1
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Ding K, Xu Q, Zhang X, Liu S. Metabolomic insights into neurological effects of BDE-47 exposure in the sea cucumber Apostichopus japonicus. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 266:115558. [PMID: 37820477 DOI: 10.1016/j.ecoenv.2023.115558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/21/2023] [Accepted: 10/06/2023] [Indexed: 10/13/2023]
Abstract
The persistent organic pollutant 2,2',4,4'-Tetrabromodiphenyl ether (BDE-47), a prevalent congener among polybrominated diphenyl ethers (PBDEs), exhibits potent bioaccumulation and toxicity. Despite extensive research into the adverse effects of BDE-47, its neurotoxicity in sea cucumbers remains unexplored. Given the crucial role of the sea cucumber's nervous system in survival and adaptation, evaluating the impacts of BDE-47 is vital for sustainable aquaculture and consumption. In this study, we employed ultra-high-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Triple-TOF-MS) to analyze metabolomic changes in neuro-related tissues of Apostichopus japonicus exposed to low (0.1 µg/L), medium (1.0 µg/L), and high (10.0 µg/L) BDE-47 concentrations. We identified significantly changed metabolites in each exposure group (87 in low, 79 in medium, and 102 in high), affecting a variety of physiological processes such as steroid hormone balance, nucleotide metabolism, energy metabolism, neurotransmitter levels, and neuroprotection. In addition, we identified concentration-dependent, common, and some other metabolic responses in the neuro-related tissues. Our findings reveal critical insights into the neurotoxic effects of BDE-47 in sea cucumbers and contribute to risk assessment related to BDE-47 exposure in the sea cucumber industry, paving the way for future neurotoxicological research in invertebrates.
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Affiliation(s)
- Kui Ding
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China; Laboratory of Marine Ecology and Environmental Science, National Laboratory for Marine Science and Technology, Qingdao 266061, China; CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
| | - Qinzeng Xu
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China; Laboratory of Marine Ecology and Environmental Science, National Laboratory for Marine Science and Technology, Qingdao 266061, China
| | - Xuelei Zhang
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China; Laboratory of Marine Ecology and Environmental Science, National Laboratory for Marine Science and Technology, Qingdao 266061, China
| | - Shilin Liu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
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2
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Zhao Y, Tabet D, Rubio Contreras D, Lao L, Kousholt AN, Weile J, Melo H, Hoeg L, Feng S, Coté AG, Lin ZY, Setiaputra D, Jonkers J, Gingras AC, Gómez Herreros F, Roth FP, Durocher D. Genome-scale mapping of DNA damage suppressors through phenotypic CRISPR-Cas9 screens. Mol Cell 2023; 83:2792-2809.e9. [PMID: 37478847 PMCID: PMC10530064 DOI: 10.1016/j.molcel.2023.06.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 04/18/2023] [Accepted: 06/21/2023] [Indexed: 07/23/2023]
Abstract
To maintain genome integrity, cells must accurately duplicate their genome and repair DNA lesions when they occur. To uncover genes that suppress DNA damage in human cells, we undertook flow-cytometry-based CRISPR-Cas9 screens that monitored DNA damage. We identified 160 genes whose mutation caused spontaneous DNA damage, a list enriched in essential genes, highlighting the importance of genomic integrity for cellular fitness. We also identified 227 genes whose mutation caused DNA damage in replication-perturbed cells. Among the genes characterized, we discovered that deoxyribose-phosphate aldolase DERA suppresses DNA damage caused by cytarabine (Ara-C) and that GNB1L, a gene implicated in 22q11.2 syndrome, promotes biogenesis of ATR and related phosphatidylinositol 3-kinase-related kinases (PIKKs). These results implicate defective PIKK biogenesis as a cause of some phenotypes associated with 22q11.2 syndrome. The phenotypic mapping of genes that suppress DNA damage therefore provides a rich resource to probe the cellular pathways that influence genome maintenance.
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Affiliation(s)
- Yichao Zhao
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Daniel Tabet
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | | | - Linjiang Lao
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Arne Nedergaard Kousholt
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Jochen Weile
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada; Donnelly Centre and Department of Computer Science, University of Toronto, 160 College Street, Toronto M5S 3E1, Canada
| | - Henrique Melo
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Lisa Hoeg
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Sumin Feng
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Atina G Coté
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Zhen-Yuan Lin
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Dheva Setiaputra
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Jos Jonkers
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | | | - Frederick P Roth
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada; Donnelly Centre and Department of Computer Science, University of Toronto, 160 College Street, Toronto M5S 3E1, Canada
| | - Daniel Durocher
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada.
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3
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Sun Y, Chang Q, Eerqing N, Hu C. Study of the method of spinal cord neuron culture in Sprague-Dawley rats. IBRAIN 2022; 9:270-280. [PMID: 37786761 PMCID: PMC10527773 DOI: 10.1002/ibra.12085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/08/2022] [Accepted: 12/11/2022] [Indexed: 10/04/2023]
Abstract
This study aimed to explore the method of culture of spinal cord neurons (SPNs) in vitro and to provide prerequisites for studying the molecular mechanism and pharmacological mechanism of spinal cord injury and repair. The spinal cord tissues of neonatal Sprague-Dawley rats were taken and digested by trypsin, followed by cytarabine (Ara-C) to inhibit the proliferation of heterogeneous cells, differential velocity adhesion, and natural growth in neuron-specific medium. Then, the morphology of SPNs was observed. Ara-C treatment inhibited the growth of heterogeneous cells and the growth of spinal neurons. Using the differential velocity adhesion method, it was found that the adhesion time of heterogeneous cells and SPNs was not significantly different, and it could not separate neurons and heterogeneous cells well. A large number of mixed cells gathered and floated, and died on the 18th day. Compared with the 20th day, the cell viability of the 18th day was better (p < 0.001). The natural growth and culture of SPNs in Neurobasal-A medium can yield neurons of higher purity and SPNs from the 12th day to the 18th day can be selected for related in vitro cell experiments.
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Affiliation(s)
- Yi‐Fei Sun
- National‐Local Joint Engineering Research Center of Translational Medicine of Anesthesiology, Institute of Neurological Disease, West China HospitalSichuan UniversityChengduChina
- Center for Epigenetics and Induced Pluripotent Stem Cells, Kennedy Krieger InstituteJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Quan‐Yuan Chang
- Department of AnesthesiologySouthwest Medical UniversityLuzhouChina
| | - Narima Eerqing
- Department of Physics and AstronomyUniversity of ExeterExeterUK
| | - Chang‐Yan Hu
- Animal Zoology DepartmentKunming Medical UniversityKunmingChina
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4
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Nishii R, Mizuno T, Rehling D, Smith C, Clark BL, Zhao X, Brown SA, Smart B, Moriyama T, Yamada Y, Ichinohe T, Onizuka M, Atsuta Y, Yang L, Yang W, Thomas PG, Stenmark P, Kato M, Yang JJ. NUDT15 polymorphism influences the metabolism and therapeutic effects of acyclovir and ganciclovir. Nat Commun 2021; 12:4181. [PMID: 34234136 PMCID: PMC8263746 DOI: 10.1038/s41467-021-24509-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 06/14/2021] [Indexed: 02/05/2023] Open
Abstract
Nucleobase and nucleoside analogs (NNA) are widely used as anti-viral and anti-cancer agents, and NNA phosphorylation is essential for the activity of this class of drugs. Recently, diphosphatase NUDT15 was linked to thiopurine metabolism with NUDT15 polymorphism associated with drug toxicity in patients. Profiling NNA drugs, we identify acyclovir (ACV) and ganciclovir (GCV) as two new NNAs metabolized by NUDT15. NUDT15 hydrolyzes ACV and GCV triphosphate metabolites, reducing their effects against cytomegalovirus (CMV) in vitro. Loss of NUDT15 potentiates cytotoxicity of ACV and GCV in host cells. In hematopoietic stem cell transplant patients, the risk of CMV viremia following ACV prophylaxis is associated with NUDT15 genotype (P = 0.015). Donor NUDT15 deficiency is linked to graft failure in patients receiving CMV-seropositive stem cells (P = 0.047). In conclusion, NUDT15 is an important metabolizing enzyme for ACV and GCV, and NUDT15 variation contributes to inter-patient variability in their therapeutic effects.
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Affiliation(s)
- Rina Nishii
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Takanori Mizuno
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Daniel Rehling
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Colton Smith
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Brandi L Clark
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xujie Zhao
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Scott A Brown
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Brandon Smart
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Takaya Moriyama
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yuji Yamada
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Tatsuo Ichinohe
- Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | | | - Yoshiko Atsuta
- Japanese Data Center for Hematopoietic Cell Transplantation, Aichi, Japan
| | - Lei Yang
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wenjian Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden. .,Department of Experimental Medical Science, Lund University, Lund, Sweden.
| | - Motohiro Kato
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan.
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA. .,Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA. .,Hematological Malignancies Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN, USA.
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5
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Messikommer A, Seipel K, Byrne S, Valk PJM, Pabst T, Luedtke NW. RNA Targeting in Acute Myeloid Leukemia. ACS Pharmacol Transl Sci 2020; 3:1225-1232. [PMID: 33344899 DOI: 10.1021/acsptsci.0c00120] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Indexed: 12/12/2022]
Abstract
Nucleosides and their analogues constitute an essential family of anticancer drugs. DNA has been the presumptive target of the front-line prodrug for acute myeloid leukemia (AML), cytarabine (ara-C), since the 1980s. Here, the biomolecular targeting of ara-C was evaluated in primary white blood cells using the ara-C mimic "AzC" and azide-alkyne "click" reactions. Fluorescent staining and microscopy revealed that metabolic incorporation of AzC into primary white blood cells was unexpectedly enhanced by the DNA polymerase inhibitor aphidicholine. According to RNaseH digestion and pull-down-and-release experiments, AzC was incorporated into short RNA fragments bound to DNA in peripheral blood monocytes (PBMCs) collected from all six healthy human donors tested. Samples from 22 AML patients (French-American-British classes M4 and M5) exhibited much more heterogeneity, with 27% incorporating AzC into RNA and 55% into DNA. The overall survival of AML patients whose samples incorporated AzC into RNA was approximately 3-fold higher as compared to that of the DNA cohort (p ≤ 0.056, χ2 = 3.65). These results suggest that the RNA primers of DNA synthesis are clinically favorable targets of ara-C, and that variable incorporation of nucleoside drugs into DNA versus RNA may enable future patient stratification into treatment-specific subgroups.
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Affiliation(s)
| | - Katja Seipel
- Department of Medical Oncology, University Hospital Inselspital and University of Bern, CH-3010 Bern, Switzerland
| | - Stephen Byrne
- Department of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Peter J M Valk
- Department of Hematology, Erasmus University Medical Center, 3000 CA Rotterdam, Netherlands
| | - Thomas Pabst
- Department of Medical Oncology, University Hospital Inselspital and University of Bern, CH-3010 Bern, Switzerland
| | - Nathan W Luedtke
- Department of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland.,Department of Chemistry, McGill University, Montreal, Quebec H3A 0B8, Canada.,Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec H3A 1A3, Canada
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6
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Structural insights into mutagenicity of anticancer nucleoside analog cytarabine during replication by DNA polymerase η. Sci Rep 2019; 9:16400. [PMID: 31704958 PMCID: PMC6841716 DOI: 10.1038/s41598-019-52703-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/22/2019] [Indexed: 01/08/2023] Open
Abstract
Cytarabine (AraC) is the mainstay chemotherapy for acute myeloid leukemia (AML). Whereas initial treatment with AraC is usually successful, most AML patients tend to relapse, and AraC treatment-induced mutagenesis may contribute to the development of chemo-resistant leukemic clones. We show here that whereas the high-fidelity replicative polymerase Polδ is blocked in the replication of AraC, the lower-fidelity translesion DNA synthesis (TLS) polymerase Polη is proficient, inserting both correct and incorrect nucleotides opposite a template AraC base. Furthermore, we present high-resolution crystal structures of human Polη with a template AraC residue positioned opposite correct (G) and incorrect (A) incoming deoxynucleotides. We show that Polη can accommodate local perturbation caused by the AraC via specific hydrogen bonding and maintain a reaction-ready active site alignment for insertion of both correct and incorrect incoming nucleotides. Taken together, the structures provide a novel basis for the ability of Polη to promote AraC induced mutagenesis in relapsed AML patients.
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7
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Yoon JH, Roy Choudhury J, Prakash L, Prakash S. Translesion synthesis DNA polymerases η, ι, and ν promote mutagenic replication through the anticancer nucleoside cytarabine. J Biol Chem 2019; 294:19048-19054. [PMID: 31685662 DOI: 10.1074/jbc.ra119.011381] [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: 10/07/2019] [Revised: 10/30/2019] [Indexed: 11/06/2022] Open
Abstract
Cytarabine (AraC) is the mainstay for the treatment of acute myeloid leukemia. Although complete remission is observed in a large proportion of patients, relapse occurs in almost all the cases. The chemotherapeutic action of AraC derives from its ability to inhibit DNA synthesis by the replicative polymerases (Pols); the replicative Pols can insert AraCTP at the 3' terminus of the nascent DNA strand, but they are blocked at extending synthesis from AraC. By extending synthesis from the 3'-terminal AraC and by replicating through AraC that becomes incorporated into DNA, translesion synthesis (TLS) DNA Pols could reduce the effectiveness of AraC in chemotherapy. Here we identify the TLS Pols required for replicating through the AraC templating residue and determine their error-proneness. We provide evidence that TLS makes a consequential contribution to the replication of AraC-damaged DNA; that TLS through AraC is conducted by three different pathways dependent upon Polη, Polι, and Polν, respectively; and that TLS by all these Pols incurs considerable mutagenesis. The prominent role of TLS in promoting proficient and mutagenic replication through AraC suggests that TLS inhibition in acute myeloid leukemia patients would increase the effectiveness of AraC chemotherapy; and by reducing mutation formation, TLS inhibition may dampen the emergence of drug-resistant tumors and thereby the high incidence of relapse in AraC-treated patients.
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Affiliation(s)
- Jung-Hoon Yoon
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas 77555
| | - Jayati Roy Choudhury
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas 77555
| | - Louise Prakash
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas 77555
| | - Satya Prakash
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas 77555
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8
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Holzer S, Rzechorzek NJ, Short IR, Jenkyn-Bedford M, Pellegrini L, Kilkenny ML. Structural Basis for Inhibition of Human Primase by Arabinofuranosyl Nucleoside Analogues Fludarabine and Vidarabine. ACS Chem Biol 2019; 14:1904-1912. [PMID: 31479243 PMCID: PMC6757278 DOI: 10.1021/acschembio.9b00367] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 09/03/2019] [Indexed: 12/17/2022]
Abstract
Nucleoside analogues are widely used in clinical practice as chemotherapy drugs. Arabinose nucleoside derivatives such as fludarabine are effective in the treatment of patients with acute and chronic leukemias and non-Hodgkin's lymphomas. Although nucleoside analogues are generally known to function by inhibiting DNA synthesis in rapidly proliferating cells, the identity of their in vivo targets and mechanism of action are often not known in molecular detail. Here we provide a structural basis for arabinose nucleotide-mediated inhibition of human primase, the DNA-dependent RNA polymerase responsible for initiation of DNA synthesis in DNA replication. Our data suggest ways in which the chemical structure of fludarabine could be modified to improve its specificity and affinity toward primase, possibly leading to less toxic and more effective therapeutic agents.
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Affiliation(s)
- Sandro Holzer
- Department
of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.
| | - Neil J. Rzechorzek
- Department
of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.
| | - Isobel R. Short
- Department
of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.
| | - Michael Jenkyn-Bedford
- Department
of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.
| | - Luca Pellegrini
- Department
of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.
| | - Mairi L. Kilkenny
- Department
of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K.
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9
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Tsesmetzis N, Paulin CBJ, Rudd SG, Herold N. Nucleobase and Nucleoside Analogues: Resistance and Re-Sensitisation at the Level of Pharmacokinetics, Pharmacodynamics and Metabolism. Cancers (Basel) 2018; 10:cancers10070240. [PMID: 30041457 PMCID: PMC6071274 DOI: 10.3390/cancers10070240] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 07/18/2018] [Accepted: 07/20/2018] [Indexed: 02/07/2023] Open
Abstract
Antimetabolites, in particular nucleobase and nucleoside analogues, are cytotoxic drugs that, starting from the small field of paediatric oncology, in combination with other chemotherapeutics, have revolutionised clinical oncology and transformed cancer into a curable disease. However, even though combination chemotherapy, together with radiation, surgery and immunotherapy, can nowadays cure almost all types of cancer, we still fail to achieve this for a substantial proportion of patients. The understanding of differences in metabolism, pharmacokinetics, pharmacodynamics, and tumour biology between patients that can be cured and patients that cannot, builds the scientific basis for rational therapy improvements. Here, we summarise current knowledge of how tumour-specific and patient-specific factors can dictate resistance to nucleobase/nucleoside analogues, and which strategies of re-sensitisation exist. We revisit well-established hurdles to treatment efficacy, like the blood-brain barrier and reduced deoxycytidine kinase activity, but will also discuss the role of novel resistance factors, such as SAMHD1. A comprehensive appreciation of the complex mechanisms that underpin the failure of chemotherapy will hopefully inform future strategies of personalised medicine.
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Affiliation(s)
- Nikolaos Tsesmetzis
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, 171 77 Stockholm, Sweden.
| | - Cynthia B J Paulin
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden.
| | - Sean G Rudd
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden.
| | - Nikolas Herold
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, 171 77 Stockholm, Sweden.
- Paediatric Oncology, Theme of Children's and Women's Health, Karolinska University Hospital Solna, 171 76 Stockholm, Sweden.
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10
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Abstract
To maintain genomic stability, ribonucleotide incorporation during DNA synthesis is controlled predominantly at the DNA polymerase level. A steric clash between the 2'-hydroxyl of an incoming ribonucleotide and a bulky active site residue, known as the "steric gate", establishes an effective mechanism for most DNA polymerases to selectively insert deoxyribonucleotides. Recent kinetic, structural, and in vivo studies have illuminated novel features about ribonucleotide exclusion and the mechanistic consequences of ribonucleotide misincorporation on downstream events, such as the bypass of a ribonucleotide in a DNA template and the subsequent extension of the DNA lesion bypass product. These important findings are summarized in this review.
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Affiliation(s)
- Jessica A Brown
- Department of Biochemistry, Ohio State University, Columbus, Ohio 43210, United States
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11
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Cavanaugh NA, Beard WA, Wilson SH. DNA polymerase beta ribonucleotide discrimination: insertion, misinsertion, extension, and coding. J Biol Chem 2010; 285:24457-65. [PMID: 20519499 DOI: 10.1074/jbc.m110.132407] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
DNA polymerases must select nucleotides that preserve Watson-Crick base pairing rules and choose substrates with the correct (deoxyribose) sugar. Sugar discrimination represents a great challenge because ribonucleotide triphosphates are present at much higher cellular concentrations than their deoxy-counterparts. Although DNA polymerases discriminate against ribonucleotides, many therapeutic nucleotide analogs that target polymerases have sugar modifications, and their efficacy depends on their ability to be incorporated into DNA. Here, we investigate the ability of DNA polymerase beta to utilize nucleotides with modified sugars. DNA polymerase beta readily inserts dideoxynucleoside triphosphates but inserts ribonucleotides nearly 4 orders of magnitude less efficiently than natural deoxynucleotides. The efficiency of ribonucleotide insertion is similar to that reported for other DNA polymerases. The poor polymerase-dependent insertion represents a key step in discriminating against ribonucleotides because, once inserted, a ribonucleotide is easily extended. Likewise, a templating ribonucleotide has little effect on insertion efficiency or fidelity. In contrast to insertion and extension of a ribonucleotide, the chemotherapeutic drug arabinofuranosylcytosine triphosphate is efficiently inserted but poorly extended. These results suggest that the sugar pucker at the primer terminus plays a crucial role in DNA synthesis; a 3'-endo sugar pucker facilitates nucleotide insertion, whereas a 2'-endo conformation inhibits insertion.
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Affiliation(s)
- Nisha A Cavanaugh
- Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709-2233, USA
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12
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Cros E, Jordheim L, Dumontet C, Galmarini CM. Problems Related to Resistance to Cytarabine in Acute Myeloid Leukemia. Leuk Lymphoma 2009; 45:1123-32. [PMID: 15359991 DOI: 10.1080/1042819032000159861] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
First-line chemotherapy treatment in acute-myeloid leukemia patients usually consists of a combination of cytarabine (ara-C) and an anthracycline. These regimens induce complete response (CR) rates in 65-80% of newly diagnosed AML patients. However, clinical outcome is unsatisfactory, as most of the patients who achieve a CR will relapse within 2 years from diagnosis, often with resistant disease and poor response to subsequent therapy. Thus, understanding the factors which contribute to the emergence of chemoresistant leukemic cells is essential to improve outcome in patients suffering from this disease. In this review, we highlight the current knowledge concerning the cellular mechanisms of resistance to ara-C. We also discuss possible strategies that may be used to overcome such resistance. Efforts to increase intracellular levels and DNA incorporation of phosphorylated ara-C using pronucleotides of ara-C are very promising. Ara-C combined with agents modulating apototic responses are expected to provide additional benefit. In the same way that combination chemotherapy has provided curative treatment of AML, a multifactorial approach of ara-C resistance should allow significant progress in the treatment of currently chemoresistant disease.
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Affiliation(s)
- Emeline Cros
- INSERM 590. 8, Avenue Rockefeller, 69373 Lyon, France
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13
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Nazarkina ZK, Lavrik OI, Khodyreva SN. Flap endonuclease 1 and its role in eukaryotic DNA metabolism. Mol Biol 2008. [DOI: 10.1134/s0026893308030035] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Batista Lobo S, Denyer M, Britland S, Javid FA. Development of an intestinal cell culture model to obtain smooth muscle cells and myenteric neurones. J Anat 2007; 211:819-29. [PMID: 17979953 PMCID: PMC2375843 DOI: 10.1111/j.1469-7580.2007.00820.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
This paper reports on the development of an entirely new intestinal smooth muscle cell (ISMC) culture model using rat neonates for use in pharmacological research applications. Segments of the duodenum, jejunum and ileum were obtained from Sprague-Dawley rat neonates. The cell extraction technique consisted of ligating both ends of the intestine and incubating (37 degrees C) in 0.25% trypsin for periods of 30-90 min. Isolated cells were suspended in DMEM-HEPES, plated and allowed to proliferate for 7 days. Cell culture quality was assessed via a series of viability tests using the dye exclusion assay. In separate experiments, tissues were exposed to trypsin for varying durations and subsequently histological procedures were applied. Cell purification techniques included differential adhesion technique for minimizing fibroblasts. Selective treatments with neurotoxin scorpion venom (30 microg mL(-1)) and anti-mitotic cytosine arabinoside (6 microm) were also applied to purify respectively ISMC and myenteric neurones selectively. The different cell populations were identified in regard to morphology and growth characteristics via immunocytochemistry using antibodies to smooth muscle alpha-actin, alpha-actinin and serotonin-5HT3 receptors. Based on both viability and cell confluence experiments, results demonstrated that intestinal cells were best obtained from segments of the ileum dissociated in trypsin for 30 min. This provided the optimum parameters to yield highly viable cells and confluent cultures. The finding was further supported by histological studies demonstrating that an optimum incubation time of 30 min is required to isolate viable cells from the muscularis externae layer. When cell cultures were treated with cytosine arabinoside, the non-neuronal cells were abolished, resulting in the proliferation of cell bodies and extended neurites. Conversely, cultures treated with scorpion venom resulted in complete abolition of neurones and proliferation of increasing numbers of ISMC, which were spindle-shaped and uniform throughout the culture. When characterized by immunocytochemistry, neurones were stained with antibody to 5HT3 receptors but not with antibodies to alpha-smooth muscle actin and alpha-actinin. Conversely, ISMC were stained with antibodies to alpha-smooth muscle actin and alpha-actinin but not with antibody to 5HT3 receptors. The present study provides evidence that our method of dissociation and selectively purifying different cell populations will allow for pharmacological investigation of each cell type on different or defined mixtures of different cell types.
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Affiliation(s)
- S Batista Lobo
- School of Pharmacy, University of Bradford and Institute of Pharmaceutical Innovation, Bradford, UK.
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15
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Szantai E, Ronai Z, Sasvari-Szekely M, Bonn G, Guttman A. Multicapillary Electrophoresis Analysis of Single-Nucleotide Sequence Variations in the Deoxycytidine Kinase Gene. Clin Chem 2006; 52:1756-62. [PMID: 16858072 DOI: 10.1373/clinchem.2006.071159] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
Background: Investigation of the genetic background of complex traits is the focus of recent interest, as several common diseases or the individual response to treatments of various illnesses have not yet been explored. These studies require the development and implementation of reliable and large-scale genotyping methods. In this report, we introduce an efficient technique based on PCR–restriction fragment length sequence variation technique for the analysis of the −360CG and −201CT single-nucleotide sequence variations in the deoxycytidine kinase gene.
Methods: A multicapillary gel electrophoresis instrument was used for the size determination of the generated DNA fragments. A healthy Hungarian population of 100 individuals was investigated to determine allele and genotype frequencies for the 2 sequence variations of interest.
Results: We found that the occurrence of the minor allele is rather low, i.e., the frequency of both the −360G and −201T variants is 1%.
Conclusions: Our technique can readily facilitate the analysis of these important sequence variations in other ethnic groups to clarify the role of these sequence variations in conjunction with arabinosylcytosine treatment in acute myeloid leukemia.
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Affiliation(s)
- Eszter Szantai
- Horváth Laboratory of Bioseparation Sciences and Institute of Analytical Chemistry and Radiochemistry, Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innsbruck, Austria
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16
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Szantai E, Ronai Z, Sasvari-Szekely M, Guttman A. Haplotyping of the deoxycytidine kinase gene by multicapillary electrophoresis. Anal Biochem 2006; 352:148-50. [PMID: 16527236 DOI: 10.1016/j.ab.2006.01.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2005] [Revised: 01/13/2006] [Accepted: 01/16/2006] [Indexed: 11/26/2022]
Affiliation(s)
- Eszter Szantai
- Horváth Laboratory of Bioseparation Sciences, Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 66, Innsbruck A-6020, Austria
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Abstract
Disease relapse remains the major cause of treatment failure in adults with acute myeloid leukaemia (AML). This reflects both the failure of current salvage regimens and the absence of effective strategies to secure long-term disease-free survival in those patients who achieve a second remission. Recent progress in understanding the pathogenesis of relapsed disease has enabled the identification of a variety of dysregulated molecular pathways and these now provide a rational basis for the design of novel targeted therapies. At the same time, advances in allogeneic stem-cell transplantation have permitted the extension of the curative potential of allografting to patients in whom it was previously contraindicated. As a result, a range of novel drug and transplant therapies has become available in patients with relapsed AML, and it is realistic to anticipate that a co-ordinated assessment of their clinical and biological impact will provide the basis for the design of future, more effective treatments in relapsed disease.
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Affiliation(s)
- Charles Craddock
- Leukaemia Unit, Department of Haematology, Queen Elizabeth Hospital, Birmingham, UK.
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18
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Shi JY, Shi ZZ, Zhang SJ, Zhu YM, Gu BW, Li G, Bai XT, Gao XD, Hu J, Jin W, Huang W, Chen Z, Chen SJ. Association between single nucleotide polymorphisms in deoxycytidine kinase and treatment response among acute myeloid leukaemia patients. ACTA ACUST UNITED AC 2004; 14:759-68. [PMID: 15564883 DOI: 10.1097/00008571-200411000-00007] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Development of resistance to 1-beta-arabinofuranosylcytosine (AraC) is a major obstacle in the treatment of patients with acute myeloid leukaemia (AML). Deficiency of functional deoxycytidine kinase (dCK) plays an important role in AraC resistance in vitro. We screened 5378 bp sequences of the dCK gene, including all exons and the 5' flanking region, and identified two single nucleotide polymorphisms (SNPs) in the regulatory region (rSNPs) with high allele frequencies. These two rSNPs (-201C>T and -360C>G) formed two major haplotypes. Genotyping with sequencing and MassARRAY system among 122 AML patients showed that those with -360CG/-201CT and -360GG/-201TT compound genotypes (n = 41) displayed a favourable response to chemotherapy whereas those with -360CC/-201CC (n = 81) tended to have a poor response (P = 0.025). Moreover, real-time quantitative reverse transcriptase-polymerase chain reaction showed that patients with -360CG/-201CT and -360GG/-201TT genotypes expressed higher level of dCK mRNA compared to those with the -360CC/-201CC genotype (P = 0.0034). Luciferase-reporter assay showed that dCK 5' regulatory region bearing -360G/-201T genotype alone had an eight-fold greater transcriptional activation activity compared to that with -360C/-201C genotype, whereas co-transfection of both -360G/-201T and -360C/-201C constructs mimicked the heterozygous genotype, which exhibited a four-fold greater activity compared to that with -360C/-201C. These results indicate that rSNP haplotypes of dCK gene may serve as a genetic marker for predicting drug responsiveness, which will be beneficial in establishing more effective AML chemotherapeutic regimens.
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Affiliation(s)
- Jing-Yi Shi
- State Key Laboratory of Medical Genomics Shanghai Institute of Hematology, Shanghai, PR China
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19
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Abstract
One strand of cellular DNA is generated as RNA-initiated discontinuous segments called Okazaki fragments that later are joined. The RNA terminated region is displaced into a 5' single-stranded flap, which is removed by the structure-specific flap endonuclease 1 (FEN1), leaving a nick for ligation. Similarly, in long-patch base excision repair, a damaged nucleotide is displaced into a flap and removed by FEN1. FEN1 is a genome stabilization factor that prevents flaps from equilibrating into structures that lead to duplications and deletions. As an endonuclease, FEN1 enters the flap from the 5' end and then tracks to cleave the flap base. Cleavage is oriented by the formation of a double flap. Analyses of FEN1 crystal structures suggest mechanisms for tracking and cleavage. Some flaps can form self-annealed and template bubble structures that interfere with FEN1. FEN1 interacts with other nucleases and helicases that allow it to act efficiently on structured flaps. Genetic and biochemical analyses continue to reveal many roles of FEN1.
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Affiliation(s)
- Yuan Liu
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA.
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20
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Mourlevat S, Troadec JD, Ruberg M, Michel PP. Prevention of dopaminergic neuronal death by cyclic AMP in mixed neuronal/glial mesencephalic cultures requires the repression of presumptive astrocytes. Mol Pharmacol 2003; 64:578-86. [PMID: 12920193 DOI: 10.1124/mol.64.3.578] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Cyclic AMP-elevating agents are highly effective in preventing the loss of dopaminergic neurons that occurs spontaneously in neuronal-glial mesencephalic cultures. We demonstrate here that cAMP causes a concomitant decline in the number of dividing non-neuronal cells, suggesting that inhibition of proliferation contributes to neuroprotection. Consistent with this hypothesis, a transient treatment with the antimitotic cytosine arabinoside, at concentrations that induce long-term repression of glial cell proliferation, mimicked the neuroprotective action of cAMP and also obviated the need for the cyclic nucleotide. Treatment with cAMP-elevating agents reduced the population of OX-42-positive microglial cells and the number of immature astrocytes expressing vimentin and low levels of the astrocytic marker glial fibrillary acidic protein. The effect on the immature astrocytes, however, seemed essential for neuroprotection. Ciliary neurotrophic factor and leukemia inhibitory factor, which stimulate astrocyte differentiation without reducing cell proliferation, failed to reproduce the protective effects of the cyclic nucleotide. Cyclic AMP did not operate by counteracting the action of the astrocyte mitogen epidermal growth factor or by reducing activation of the mitogen-activated protein kinase signaling pathway. The neuroprotective and antiproliferative actions of cAMP, however, were closely mimicked by olomoucine and roscovitine, potent inhibitors of the cyclin-dependent kinase CDK1 that are structurally related to cAMP. Measurement of CDK1 activity confirmed that neuroprotection was closely correlated with inhibition of this kinase by cAMP. In summary, neuroprotection of mesencephalic dopaminergic neurons by cAMP most probably requires the repression of presumptive astrocytes through inhibition of CDK1.
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Affiliation(s)
- Sophie Mourlevat
- INSERM 289, Experimental Neurology and Therapeutics, Bâtiment Pharmacie, Hôpital de la Salpêtrière, 47 bd de l'Hôpital, 75013 Paris, France
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21
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Galmarini CM, Thomas X, Calvo F, Rousselot P, Rabilloud M, El Jaffari A, Cros E, Dumontet C. In vivo mechanisms of resistance to cytarabine in acute myeloid leukaemia. Br J Haematol 2002; 117:860-8. [PMID: 12060121 DOI: 10.1046/j.1365-2141.2002.03538.x] [Citation(s) in RCA: 134] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Factors that reduce the intracellular concentration of triphosphorylated cytarabine (ara-CTP), the active form of cytarabine (ara-C), may induce chemoresistance in acute myeloid leukaemia (AML) patients. These factors include reduced influx of ara-C by the hENT1 transporter, reduced phosphorylation by deoxycytidine kinase (dCK), and increased degradation by high Km cytoplasmic 5'-nucleotidase (5NT) and/or cytidine deaminase (CDD). Increased levels of DNA polymerase alpha (DNA POL) and reduced levels of topoisomerase I (TOPO I) and topoisomerase II (TOPO II) have also been detected in ara-C-resistant cell lines. To determine whether these factors are implicated in clinical ara-C resistance, we analysed the expression of these parameters at diagnosis, using reverse transcription polymerase chain reaction, in the blast cells of 123 AML patients treated with ara-C. At diagnosis, hENT1, dCK, CDD, 5NT, TOPO I, TOPO II, DNA POL and MDR1 were expressed in 83%, 22%, 7%, 37%, 59%, 37%, 39% and 16% of patients respectively. In univariate analysis, patients with expression of 5NT or DNA POL at diagnosis had significantly shorter disease-free survival (DFS). In multivariate analysis, DNA POL positivity and hENT1 deficiency were related to a shorter DFS. In univariate analysis, patients with 5NT-positive blasts had significantly shorter overall survival (OS). In multivariate analysis, shorter OS was related to DNA POL positivity. These results suggest that expression of DNA POL, 5NT and hENT1 at diagnosis may be resistance mechanisms to ara-C in AML patients.
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Affiliation(s)
- Carlos M Galmarini
- Unité INSERM 453, Laboratoire de Cytologie Analytique, Faculté de Médecine Rockefeller, 8 avenue Rockefeller, 69373 Lyon, France.
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22
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Abstract
DNA primases are enzymes whose continual activity is required at the DNA replication fork. They catalyze the synthesis of short RNA molecules used as primers for DNA polymerases. Primers are synthesized from ribonucleoside triphosphates and are four to fifteen nucleotides long. Most DNA primases can be divided into two classes. The first class contains bacterial and bacteriophage enzymes found associated with replicative DNA helicases. These prokaryotic primases contain three distinct domains: an amino terminal domain with a zinc ribbon motif involved in binding template DNA, a middle RNA polymerase domain, and a carboxyl-terminal region that either is itself a DNA helicase or interacts with a DNA helicase. The second major primase class comprises heterodimeric eukaryotic primases that form a complex with DNA polymerase alpha and its accessory B subunit. The small eukaryotic primase subunit contains the active site for RNA synthesis, and its activity correlates with DNA replication during the cell cycle.
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Affiliation(s)
- D N Frick
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York 10595, USA.
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23
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Carbone GM, Catapano CV, Fernandes DJ. Imbalanced DNA synthesis induced by cytosine arabinoside and fludarabine in human leukemia cells11Abbreviations: araC, 1-β-d-arabinofuranosylcytosine (cytosine arabinoside); araA, 1-β-d-arabinofuranosyladenine; BrdUrd, 5-bromo-2′-deoxyuridine; FaraA, 1-β-d-arabinofuranosyl-2-fluoroadenine (fludarabine); ic50, concentration that reduces cloning efficiency by 50%; GAPDH, glyceraldehyde-3-phosphate dehydrogenase; PALA, N-(phosphonacetyl)-l-aspartate; and SSC, standard saline citrate. Biochem Pharmacol 2001; 62:101-10. [PMID: 11377401 DOI: 10.1016/s0006-2952(01)00637-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Previous studies have demonstrated that cytosine arabinoside (araC) induces an accumulation of Okazaki fragments, while fludarabine (FaraA) inhibits Okazaki fragment synthesis. We extended these observations in the present study to provide insights into various mechanisms by which these anticancer drugs affect DNA replication and induce genomic instability in human CEM leukemia cells. Neither araC nor FaraA induced a detectable amount of re-replicated DNA in S-phase cells, which indicated that drug-induced alterations in Okazaki fragment synthesis were not accompanied by DNA re-replication. Synthesis on both leading and lagging DNA strands within the c-myc locus was measured in cells incubated with equitoxic concentrations of araC or FaraA. In araC-treated cells, nascent DNA from the lagging strand was enriched about 5-fold compared with the leading strand. In contrast, FaraA did not induce any replication imbalance. AraC- and FaraA induced changes in the frequency of N-(phosphonacetyl)-l-aspartate (PALA) resistance and the extent of CAD gene amplification were monitored as markers of drug-induced genomic instability. At concentrations that reduced cloning efficiency by 50% (IC(50)), araC increased the frequency of PALA resistance about 4-fold, while FaraA did not have a significant effect on the frequency of PALA resistance. Pretreatment with araC also increased the extent of CAD gene amplification. We propose that the imbalanced DNA synthesis induced by araC leads to the accumulation of Okazaki fragments on the lagging arms and single-stranded DNA regions on the leading arms of replication forks. The formation of these abnormal replication structures was associated with the generation of genomic instability.
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Affiliation(s)
- G M Carbone
- Department of Experimental Oncology, Hollings Cancer Center, Medical University of South Carolina, 86 Jonathan Lucas Street, P.O. Box 250955, Charleston, SC 29425, USA
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24
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Veuger MJ, Honders MW, Landegent JE, Willemze R, Barge RM. A novel RT-PCR-based protein activity truncation assay for direct assessment of deoxycytidine kinase in small numbers of purified leukemic cells. Leukemia 2000; 14:1678-84. [PMID: 10995016 DOI: 10.1038/sj.leu.2401880] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In vitro studies have demonstrated that deoxycytidine kinase (dCK) plays a crucial role in the mechanism of resistance to cytarabine (AraC). The resistant phenotype in vitro is always a result of mutational inactivation of dCK, leading to defects in the metabolic pathways of AraC. Although inactivation of dCK has shown to be one of the major mechanism of resistance to AraC in vitro, limited in vivo data are available. To improve research concerning the involvement of dCK inactivation in patients with acute myeloid leukemia (AML), we have set up a protocol that allows direct assessment of dCK expression and activity in primary human cells. In this protein activity truncation assay (PAT assay), the complete coding region of dCK is amplified by RT-PCR and a T7 RNA polymerase promoter sequence is introduced upstream of the coding region in a nested PCR reaction. After in vitro transcription-translation dCK proteins are analyzed for their molecular weight and phosphorylating capacities. We show that this relatively quick method can be used in purified, primary human leukemic blasts. In addition, inactivation of dCK by point mutations, deletions or genomic rearrangements can easily be detected in AraC-resistant cell lines. This novel assay may contribute to further elucidate the mechanism of AraC resistance in vivo.
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Affiliation(s)
- M J Veuger
- Department of Hematology, Leiden University Medical Center, The Netherlands
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25
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High incidence of alternatively spliced forms of deoxycytidine kinase in patients with resistant acute myeloid leukemia. Blood 2000. [DOI: 10.1182/blood.v96.4.1517.h8001517_1517_1524] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Deficiency of functional deoxycytidine kinase (dCK) is a common characteristic for in vitro resistance to cytarabine (AraC). To investigate whether dCK is also a target for induction of AraC resistance in patients with acute myeloid leukemia (AML), we determined dCK messenger RNA (mRNA) expression in (purified) leukemic blasts and phytohemagglutinin-stimulated T cells (PHA T cells) from patients with chemotherapy-sensitive and chemotherapy-resistant AML. In control samples from healthy donors (PHA T cells and bone marrow), only wild-type dCK complementary DNA (cDNA) was amplified. Also, in (purified) leukemic blasts from patients with sensitive AML, only wild-type dCK cDNAs were observed. These cDNAs coded for active dCK proteins in vitro. However, in 7 of 12 (purified) leukemic blast samples from patients with resistant AML, additional polymerase chain reaction fragments with a deletion of exon 5, exons 3 to 4, exons 3 to 6, or exons 2 to 6 were detected in coexpression with wild-type dCK. Deletion of exons 3 to 6 was also identified in 6 of 12 PHA T cells generated from the patients with resistant AML. The deleted dCK mRNAs were formed by alternative splicing and did code for inactive dCK proteins in vitro. These findings suggest that the presence of inactive, alternatively spliced dCK mRNA transcripts in resistant AML blasts may contribute to the process of AraC resistance in patients with AML.
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26
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High incidence of alternatively spliced forms of deoxycytidine kinase in patients with resistant acute myeloid leukemia. Blood 2000. [DOI: 10.1182/blood.v96.4.1517] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AbstractDeficiency of functional deoxycytidine kinase (dCK) is a common characteristic for in vitro resistance to cytarabine (AraC). To investigate whether dCK is also a target for induction of AraC resistance in patients with acute myeloid leukemia (AML), we determined dCK messenger RNA (mRNA) expression in (purified) leukemic blasts and phytohemagglutinin-stimulated T cells (PHA T cells) from patients with chemotherapy-sensitive and chemotherapy-resistant AML. In control samples from healthy donors (PHA T cells and bone marrow), only wild-type dCK complementary DNA (cDNA) was amplified. Also, in (purified) leukemic blasts from patients with sensitive AML, only wild-type dCK cDNAs were observed. These cDNAs coded for active dCK proteins in vitro. However, in 7 of 12 (purified) leukemic blast samples from patients with resistant AML, additional polymerase chain reaction fragments with a deletion of exon 5, exons 3 to 4, exons 3 to 6, or exons 2 to 6 were detected in coexpression with wild-type dCK. Deletion of exons 3 to 6 was also identified in 6 of 12 PHA T cells generated from the patients with resistant AML. The deleted dCK mRNAs were formed by alternative splicing and did code for inactive dCK proteins in vitro. These findings suggest that the presence of inactive, alternatively spliced dCK mRNA transcripts in resistant AML blasts may contribute to the process of AraC resistance in patients with AML.
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Cline SD, Osheroff N. Cytosine arabinoside lesions are position-specific topoisomerase II poisons and stimulate DNA cleavage mediated by the human type II enzymes. J Biol Chem 1999; 274:29740-3. [PMID: 10514448 DOI: 10.1074/jbc.274.42.29740] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cytosine arabinoside (araC) is an important drug used for the treatment of human leukemias. In order to exert its cytotoxic effects, araC must be incorporated into chromosomal DNA. Although specific DNA lesions that involve base loss or modification stimulate nucleic acid cleavage mediated by type II topoisomerases, the effects of deoxyribose sugar ring modification on enzyme activity have not been examined. Therefore, the effects of incorporated araC residues on the DNA cleavage/religation equilibrium of human topoisomerase IIalpha and beta were characterized. AraC lesions were position-specific topoisomerase II poisons and stimulated DNA scission mediated by both human type II enzymes. However, the positional specificity of araC residues differed from that previously reported for other cleavage-enhancing DNA lesions. Finally, additive or synergistic increases in DNA cleavage were observed in the presence of araC lesions and etoposide. These findings broaden the range of DNA lesions known to alter topoisomerase II function and raise the possibility that this enzyme may mediate some of the cellular effects of araC.
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Affiliation(s)
- S D Cline
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA
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28
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Mazur DJ, Perrino FW. Identification and expression of the TREX1 and TREX2 cDNA sequences encoding mammalian 3'-->5' exonucleases. J Biol Chem 1999; 274:19655-60. [PMID: 10391904 DOI: 10.1074/jbc.274.28.19655] [Citation(s) in RCA: 210] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The 3'-->5' exonucleases catalyze the excision of nucleoside monophosphates from the 3' termini of DNA. We have identified the cDNA sequences encoding two 3'-->5' exonucleases (TREX1 and TREX2) from mammalian cells. The TREX1 and TREX2 proteins are 304 and 236 amino acids in length, respectively. Analysis of the TREX1 and TREX2 sequences identifies three conserved motifs that likely generate the exonuclease active site in these enzymes. The specific amino acids in these three conserved motifs suggest that these mammalian exonucleases are most closely related to the proofreading exonucleases of the bacterial replicative DNA polymerases and the RNase T enzymes. Expression of TREX1 and TREX2 in Escherichia coli demonstrates that these recombinant proteins are active 3'-->5' exonucleases. The recombinant TREX1 protein was purified, and exonuclease activity was measured using single-stranded, partial duplex, and mispaired oligonucleotide DNA substrates. The greatest activity of the TREX1 protein was detected using a partial duplex DNA containing five mispaired nucleotides at the 3' terminus. No activity was detected using single-stranded RNA or an RNA-DNA partial duplex. Identification of the TREX1 and TREX2 cDNA sequences provides the genetic tools to investigate the physiological roles of these exonucleases in mammalian DNA replication, repair, and recombination pathways.
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Affiliation(s)
- D J Mazur
- Wake Forest University School of Medicine, Department of Biochemistry, Winston-Salem, North Carolina 27157, USA
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29
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Braess J, Wegendt C, Feuring-Buske M, Riggert J, Kern W, Hiddemann W, Schleyer E. Leukaemic blasts differ from normal bone marrow mononuclear cells and CD34+ haemopoietic stem cells in their metabolism of cytosine arabinoside. Br J Haematol 1999. [DOI: 10.1111/j.1365-2141.1999.01338.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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