweden
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42
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Kunos CA, Capala J, Kohn EC, Ivy SP. Radiopharmaceuticals for Persistent or Recurrent Uterine Cervix Cancer. Front Oncol 2019; 9:560. [PMID: 31297338 PMCID: PMC6607970 DOI: 10.3389/fonc.2019.00560] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 06/10/2019] [Indexed: 01/02/2023] Open
Abstract
Uterine cervix cancers pose therapeutic challenges because of an overactive ribonucleotide reductase, which provides on-demand deoxyribonucleotides for DNA replication or for a DNA damage repair response. Ribonucleotide reductase overactivity bestows cancer cell resistance to the effects of radiotherapy and chemotherapy used to treat disease; but nevertheless, this same biologic overexpression provides opportune vulnerabilities relatively specific to uterine cervix cancers for new therapeutic strategies to take advantage. The discovery of human epidermal growth factor receptor 2 (ErbB2 or HER2) overexpression on metastatic uterine cervix cancer cells provides an opportunity for clinical trials of targeted radiopharmaceuticals in combination with DNA damage response modifying drugs. The National Cancer Institute's clinical trial infrastructure and its experimental therapeutics portfolio can now offer clinical trial evaluation of molecularly-targeted and tolerated radiopharmaceutical-drug combinations for women with persistent or recurrent metastatic uterine cervix cancer. This article discusses the current thinking of the National Cancer Institute in regard to attractive radiopharmaceutical strategies for this disease and others.
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Affiliation(s)
- Charles A Kunos
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD, United States
| | - Jacek Capala
- Radiation Research Program, National Cancer Institute, Bethesda, MD, United States
| | - Elise C Kohn
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD, United States
| | - Susan Percy Ivy
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD, United States
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43
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Wanrooij PH, Chabes A. Ribonucleotides in mitochondrial DNA. FEBS Lett 2019; 593:1554-1565. [PMID: 31093968 DOI: 10.1002/1873-3468.13440] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/09/2019] [Accepted: 05/09/2019] [Indexed: 01/05/2023]
Abstract
The incorporation of ribonucleotides (rNMPs) into DNA during genome replication has gained substantial attention in recent years and has been shown to be a significant source of genomic instability. Studies in yeast and mammals have shown that the two genomes, the nuclear DNA (nDNA) and the mitochondrial DNA (mtDNA), differ with regard to their rNMP content. This is largely due to differences in rNMP repair - whereas rNMPs are efficiently removed from the nuclear genome, mitochondria lack robust mechanisms for removal of single rNMPs incorporated during DNA replication. In this minireview, we describe the processes that determine the frequency of rNMPs in the mitochondrial genome and summarise recent findings regarding the effect of incorporated rNMPs on mtDNA stability and function.
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Affiliation(s)
- Paulina H Wanrooij
- Department of Medical Biochemistry and Biophysics, Umeå University, Sweden
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics, Umeå University, Sweden.,Laboratory for Molecular Infection Medicine Sweden, Umeå University, Sweden
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44
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Assessment of the radioprotective effect of propolis in breast cancer patients undergoing radiotherapy. New perspective for an old honey bee product. JOURNAL OF RADIATION RESEARCH AND APPLIED SCIENCES 2019. [DOI: 10.1016/j.jrras.2016.06.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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45
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Misko TA, Liu YT, Harris ME, Oleinick NL, Pink J, Lee HY, Dealwis CG. Structure-guided design of anti-cancer ribonucleotide reductase inhibitors. J Enzyme Inhib Med Chem 2019; 34:438-450. [PMID: 30734609 PMCID: PMC6328008 DOI: 10.1080/14756366.2018.1545226] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Ribonucleotide reductase (RR) catalyses the rate-limiting step of dNTP synthesis, establishing it as an important cancer target. While RR is traditionally inhibited by nucleoside-based antimetabolites, we recently discovered a naphthyl salicyl acyl hydrazone-based inhibitor (NSAH) that binds reversibly to the catalytic site (C-site). Here we report the synthesis and in vitro evaluation of 13 distinct compounds (TP1-13) with improved binding to hRR over NSAH (TP8), with lower KD’s and more predicted residue interactions. Moreover, TP6 displayed the greatest growth inhibiting effect in the Panc1 pancreatic cancer cell line with an IC50 of 0.393 µM. This represents more than a 2-fold improvement over NSAH, making TP6 the most potent compound against pancreatic cancer emerging from the hydrazone inhibitors. NSAH was optimised by the addition of cyclic and polar groups replacing the naphthyl moiety, which occupies the phosphate-binding pocket in the C-site, establishing a new direction in inhibitor design.
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Affiliation(s)
- Tessianna A Misko
- a Department of Pharmacology, School of Medicine , Case Western Reserve University , Cleveland , OH , USA
| | - Yi-Ting Liu
- b School of Pharmacy, College of Pharmacy , Taipei Medical University , Taipei , Taiwan
| | - Michael E Harris
- c Department of Chemistry , University of Florida , Gainesville , FL , United States
| | - Nancy L Oleinick
- d Department of Radiation Oncology, School of Medicine , Case Western Reserve University , Cleveland , OH , USA
| | - John Pink
- e Case Comprehensive Cancer Center, School of Medicine , Case Western Reserve University , Cleveland , OH , USA
| | - Hsueh-Yun Lee
- b School of Pharmacy, College of Pharmacy , Taipei Medical University , Taipei , Taiwan.,f Ph.D Program in Biotechnology Research and Development, College of Pharmacy , Taipei Medical University , Taipei , Taiwan
| | - Chris G Dealwis
- a Department of Pharmacology, School of Medicine , Case Western Reserve University , Cleveland , OH , USA.,g Department of Chemistry, Center for Proteomics , Case Western Reserve University , Cleveland , OH , USA
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46
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Kunos CA, Capala J, Ivy SP. Radiopharmaceuticals for Relapsed or Refractory Leukemias. Front Oncol 2019; 9:97. [PMID: 30859091 PMCID: PMC6397856 DOI: 10.3389/fonc.2019.00097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Accepted: 02/04/2019] [Indexed: 12/21/2022] Open
Abstract
Radiopharmaceuticals, meaning drugs that hold a radionuclide intended for use in cancer patients for treatment of their disease or for palliation of their disease-related symptoms, have gained new interest for clinical development in adult patients with relapsed or refractory leukemia. About one-third of adult patients outlive their leukemia, with the remainder unable to attain complete remission status following the first phase of treatment due to refractory bone marrow or blood residual microscopic disease. The National Cancer Institute (NCI) Cancer Therapy Evaluation Program conducted 49 phase 1-1b trials in adult patients with leukemia between 1986 and 2017 in an effort to discover tolerated and effective therapeutic drug combinations intended to improve remission and mortality rates. None of these trials involved radiopharmaceuticals. In this article, the NCI perspective on the challenges encountered in and on the future potential of radiopharmaceuticals alone or in combination for adult patients with relapsed or refractory leukemia is discussed. An effort is underway already to build-up the NCI's clinical trial enterprise infrastructure for radiopharmaceutical clinical development.
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Affiliation(s)
- Charles A Kunos
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD, United States
| | - Jacek Capala
- Radiation Research Program, National Cancer Institute, Bethesda, MD, United States
| | - Susan Percy Ivy
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD, United States
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47
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Penque BA, Su L, Wang J, Ji W, Bale A, Luh F, Fulbright RK, Sarmast U, Sega AG, Konstantino M, Spencer-Manzon M, Pierce R, Yen Y, Lakhani SA. A homozygous variant in RRM2B is associated with severe metabolic acidosis and early neonatal death. Eur J Med Genet 2018; 62:103574. [PMID: 30439532 DOI: 10.1016/j.ejmg.2018.11.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 10/23/2018] [Accepted: 11/09/2018] [Indexed: 11/26/2022]
Abstract
RRM2B encodes the crucial p53-inducible ribonucleotide reductase small subunit 2 homolog (p53R2), which is required for DNA synthesis throughout the cell cycle. Mutations in this gene have been associated with a lethal mitochondrial depletion syndrome. Here we present the case of an infant with a novel homozygous p.Asn221Ser mutation in RRM2B who developed hypotonia, failure to thrive, sensorineural hearing loss, and severe metabolic lactic acidosis, ultimately progressing to death at 3 months of age. Through molecular modeling using the X-ray crystal structure of p53R2, we demonstrate that this mutation likely causes disruption of a highly conserved helix region of the protein by altering intramolecular interactions. This report expands our knowledge of potential pathogenic RRM2B mutations as well as our understanding of the molecular function of p53R2 and its role in the pathogenesis of mitochondrial DNA depletion.
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Affiliation(s)
- Brent A Penque
- Pediatric Genomics Discovery Program, Department of Pediatrics, Section of Critical Care Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Leila Su
- Department of Cancer Biology and Drug Discovery, College of Medical Technology, Taipei Medical University, Taipei, 110, Taiwan; Sino-American Cancer Foundation, Temple City, CA, USA
| | - Jianghai Wang
- Department of Cancer Biology and Drug Discovery, College of Medical Technology, Taipei Medical University, Taipei, 110, Taiwan; Sino-American Cancer Foundation, Temple City, CA, USA
| | - Weizhen Ji
- Pediatric Genomics Discovery Program, Department of Pediatrics, Section of Critical Care Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Allen Bale
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Frank Luh
- Department of Cancer Biology and Drug Discovery, College of Medical Technology, Taipei Medical University, Taipei, 110, Taiwan; Sino-American Cancer Foundation, Temple City, CA, USA
| | - Robert K Fulbright
- Department of Radiology and Biomedical Imaging, Yale University School of Medicine, New Haven, CT, USA
| | - Uzair Sarmast
- Department of Radiology and Biomedical Imaging, Yale University School of Medicine, New Haven, CT, USA
| | - Annalisa G Sega
- Pediatric Genomics Discovery Program, Department of Pediatrics, Section of Critical Care Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Monica Konstantino
- Pediatric Genomics Discovery Program, Department of Pediatrics, Section of Critical Care Medicine, Yale University School of Medicine, New Haven, CT, USA
| | | | - Richard Pierce
- Pediatric Genomics Discovery Program, Department of Pediatrics, Section of Critical Care Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Yun Yen
- Department of Cancer Biology and Drug Discovery, College of Medical Technology, Taipei Medical University, Taipei, 110, Taiwan; Sino-American Cancer Foundation, Temple City, CA, USA.
| | - Saquib A Lakhani
- Pediatric Genomics Discovery Program, Department of Pediatrics, Section of Critical Care Medicine, Yale University School of Medicine, New Haven, CT, USA.
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48
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Kimoloi S. Modulation of the de novo purine nucleotide pathway as a therapeutic strategy in mitochondrial myopathy. Pharmacol Res 2018; 138:37-42. [PMID: 30267763 DOI: 10.1016/j.phrs.2018.09.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 09/25/2018] [Accepted: 09/25/2018] [Indexed: 11/17/2022]
Abstract
Mitochondrial myopathy (MM) is characterised by muscle weakness, exercise intolerance and various histopathological changes. Recently, a subset of MM has also been associated with aberrant activation of mammalian target of rapamycin complex 1 (mTORC1) in skeletal muscle. This aberrant mTORC1 activation promotes increased de novo nucleotide synthesis, which contributes to abnormal expansion and imbalance of skeletal muscle deoxyribonucleoside triphosphates (dNTP) pools. However, the exact mechanism via which mTORC1-stimulated de novo nucleotide biosynthesis ultimately disturbs muscle dNTP pools remains unclear. In this article, it is proposed that mTORC1-stimulated de novo nucleotide synthesis in skeletal muscle cells with respiratory chain dysfunction promotes an asymmetric increase of purine nucleotides, probably due to NAD+ deficiency. This in turn could disrupt purine nucleotide-dependent allosteric feedback regulatory mechanisms, ultimately leading to dNTP pools aberration. Pharmacological down-modulation of aminoimidazole carboxamide ribonucleotide transformylase/inosine monophosphate cyclohydrolase (ATIC) activity is also proposed as a potential therapeutic strategy in MM exhibiting mTORC1-driven abnormal metabolic reprogramming, including aberrant dNTPs pools.
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Affiliation(s)
- Sammy Kimoloi
- Center for Physiology and Pathophysiology, Institute of Vegetative Physiology, Medical Faculty, University of Cologne, Robert Koch Street 39, Cologne, Germany; Department of Medical Laboratory Sciences, Masinde Muliro University of Science and Technology, P.O Box 190-50100, Kakamega, Kenya.
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49
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Gustafsson NMS, Färnegårdh K, Bonagas N, Ninou AH, Groth P, Wiita E, Jönsson M, Hallberg K, Lehto J, Pennisi R, Martinsson J, Norström C, Hollers J, Schultz J, Andersson M, Markova N, Marttila P, Kim B, Norin M, Olin T, Helleday T. Targeting PFKFB3 radiosensitizes cancer cells and suppresses homologous recombination. Nat Commun 2018; 9:3872. [PMID: 30250201 PMCID: PMC6155239 DOI: 10.1038/s41467-018-06287-x] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 08/24/2018] [Indexed: 12/16/2022] Open
Abstract
The glycolytic PFKFB3 enzyme is widely overexpressed in cancer cells and an emerging anti-cancer target. Here, we identify PFKFB3 as a critical factor in homologous recombination (HR) repair of DNA double-strand breaks. PFKFB3 rapidly relocates into ionizing radiation (IR)-induced nuclear foci in an MRN-ATM-γH2AX-MDC1-dependent manner and co-localizes with DNA damage and HR repair proteins. PFKFB3 relocalization is critical for recruitment of HR proteins, HR activity, and cell survival upon IR. We develop KAN0438757, a small molecule inhibitor that potently targets PFKFB3. Pharmacological PFKFB3 inhibition impairs recruitment of ribonucleotide reductase M2 and deoxynucleotide incorporation upon DNA repair, and reduces dNTP levels. Importantly, KAN0438757 induces radiosensitization in transformed cells while leaving non-transformed cells unaffected. In summary, we identify a key role for PFKFB3 enzymatic activity in HR repair and present KAN0438757, a selective PFKFB3 inhibitor that could potentially be used as a strategy for the treatment of cancer.
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Affiliation(s)
- Nina M S Gustafsson
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, 171 21, Stockholm, Sweden.
- Kancera AB, Karolinska Science Park, 171 48, Solna, Sweden.
| | - Katarina Färnegårdh
- Kancera AB, Karolinska Science Park, 171 48, Solna, Sweden
- Drug Discovery and Development Platform, Science for Life Laboratory, Department of Organic Chemistry, Stockholm University, Box 1030, S-171 21, Solna, Sweden
| | - Nadilly Bonagas
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, 171 21, Stockholm, Sweden
| | - Anna Huguet Ninou
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, 171 21, Stockholm, Sweden
- Kancera AB, Karolinska Science Park, 171 48, Solna, Sweden
| | - Petra Groth
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, 171 21, Stockholm, Sweden
| | - Elisee Wiita
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, 171 21, Stockholm, Sweden
| | | | - Kenth Hallberg
- SARomics Biostructures AB, Medicon Village, SE-223 81, Lund, Sweden
- Sprint Bioscience, 141 57, Huddinge, Sweden
| | - Jemina Lehto
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, 171 21, Stockholm, Sweden
- Kancera AB, Karolinska Science Park, 171 48, Solna, Sweden
| | - Rosa Pennisi
- Department of Sciences, Roma Tre University, 446 00146 Rome, Italy
| | | | | | - Jessica Hollers
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Johan Schultz
- Kancera AB, Karolinska Science Park, 171 48, Solna, Sweden
| | | | | | - Petra Marttila
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, 171 21, Stockholm, Sweden
| | - Baek Kim
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Pharmacy, Kyung-Hee University, 02447, Seoul, South Korea
| | - Martin Norin
- Kancera AB, Karolinska Science Park, 171 48, Solna, Sweden
| | - Thomas Olin
- Kancera AB, Karolinska Science Park, 171 48, Solna, Sweden
| | - Thomas Helleday
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, 171 21, Stockholm, Sweden.
- Sheffield Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, S10 2RX, Sheffield, UK.
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50
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Pohjoismäki JLO, Forslund JME, Goffart S, Torregrosa-Muñumer R, Wanrooij S. Known Unknowns of Mammalian Mitochondrial DNA Maintenance. Bioessays 2018; 40:e1800102. [DOI: 10.1002/bies.201800102] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 06/18/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Jaakko L. O. Pohjoismäki
- Department of Environmental and Biological Sciences, University of Eastern Finland; 80101 Joensuu Finland
| | | | - Steffi Goffart
- Department of Environmental and Biological Sciences, University of Eastern Finland; 80101 Joensuu Finland
| | - Rubén Torregrosa-Muñumer
- Department of Environmental and Biological Sciences, University of Eastern Finland; 80101 Joensuu Finland
| | - Sjoerd Wanrooij
- Department of Medical Biochemistry and Biophysics, Umeå University; 90187 Umeå Sweden
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