51
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Wei Z, Shen X, Ni B, Luo G, Tian Y, Sun Y. Contribution of hepatitis B virus X protein-induced aberrant microRNA expression to hepatocellular carcinoma pathogenesis. ACTA ACUST UNITED AC 2019; 43:113-123. [PMID: 31320813 PMCID: PMC6620039 DOI: 10.3906/biy-1807-196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The hepatitis B virus-encoded X (HBX) protein plays important roles in Hepatocellular carcinoma (HCC). Previous studies have demonstrated that HBX can induce alterations in the expression of numerous microRNAs (miRNAs) involved in the carcinogenesis of various tumors. However, the global profile of liver miRNA changes induced by HBX has not been characterized. In this study, we conducted a miRNA microarray analysis to investigate the influence of HBX on the expression of total miRNAs in liver in relation to HCC. Comparative analysis of the data from human normal liver cells (L02) and human HCC cells (HepG2), with or without HBX, identified 19 differentially expressed miRNAs, including 5 with known association to HBX. Target gene prediction for the aberrantly expressed miRNAs identified a total of 304 potential target genes, involved in sundry pathways. Finally, pathway analysis of the HBXinduced miRNAs pathway showed that 5 of the total miRNAs formed an internetwork, suggesting that HBX might exert its pathological effects on hepatic cells through functional synergy with miRNAs that regulated common pathways in liver cells. Therefore, this work provides new insights into the mechanisms of HCC as well as potential diagnostic markers or therapeutic targets for use in clinical management of HCC.
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Affiliation(s)
- Zhiyuan Wei
- Institute of Immunology, PLA, Army Medical University (Third Military Medical University) , Chongqing , P.R. China.,Southwest Hospital, Army Medical University (Third Military Medical University) , Chongqing , P. R. China
| | - Xiaohe Shen
- Department of Microbiology and Immunology, Shanxi Medical University , Taiyuan, Shanxi , P.R. China
| | - Bing Ni
- Department of Pathophysiology and High Altitude Pathology, Army Medical University (Third Military Medical University) , Chongqing , P.R. China.,Institute of Immunology, PLA, Army Medical University (Third Military Medical University) , Chongqing , P.R. China
| | - Gaoxing Luo
- Southwest Hospital, Army Medical University (Third Military Medical University) , Chongqing , P. R. China
| | - Yi Tian
- Institute of Immunology, PLA, Army Medical University (Third Military Medical University) , Chongqing , P.R. China
| | - Yi Sun
- Southwest Hospital, Army Medical University (Third Military Medical University) , Chongqing , P. R. China
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52
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Shishodia S, Zhang D, El-Sagheer AH, Brown T, Claridge TDW, Schofield CJ, Hopkinson RJ. NMR analyses on N-hydroxymethylated nucleobases - implications for formaldehyde toxicity and nucleic acid demethylases. Org Biomol Chem 2018; 16:4021-4032. [PMID: 29767200 PMCID: PMC5977384 DOI: 10.1039/c8ob00734a] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 03/29/2018] [Indexed: 12/14/2022]
Abstract
Formaldehyde is produced in cells by enzyme-catalysed demethylation reactions, including those occurring on N-methylated nucleic acids. Formaldehyde reacts with nucleobases to form N-hydroxymethylated adducts that may contribute to its toxicity/carcinogenicity when added exogenously, but the chemistry of these reactions has been incompletely defined. We report NMR studies on the reactions of formaldehyde with canonical/modified nucleobases. The results reveal that hydroxymethyl hemiaminals on endocyclic nitrogens, as observed with thymidine and uridine monophosphates, are faster to form than equivalent hemiaminals on exocyclic nitrogens; however, the exocyclic adducts, as formed with adenine, guanine and cytosine, are more stable in solution. Nucleic acid demethylase (FTO)-catalysed hydroxylation of (6-methyl)adenosine results in (6-hydroxymethyl)adenosine as the major observed product; by contrast no evidence for a stable 3-hydroxymethyl adduct was accrued with FTO-catalysed oxidation of (3-methyl)thymidine. Collectively, our results imply N-hydroxymethyled adducts of nucleic acid bases, formed either by reactions with formaldehyde or via demethylase catalysis, have substantially different stabilities, with some being sufficiently stable to have functional roles in disease or the regulation of nucleic acid/nucleobase activity.
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Affiliation(s)
- S. Shishodia
- Chemistry Research Laboratory
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
| | - D. Zhang
- Chemistry Research Laboratory
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
| | - A. H. El-Sagheer
- Chemistry Research Laboratory
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
- Chemistry Branch, Department of Science and Mathematics
, Faculty of Petroleum and Mining Engineering
, Suez University
,
43721 Suez
, Egypt
| | - T. Brown
- Chemistry Research Laboratory
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
| | - T. D. W. Claridge
- Chemistry Research Laboratory
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
| | - C. J. Schofield
- Chemistry Research Laboratory
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
| | - R. J. Hopkinson
- Chemistry Research Laboratory
,
12 Mansfield Road
, Oxford
, OX1 3TA
, UK
- Leicester Institute of Structural and Chemical Biology and Department of Chemistry
, University of Leicester
,
Henry Wellcome Building
, Lancaster Road
, Leicester
, LE1 7RH
, UK
.
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53
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Parashar S, Cheishvili D, Mahmood N, Arakelian A, Tanvir I, Khan HA, Kremer R, Mihalcioiu C, Szyf M, Rabbani SA. DNA methylation signatures of breast cancer in peripheral T-cells. BMC Cancer 2018; 18:574. [PMID: 29776342 PMCID: PMC5960123 DOI: 10.1186/s12885-018-4482-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 05/07/2018] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Immune surveillance acts as a defense mechanism in cancer, and its disruption is involved in cancer progression. DNA methylation reflects the phenotypic identity of cells and recent data suggested that DNA methylation profiles of T cells and peripheral blood mononuclear cells (PBMC) are altered in cancer progression. METHODS We enrolled 19 females with stage 1 and 2, nine with stage 3 and 4 and 9 age matched healthy women. T cells were isolated from peripheral blood and extracted DNA was subjected to Illumina 450 K DNA methylation array analysis. Raw data was analyzed by BMIQ, ChAMP and ComBat followed by validation of identified genes by pyrosequencing. RESULTS Analysis of data revealed ~ 10,000 sites that correlated with breast cancer progression and established a list of 89 CG sites that were highly correlated (p < 0.01, r > 0.7, r < - 0.7) with breast cancer progression. The vast majority of these sites were hypomethylated and enriched in genes with functions in the immune system. CONCLUSIONS The study points to the possibility of using DNA methylation signatures as a noninvasive method for early detection of breast cancer and its progression which need to be tested in clinical studies.
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Affiliation(s)
- Surabhi Parashar
- Department of Medicine, McGill University Health Center, 1001 Décarie Blvd., Room EM1.3232, Montréal, QC, H4A3J1, Canada
| | - David Cheishvili
- Department of Pharmacology and Therapeutics, McGill University Health Center, Montreal, QC, Canada.,Present address: Montreal EpiTerapia Inc., Montreal, QC, Canada
| | - Niaz Mahmood
- Department of Medicine, McGill University Health Center, 1001 Décarie Blvd., Room EM1.3232, Montréal, QC, H4A3J1, Canada
| | - Ani Arakelian
- Department of Medicine, McGill University Health Center, 1001 Décarie Blvd., Room EM1.3232, Montréal, QC, H4A3J1, Canada
| | | | | | - Richard Kremer
- Department of Medicine, McGill University Health Center, 1001 Décarie Blvd., Room EM1.3232, Montréal, QC, H4A3J1, Canada
| | - Catalin Mihalcioiu
- Department of Medicine, McGill University Health Center, 1001 Décarie Blvd., Room EM1.3232, Montréal, QC, H4A3J1, Canada
| | - Moshe Szyf
- Department of Pharmacology and Therapeutics, McGill University Health Center, Montreal, QC, Canada
| | - Shafaat A Rabbani
- Department of Medicine, McGill University Health Center, 1001 Décarie Blvd., Room EM1.3232, Montréal, QC, H4A3J1, Canada.
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54
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Papaluca A, Wagner JR, Saragovi HU, Ramotar D. UNG-1 and APN-1 are the major enzymes to efficiently repair 5-hydroxymethyluracil DNA lesions in C. elegans. Sci Rep 2018; 8:6860. [PMID: 29717169 PMCID: PMC5931555 DOI: 10.1038/s41598-018-25124-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/13/2018] [Indexed: 11/16/2022] Open
Abstract
In Caenorhabditis elegans, two DNA glycosylases, UNG-1 and NTH-1, and two AP endonucleases, APN-1 and EXO-3, have been characterized from the base-excision repair (BER) pathway that repairs oxidatively modified DNA bases. UNG-1 removes uracil, while NTH-1 can remove 5-hydroxymethyluracil (5-hmU), an oxidation product of thymine, as well as other lesions. Both APN-1 and EXO-3 can incise AP sites and remove 3′-blocking lesions at DNA single strand breaks, and only APN-1 possesses 3′- to 5′-exonulease and nucleotide incision repair activities. We used C. elegans mutants to study the role of the BER pathway in processing 5-hmU. We observe that ung-1 mutants exhibited a decrease in brood size and lifespan, and an elevated level of germ cell apoptosis when challenged with 5-hmU. These phenotypes were exacerbated by RNAi downregulation of apn-1 in the ung-1 mutant. The nth-1 or exo-3 mutants displayed wild type phenotypes towards 5-hmU. We show that partially purified UNG-1 can act on 5-hmU lesion in vitro. We propose that UNG-1 removes 5-hmU incorporated into the genome and the resulting AP site is cleaved by APN-1 or EXO-3. In the absence of UNG-1, the 5-hmU is removed by NTH-1 creating a genotoxic 3′-blocking lesion that requires the action of APN-1.
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Affiliation(s)
- Arturo Papaluca
- Maisonneuve-Rosemont Hospital, Research Center, Université de Montréal, Department of Medicine, 5415 Boul. de l'Assomption, Montréal, Québec, H1T2M4, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Department of Pharmacology and Therapeutics, McGill University, Department of Pharmacology and Therapeutics, 3755 Chemin de la Côte Sainte-Catherine, Québec, Montréal, H3T1E2, Canada
| | - J Richard Wagner
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12 Avenue Nord, Sherbrooke, Québec, J1H5N4, Canada
| | - H Uri Saragovi
- Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Department of Pharmacology and Therapeutics, McGill University, Department of Pharmacology and Therapeutics, 3755 Chemin de la Côte Sainte-Catherine, Québec, Montréal, H3T1E2, Canada
| | - Dindial Ramotar
- Maisonneuve-Rosemont Hospital, Research Center, Université de Montréal, Department of Medicine, 5415 Boul. de l'Assomption, Montréal, Québec, H1T2M4, Canada.
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55
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Dattani A, Sridhar D, Aziz Aboobaker A. Planarian flatworms as a new model system for understanding the epigenetic regulation of stem cell pluripotency and differentiation. Semin Cell Dev Biol 2018; 87:79-94. [PMID: 29694837 DOI: 10.1016/j.semcdb.2018.04.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 04/21/2018] [Indexed: 12/11/2022]
Abstract
Planarian flatworms possess pluripotent stem cells (neoblasts) that are able to differentiate into all cell types that constitute the adult body plan. Consequently, planarians possess remarkable regenerative capabilities. Transcriptomic studies have revealed that gene expression is coordinated to maintain neoblast pluripotency, and ensure correct lineage specification during differentiation. But as yet they have not revealed how this regulation of expression is controlled. In this review, we propose that planarians represent a unique and effective system to study the epigenetic regulation of these processes in an in vivo context. We consolidate evidence suggesting that although DNA methylation is likely present in some flatworm lineages, it does not regulate neoblast function in Schmidtea mediterranea. A number of phenotypic studies have documented the role of histone modification and chromatin remodelling complexes in regulating distinct neoblast processes, and we focus on four important examples of planarian epigenetic regulators: Nucleosome Remodeling Deacetylase (NuRD) complex, Polycomb Repressive Complex (PRC), the SET1/MLL methyltransferases, and the nuclear PIWI/piRNA complex. Given the recent advent of ChIP-seq in planarians, we propose future avenues of research that will identify the genomic targets of these complexes allowing for a clearer picture of how neoblast processes are coordinated at the epigenetic level. These insights into neoblast biology may be directly relevant to mammalian stem cells and disease. The unique biology of planarians will also allow us to investigate how extracellular signals feed into epigenetic regulatory networks to govern concerted neoblast responses during regenerative polarity, tissue patterning, and remodelling.
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Affiliation(s)
- Anish Dattani
- Department of Zoology, South Parks Road, University of Oxford, OX1 3PS, UK.
| | - Divya Sridhar
- Department of Zoology, South Parks Road, University of Oxford, OX1 3PS, UK
| | - A Aziz Aboobaker
- Department of Zoology, South Parks Road, University of Oxford, OX1 3PS, UK.
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56
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Hu J, Guan W, Liu P, Dai J, Tang K, Xiao H, Qian Y, Sharrow AC, Ye Z, Wu L, Xu H. Endoglin Is Essential for the Maintenance of Self-Renewal and Chemoresistance in Renal Cancer Stem Cells. Stem Cell Reports 2018; 9:464-477. [PMID: 28793246 PMCID: PMC5550272 DOI: 10.1016/j.stemcr.2017.07.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 07/10/2017] [Accepted: 07/11/2017] [Indexed: 12/26/2022] Open
Abstract
Renal cell carcinoma (RCC) is a deadly malignancy due to its tendency to metastasize and resistance to chemotherapy. Stem-like tumor cells often confer these aggressive behaviors. We discovered an endoglin (CD105)-expressing subpopulation in human RCC xenografts and patient samples with a greater capability to form spheres in vitro and tumors in mice at low dilutions than parental cells. Knockdown of CD105 by short hairpin RNA and CRISPR/cas9 reduced stemness markers and sphere-formation ability while accelerating senescence in vitro. Importantly, downregulation of CD105 significantly decreased the tumorigenicity and gemcitabine resistance. This loss of stem-like properties can be rescued by CDA, MYC, or NANOG, and CDA might act as a demethylase maintaining MYC and NANOG. In this study, we showed that Endoglin (CD105) expression not only demarcates a cancer stem cell subpopulation but also confers self-renewal ability and contributes to chemoresistance in RCC.
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Affiliation(s)
- Junhui Hu
- Department of Urology and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan 430030, China; Department of Pediatric Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan 430030, China; Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Wei Guan
- Department of Urology and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan 430030, China
| | - Peijun Liu
- Department of Urology and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan 430030, China
| | - Jin Dai
- Department of Urology, The First Affiliated Hospital of Yangtze University, Jingzhou 434000, China
| | - Kun Tang
- Department of Urology and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan 430030, China
| | - Haibing Xiao
- Department of Urology and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan 430030, China
| | - Yuan Qian
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Allison C Sharrow
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Zhangqun Ye
- Department of Urology and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan 430030, China
| | - Lily Wu
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA; Department of Urology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA.
| | - Hua Xu
- Department of Urology and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology (HUST), Wuhan 430030, China.
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57
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Lavelle D, Engel JD, Saunthararajah Y. Fetal Hemoglobin Induction by Epigenetic Drugs. Semin Hematol 2018; 55:60-67. [PMID: 29958562 DOI: 10.1053/j.seminhematol.2018.04.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 04/13/2018] [Indexed: 12/11/2022]
Abstract
Fetal hemoglobin (HbF) inhibits the root cause of sickle pathophysiology, sickle hemoglobin polymerization. Individuals who naturally express high levels of HbF beyond infancy thus receive some protection from sickle complications. To mimic this natural genetic experiment using drugs, one guiding observation was that HbF is increased during recovery of bone marrow from extreme stress. This led to evaluation and approval of the cytotoxic (cell killing) drug hydroxyurea to treat sickle cell disease. Cytotoxic approaches are limited in potency and sustainability, however, since they require hematopoietic reserves sufficient to repeatedly mount recoveries from stress that destroys their counterparts, and such reserves are finite. HbF induction even by stress ultimately involves chromatin remodeling of the gene for HbF (HBG), therefore, a logical alternative approach is to directly inhibit epigenetic enzymes that repress HBG-implicated enzymes include DNA methyltransferase 1, histone deacetylases, lysine demethylase 1, protein arginine methyltransferase 5, euchromatic histone lysine methyltransferase 2 and chromodomain helicase DNA-binding protein 4. Clinical proof-of-principle that this alternative, noncytotoxic approach can generate substantial HbF and total hemoglobin increases has already been generated. Thus, with continued careful attention to fundamental biological and pharmacologic considerations (reviewed herein), there is potential that rational, molecular-targeted, safe and highly potent disease-modifying therapy can be realized for patients with sickle cell disease, with the accessibility and cost-effective properties needed for world-wide effect.
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Affiliation(s)
- Donald Lavelle
- Department of Medicine, University of Illinois Hospital and Health Sciences System, Chicago, IL; Department of Medicine, Jesse Brown VA Medical Center, Chicago, IL
| | | | - Yogen Saunthararajah
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH.
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58
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Jiang HP, Xiong J, Liu FL, Ma CJ, Tang XL, Yuan BF, Feng YQ. Modified nucleoside triphosphates exist in mammals. Chem Sci 2018; 9:4160-4167. [PMID: 29780546 PMCID: PMC5941283 DOI: 10.1039/c7sc05472f] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 03/31/2018] [Indexed: 12/21/2022] Open
Abstract
By establishing a chemical labeling method in combination with liquid chromatography-mass spectrometry analysis, we reported the widespread existence of various modified nucleoside triphosphates in eukaryotes.
DNA and RNA contain diverse chemical modifications that exert important influences in a variety of cellular processes. In addition to enzyme-mediated modifications of DNA and RNA, previous in vitro studies showed that pre-modified nucleoside triphosphates (NTPs) can be incorporated into DNA and RNA during replication and transcription. Herein, we established a chemical labeling method in combination with liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS) analysis for the determination of endogenous NTPs in the mammalian cells and tissues. We synthesized 8-(diazomethyl)quinoline (8-DMQ) that could efficiently react with the phosphate group under mild condition to label NTPs. The developed method allowed sensitive detection of NTPs, with the detection limits improved by 56–137 folds. The results showed that 12 types of endogenous modified NTPs were distinctly determined in the mammalian cells and tissues. In addition, the majority of these modified NTPs exhibited significantly decreased contents in human hepatocellular carcinoma (HCC) tissues compared to tumor-adjacent normal tissues. Taken together, our study revealed the widespread existence of various modified NTPs in eukaryotes.
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Affiliation(s)
- Han-Peng Jiang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , Department of Chemistry , Wuhan University , Wuhan 430072 , P. R. China . ; ; Tel: +86-27-68755595
| | - Jun Xiong
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , Department of Chemistry , Wuhan University , Wuhan 430072 , P. R. China . ; ; Tel: +86-27-68755595
| | - Fei-Long Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , Department of Chemistry , Wuhan University , Wuhan 430072 , P. R. China . ; ; Tel: +86-27-68755595
| | - Cheng-Jie Ma
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , Department of Chemistry , Wuhan University , Wuhan 430072 , P. R. China . ; ; Tel: +86-27-68755595
| | - Xing-Lin Tang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , Department of Chemistry , Wuhan University , Wuhan 430072 , P. R. China . ; ; Tel: +86-27-68755595
| | - Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , Department of Chemistry , Wuhan University , Wuhan 430072 , P. R. China . ; ; Tel: +86-27-68755595
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education) , Department of Chemistry , Wuhan University , Wuhan 430072 , P. R. China . ; ; Tel: +86-27-68755595
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59
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Gonzalez C, Sanchez A, Collins J, Lisova K, Lee JT, Michael van Dam R, Alejandro Barbieri M, Ramachandran C, Wnuk SF. The 4-N-acyl and 4-N-alkyl gemcitabine analogues with silicon-fluoride-acceptor: Application to 18F-Radiolabeling. Eur J Med Chem 2018; 148:314-324. [PMID: 29471120 PMCID: PMC5841594 DOI: 10.1016/j.ejmech.2018.02.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 01/24/2018] [Accepted: 02/06/2018] [Indexed: 01/05/2023]
Abstract
The coupling of gemcitabine with functionalized carboxylic acids using peptide coupling conditions afforded 4-N-alkanoyl analogues with a terminal alkyne or azido moiety. Reaction of 4-N-tosylgemcitabine with azidoalkyl amine provided 4-N-alkyl gemcitabine with a terminal azido group. Click reaction with silane building blocks afforded 4-N-alkanoyl or 4-N-alkyl gemcitabine analogues suitable for fluorination. RP-HPLC analysis indicated better chemical stability of 4-N-alkyl gemcitabine analogues versus 4-N-alkanoyl analogues in acidic aqueous conditions. The 4-N-alkanoyl gemcitabine analogues showed potent cytostatic activity against L1210 cell line, but cytotoxicity of the 4-N-alkylgemcitabine analogues was low. However, 4-N-alkanoyl and 4-N-alkyl analogues had comparable antiproliferative activities in the HEK293 cells. The 4-N-alkyl analogue with a terminal azide group was shown to be localized inside HEK293 cells by fluorescence microscopy after labelling with Fluor 488-alkyne. The [18F]4-N-alkyl or alkanoyl silane gemcitabine analogues were successfully synthesized using microscale and conventional silane-labeling radiochemical protocols. Preliminary positron-emission tomography (PET) imaging in mice showed the biodistribution of [18F]4-N-alkyl to have initial concentration in the liver, kidneys and GI tract followed by increasing signal in the bone.
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Affiliation(s)
- Cesar Gonzalez
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, 33199, United States
| | - Andersson Sanchez
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, 33199, United States
| | - Jeffrey Collins
- Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, United States
| | - Ksenia Lisova
- Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, United States; Physics & Biology in Medicine Interdepartmental Graduate Program, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, United States
| | - Jason T Lee
- Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, United States
| | - R Michael van Dam
- Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, United States; Physics & Biology in Medicine Interdepartmental Graduate Program, David Geffen School of Medicine, UCLA, Los Angeles, CA, 90095, United States
| | - M Alejandro Barbieri
- Department of Biological Sciences, Florida International University, Miami, FL, 33199, United States
| | | | - Stanislaw F Wnuk
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, 33199, United States.
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61
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Carell T, Kurz MQ, Müller M, Rossa M, Spada F. Non-canonical Bases in the Genome: The Regulatory Information Layer in DNA. Angew Chem Int Ed Engl 2018; 57:4296-4312. [DOI: 10.1002/anie.201708228] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Thomas Carell
- Center for Integrated Protein Science; Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstrasse 5-13 81377 Munich Germany
| | - Matthias Q. Kurz
- Center for Integrated Protein Science; Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstrasse 5-13 81377 Munich Germany
| | - Markus Müller
- Center for Integrated Protein Science; Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstrasse 5-13 81377 Munich Germany
| | - Martin Rossa
- Center for Integrated Protein Science; Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstrasse 5-13 81377 Munich Germany
| | - Fabio Spada
- Center for Integrated Protein Science; Department of Chemistry; Ludwig-Maximilians-Universität München; Butenandtstrasse 5-13 81377 Munich Germany
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62
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Schmidt V, Nagar R, Martinez LA. Control of Nucleotide Metabolism Enables Mutant p53's Oncogenic Gain-of-Function Activity. Int J Mol Sci 2017; 18:ijms18122759. [PMID: 29257071 PMCID: PMC5751358 DOI: 10.3390/ijms18122759] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/06/2017] [Accepted: 12/08/2017] [Indexed: 12/25/2022] Open
Abstract
Since its discovery as an oncoprotein in 1979, investigation into p53's many identities has completed a full circle and today it is inarguably the most extensively studied tumor suppressor (wild-type p53 form or WTp53) and oncogene (mutant p53 form or mtp53) in cancer research. After the p53 protein was declared "Molecule of the Year" by Science in 1993, the p53 field exploded and a plethora of excellent reviews is now available on every aspect of p53 genetics and functional repertoire in a cell. Nevertheless, new functions of p53 continue to emerge. Here, we discuss a novel mechanism that contributes to mtp53's Gain of Functions GOF (gain-of-function) activities and involves the upregulation of both nucleotide de novo synthesis and nucleoside salvage pathways.
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Affiliation(s)
- Valentina Schmidt
- Department of Pathology, Stony Brook University, Stony Brook, NY 11794, USA.
| | - Rachana Nagar
- Department of Pathology, Stony Brook University, Stony Brook, NY 11794, USA.
| | - Luis A Martinez
- Department of Pathology, Stony Brook University, Stony Brook, NY 11794, USA.
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63
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Schaich MA, Smith MR, Cloud AS, Holloran SM, Freudenthal BD. Structures of a DNA Polymerase Inserting Therapeutic Nucleotide Analogues. Chem Res Toxicol 2017; 30:1993-2001. [PMID: 28862449 PMCID: PMC6494084 DOI: 10.1021/acs.chemrestox.7b00173] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Members of the nucleoside analogue class of cancer therapeutics compete with canonical nucleotides to disrupt numerous cellular processes, including nucleotide homeostasis, DNA and RNA synthesis, and nucleotide metabolism. Nucleoside analogues are triphosphorylated and subsequently inserted into genomic DNA, contributing to the efficacy of therapeutic nucleosides in multiple ways. In some cases, the altered base acts as a mutagen, altering the DNA sequence to promote cellular death; in others, insertion of the altered nucleotide triggers DNA repair pathways, which produce lethal levels of cytotoxic intermediates such as single and double stranded DNA breaks. As a prerequisite to many of these biological outcomes, the modified nucleotide must be accommodated in the DNA polymerase active site during nucleotide insertion. Currently, the molecular contacts that mediate DNA polymerase insertion of modified nucleotides remain unknown for multiple therapeutic compounds, despite decades of clinical use. To determine how modified bases are inserted into duplex DNA, we used mammalian DNA polymerase β (pol β) to visualize the structural conformations of four therapeutically relevant modified nucleotides, 6-thio-2'-deoxyguanosine-5'-triphosphate (6-TdGTP), 5-fluoro-2'-deoxyuridine-5'-triphosphate (5-FdUTP), 5-formyl-deoxycytosine-5'-triphosphate (5-FodCTP), and 5-formyl-deoxyuridine-5'-triphosphate (5-FodUTP). Together, the structures reveal a pattern in which the modified nucleotides utilize Watson-Crick base pairing interactions similar to that of unmodified nucleotides. The nucleotide modifications were consistently positioned in the major groove of duplex DNA, accommodated by an open cavity in pol β. These results provide novel information for the rational design of new therapeutic nucleoside analogues and a greater understanding of how modified nucleotides are tolerated by polymerases.
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Affiliation(s)
| | | | | | | | - Bret D. Freudenthal
- Corresponding Author 4015 Wahl Hall West, Laboratory of Genome Maintenance and Structural Biology, Department of Biochemistry and Molecular Biology, and Department of Cancer Biology, University of Kansas Medical Center Kansas City, Kansas 66160. Phone: 913-588-5560,
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64
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Schutsky EK, Nabel CS, Davis A, DeNizio JE, Kohli RM. APOBEC3A efficiently deaminates methylated, but not TET-oxidized, cytosine bases in DNA. Nucleic Acids Res 2017; 45:7655-7665. [PMID: 28472485 PMCID: PMC5570014 DOI: 10.1093/nar/gkx345] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 04/18/2017] [Indexed: 12/21/2022] Open
Abstract
AID/APOBEC family enzymes are best known for deaminating cytosine bases to uracil in single-stranded DNA, with characteristic sequence preferences that can produce mutational signatures in targets such as retroviral and cancer cell genomes. These deaminases have also been proposed to function in DNA demethylation via deamination of either 5-methylcytosine (mC) or TET-oxidized mC bases (ox-mCs), which include 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine. One specific family member, APOBEC3A (A3A), has been shown to readily deaminate mC, raising the prospect of broader activity on ox-mCs. To investigate this claim, we developed a novel assay that allows for parallel profiling of activity on all modified cytosines. Our steady-state kinetic analysis reveals that A3A discriminates against all ox-mCs by >3700-fold, arguing that ox-mC deamination does not contribute substantially to demethylation. A3A is, by contrast, highly proficient at C/mC deamination. Under conditions of excess enzyme, C/mC bases can be deaminated to completion in long DNA segments, regardless of sequence context. Interestingly, under limiting A3A, the sequence preferences observed with targeting unmodified cytosine are further exaggerated when deaminating mC. Our study informs how methylation, oxidation, and deamination can interplay in the genome and suggests A3A's potential utility as a biotechnological tool to discriminate between cytosine modification states.
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Affiliation(s)
- Emily K. Schutsky
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christopher S. Nabel
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Amy K. F. Davis
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jamie E. DeNizio
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rahul M. Kohli
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
- To whom correspondence should be addressed. Tel: +1 215 573 7523; Fax: +1 215 348 5111;
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65
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Luengo A, Gui DY, Vander Heiden MG. Targeting Metabolism for Cancer Therapy. Cell Chem Biol 2017; 24:1161-1180. [PMID: 28938091 PMCID: PMC5744685 DOI: 10.1016/j.chembiol.2017.08.028] [Citation(s) in RCA: 614] [Impact Index Per Article: 87.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 08/06/2017] [Accepted: 08/30/2017] [Indexed: 12/11/2022]
Abstract
Metabolic reprogramming contributes to tumor development and introduces metabolic liabilities that can be exploited to treat cancer. Chemotherapies targeting metabolism have been effective cancer treatments for decades, and the success of these therapies demonstrates that a therapeutic window exists to target malignant metabolism. New insights into the differential metabolic dependencies of tumors have provided novel therapeutic strategies to exploit altered metabolism, some of which are being evaluated in preclinical models or clinical trials. Here, we review our current understanding of cancer metabolism and discuss how this might guide treatments targeting the metabolic requirements of tumor cells.
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Affiliation(s)
- Alba Luengo
- The Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Dan Y Gui
- The Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Matthew G Vander Heiden
- The Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Dana-Farber Cancer Institute, Boston, MA 02115, USA.
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66
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Molokie R, Lavelle D, Gowhari M, Pacini M, Krauz L, Hassan J, Ibanez V, Ruiz MA, Ng KP, Woost P, Radivoyevitch T, Pacelli D, Fada S, Rump M, Hsieh M, Tisdale JF, Jacobberger J, Phelps M, Engel JD, Saraf S, Hsu LL, Gordeuk V, DeSimone J, Saunthararajah Y. Oral tetrahydrouridine and decitabine for non-cytotoxic epigenetic gene regulation in sickle cell disease: A randomized phase 1 study. PLoS Med 2017; 14:e1002382. [PMID: 28880867 PMCID: PMC5589090 DOI: 10.1371/journal.pmed.1002382] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 08/03/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Sickle cell disease (SCD), a congenital hemolytic anemia that exacts terrible global morbidity and mortality, is driven by polymerization of mutated sickle hemoglobin (HbS) in red blood cells (RBCs). Fetal hemoglobin (HbF) interferes with this polymerization, but HbF is epigenetically silenced from infancy onward by DNA methyltransferase 1 (DNMT1). METHODS AND FINDINGS To pharmacologically re-induce HbF by DNMT1 inhibition, this first-in-human clinical trial (NCT01685515) combined 2 small molecules-decitabine to deplete DNMT1 and tetrahydrouridine (THU) to inhibit cytidine deaminase (CDA), the enzyme that otherwise rapidly deaminates/inactivates decitabine, severely limiting its half-life, tissue distribution, and oral bioavailability. Oral decitabine doses, administered after oral THU 10 mg/kg, were escalated from a very low starting level (0.01, 0.02, 0.04, 0.08, or 0.16 mg/kg) to identify minimal doses active in depleting DNMT1 without cytotoxicity. Patients were SCD adults at risk of early death despite standard-of-care, randomized 3:2 to THU-decitabine versus placebo in 5 cohorts of 5 patients treated 2X/week for 8 weeks, with 4 weeks of follow-up. The primary endpoint was ≥ grade 3 non-hematologic toxicity. This endpoint was not triggered, and adverse events (AEs) were not significantly different in THU-decitabine-versus placebo-treated patients. At the decitabine 0.16 mg/kg dose, plasma concentrations peaked at approximately 50 nM (Cmax) and remained elevated for several hours. This dose decreased DNMT1 protein in peripheral blood mononuclear cells by >75% and repetitive element CpG methylation by approximately 10%, and increased HbF by 4%-9% (P < 0.001), doubling fetal hemoglobin-enriched red blood cells (F-cells) up to approximately 80% of total RBCs. Total hemoglobin increased by 1.2-1.9 g/dL (P = 0.01) as reticulocytes simultaneously decreased; that is, better quality and efficiency of HbF-enriched erythropoiesis elevated hemoglobin using fewer reticulocytes. Also indicating better RBC quality, biomarkers of hemolysis, thrombophilia, and inflammation (LDH, bilirubin, D-dimer, C-reactive protein [CRP]) improved. As expected with non-cytotoxic DNMT1-depletion, platelets increased and neutrophils concurrently decreased, but not to an extent requiring treatment holds. As an early phase study, limitations include small patient numbers at each dose level and narrow capacity to evaluate clinical benefits. CONCLUSION Administration of oral THU-decitabine to patients with SCD was safe in this study and, by targeting DNMT1, upregulated HbF in RBCs. Further studies should investigate clinical benefits and potential harms not identified to date. TRIAL REGISTRATION ClinicalTrials.gov, NCT01685515.
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Affiliation(s)
- Robert Molokie
- Department of Medicine, University of Illinois Hospital and Health Sciences System, Chicago, Illinois, United States of America
- Jesse Brown VA Medical Center, Chicago, Illinois, United States of America
| | - Donald Lavelle
- Department of Medicine, University of Illinois Hospital and Health Sciences System, Chicago, Illinois, United States of America
- Jesse Brown VA Medical Center, Chicago, Illinois, United States of America
| | - Michel Gowhari
- Department of Medicine, University of Illinois Hospital and Health Sciences System, Chicago, Illinois, United States of America
| | - Michael Pacini
- Department of Medicine, University of Illinois Hospital and Health Sciences System, Chicago, Illinois, United States of America
| | - Lani Krauz
- Department of Medicine, University of Illinois Hospital and Health Sciences System, Chicago, Illinois, United States of America
| | - Johara Hassan
- Department of Medicine, University of Illinois Hospital and Health Sciences System, Chicago, Illinois, United States of America
| | - Vinzon Ibanez
- Jesse Brown VA Medical Center, Chicago, Illinois, United States of America
| | - Maria A. Ruiz
- Jesse Brown VA Medical Center, Chicago, Illinois, United States of America
| | - Kwok Peng Ng
- Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Philip Woost
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Tomas Radivoyevitch
- Department of Quantitative Health Sciences, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Daisy Pacelli
- Department of Medicine, University of Illinois Hospital and Health Sciences System, Chicago, Illinois, United States of America
| | - Sherry Fada
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Matthew Rump
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Matthew Hsieh
- Molecular and Clinical Hematology Section, National Institutes of Health, Bethesda, Maryland, United States of America
| | - John F. Tisdale
- Molecular and Clinical Hematology Section, National Institutes of Health, Bethesda, Maryland, United States of America
| | - James Jacobberger
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Mitch Phelps
- College of Pharmacy, The Ohio State University, Columbus, Ohio, United States of America
| | - James Douglas Engel
- Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Santhosh Saraf
- Department of Medicine, University of Illinois Hospital and Health Sciences System, Chicago, Illinois, United States of America
| | - Lewis L. Hsu
- Department of Medicine, University of Illinois Hospital and Health Sciences System, Chicago, Illinois, United States of America
| | - Victor Gordeuk
- Department of Medicine, University of Illinois Hospital and Health Sciences System, Chicago, Illinois, United States of America
| | - Joseph DeSimone
- Department of Medicine, University of Illinois Hospital and Health Sciences System, Chicago, Illinois, United States of America
| | - Yogen Saunthararajah
- Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
- Department of Hematology and Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, United States of America
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Hoffmann JS, Cordelier P. Proper sister chromatid disjunction requires CDA and PARP-1. Cell Cycle 2017; 16:1239-1240. [PMID: 28598299 DOI: 10.1080/15384101.2017.1326767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Jean-Sébastien Hoffmann
- a Equipe « Labellisée Ligue contre le Cancer», Laboratoire d'excellence TOUCAN , INSERM U 1037; CNRS ERL 5294; CRCT (Cancer Research Center of Toulouse) , Oncopole , Toulouse , France.,b Université Paul Sabatier, University of Toulouse III , Toulouse , France
| | - Pierre Cordelier
- a Equipe « Labellisée Ligue contre le Cancer», Laboratoire d'excellence TOUCAN , INSERM U 1037; CNRS ERL 5294; CRCT (Cancer Research Center of Toulouse) , Oncopole , Toulouse , France.,b Université Paul Sabatier, University of Toulouse III , Toulouse , France
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68
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SHISA3 Promoter Methylation Is a Potential Diagnostic and Prognostic Biomarker for Laryngeal Squamous Cell Carcinoma. BIOMED RESEARCH INTERNATIONAL 2017; 2017:9058749. [PMID: 28299336 PMCID: PMC5337399 DOI: 10.1155/2017/9058749] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Revised: 11/03/2016] [Accepted: 01/10/2017] [Indexed: 12/16/2022]
Abstract
The purpose of this study was to evaluate the contribution of SHISA3 promoter methylation to laryngeal squamous cell carcinoma (LSCC). SHISA3 promoter methylation status and expression were determined using methylation-specific polymerase chain reaction (MSP) and quantitative real-time PCR (qRT-PCR) in 93 paired LSCC and adjacent normal tissues, respectively. Furthermore, the regulatory function of the SHISA3 promoter fragment was analyzed using a luciferase reporter assay. The results reveal that there is a significant increase in SHISA3 methylation in LSCC tissues compared with corresponding nontumor tissues (P = 4.58E − 12). The qRT-PCR results show a significant association between SHISA3 methylation and expression in LSCC (P = 1.67E − 03). In addition, the area under the receiver operating characteristic curve was 0.91. Consequently, a log-rank test and multivariate Cox analysis suggest that SHISA3 promoter hypermethylation is a predictor of poor overall survival for LSCC (log-rank P = 0.024; HR = 2.71; 95% CI = 1.024–7.177; P = 0.047). The results indicate that SHISA3 promoter hypermethylation might increase the risk of LSCC through regulation of gene expression and is a potential diagnostic and prognostic biomarker for LSCC.
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69
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Mameri H, Bièche I, Meseure D, Marangoni E, Buhagiar-Labarchède G, Nicolas A, Vacher S, Onclercq-Delic R, Rajapakse V, Varma S, Reinhold WC, Pommier Y, Amor-Guéret M. Cytidine Deaminase Deficiency Reveals New Therapeutic Opportunities against Cancer. Clin Cancer Res 2016; 23:2116-2126. [PMID: 27601591 DOI: 10.1158/1078-0432.ccr-16-0626] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 07/25/2016] [Accepted: 08/25/2016] [Indexed: 12/21/2022]
Abstract
Purpose: One of the main challenges in cancer therapy is the identification of molecular mechanisms mediating resistance or sensitivity to treatment. Cytidine deaminase (CDA) was reported to be downregulated in cells derived from patients with Bloom syndrome, a genetic disease associated with a strong predisposition to a wide range of cancers. The purpose of this study was to determine whether CDA deficiency could be associated with tumors from the general population and could constitute a predictive marker of susceptibility to antitumor drugs.Experimental Design: We analyzed CDA expression in silico, in large datasets for cancer cell lines and tumors and in various cancer cell lines and primary tumor tissues using IHC, PDXs, qRT-PCR, and Western blotting. We also studied the mechanism underlying CDA silencing and searched for molecules that might target specifically CDA-deficient tumor cells using in silico analysis coupled to classical cellular experimental approaches.Results: We found that CDA expression is downregulated in about 60% of cancer cells and tissues. We demonstrate that DNA methylation is a prevalent mechanism of CDA silencing in tumors. Finally, we show that CDA-deficient tumor cells can be specifically targeted with epigenetic treatments and with the anticancer drug aminoflavone.Conclusions: CDA expression status identifies new subgroups of cancers, and CDA deficiency appears to be a novel and relevant predictive marker of susceptibility to antitumor drugs, opening up new possibilities for treating cancer. Clin Cancer Res; 23(8); 2116-26. ©2016 AACR.
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Affiliation(s)
- Hamza Mameri
- Institut Curie, PSL Research University, UMR 3348, 91405 Orsay, France.,CNRS UMR 3348, Centre Universitaire, Bât. 110, 91405 Orsay, France.,Université Paris Sud, Université Paris-Saclay, UMR 3348, 91405 Orsay, France
| | - Ivan Bièche
- Institut Curie, Genetic Department, 26, rue d'Ulm, 75005 Paris, France
| | - Didier Meseure
- Institut Curie, Platform of Investigative Pathology, 26, rue d'Ulm, 75005 Paris, France
| | - Elisabetta Marangoni
- Institut Curie, PSL Research University, Translational Research Department, 26, rue d'Ulm, 75005 Paris, France
| | - Géraldine Buhagiar-Labarchède
- Institut Curie, PSL Research University, UMR 3348, 91405 Orsay, France.,CNRS UMR 3348, Centre Universitaire, Bât. 110, 91405 Orsay, France.,Université Paris Sud, Université Paris-Saclay, UMR 3348, 91405 Orsay, France
| | - André Nicolas
- Institut Curie, Platform of Investigative Pathology, 26, rue d'Ulm, 75005 Paris, France.,Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, 20892
| | - Sophie Vacher
- Institut Curie, Genetic Department, 26, rue d'Ulm, 75005 Paris, France
| | - Rosine Onclercq-Delic
- Institut Curie, PSL Research University, UMR 3348, 91405 Orsay, France.,CNRS UMR 3348, Centre Universitaire, Bât. 110, 91405 Orsay, France.,Université Paris Sud, Université Paris-Saclay, UMR 3348, 91405 Orsay, France
| | - Vinodh Rajapakse
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, 20892
| | - Sudhir Varma
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, 20892
| | - William C Reinhold
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, 20892
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, 20892
| | - Mounira Amor-Guéret
- Institut Curie, PSL Research University, UMR 3348, 91405 Orsay, France. .,CNRS UMR 3348, Centre Universitaire, Bât. 110, 91405 Orsay, France.,Université Paris Sud, Université Paris-Saclay, UMR 3348, 91405 Orsay, France
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70
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Liu NQ, De Marchi T, Timmermans A, Trapman-Jansen AMAC, Foekens R, Look MP, Smid M, van Deurzen CHM, Span PN, Sweep FCGJ, Brask JB, Timmermans-Wielenga V, Foekens JA, Martens JWM, Umar A. Prognostic significance of nuclear expression of UMP-CMP kinase in triple negative breast cancer patients. Sci Rep 2016; 6:32027. [PMID: 27558661 PMCID: PMC4997324 DOI: 10.1038/srep32027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 07/27/2016] [Indexed: 11/09/2022] Open
Abstract
We have previously identified UMP-CMP kinase (CMPK1) as a prognostic marker for triple negative breast cancer (TNBC) by mass spectrometry (MS). In this study we evaluated CMPK1 association to prognosis in an independent set of samples by immunohistochemistry (IHC) and assessed biological pathways associated to its expression through gene set enrichment analysis (GSEA). A total of 461 TNBC paraffin-embedded tissues were collected from different academic hospitals in Europe, incorporated into tissue micro-arrays (TMA), and stained for CMPK1 expression. We also collected gene expression data of 60 samples, which were also present in the TMA, for GSEA correlation analysis. CMPK1 IHC staining showed both cytoplasmic and nuclear components. While cytoplasmic CMPK1 did not show any association to metastasis free survival (MFS), nuclear CMPK1 was associated to poor prognosis independently from other prognostic factors in stratified Cox regression analyses. GSEA correlation analysis of the nuclear CMPK1-stratified gene expression dataset showed a significant enrichment of extracellular matrix (ECM; positive correlation) and cell cycle (negative correlation) associated genes. We have shown here that nuclear CMPK1 is indicative of poor prognosis in TNBCs and that its expression may be related to dysregulation of ECM and cell cycle molecules.
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Affiliation(s)
- Ning Qing Liu
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.,Postgraduate School of Molecular Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Tommaso De Marchi
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.,Postgraduate School of Molecular Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Annemieke Timmermans
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Anita M A C Trapman-Jansen
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Renée Foekens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Maxime P Look
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Carolien H M van Deurzen
- Department of Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Paul N Span
- Department of Radiation Oncology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Fred C G J Sweep
- Department of Laboratory Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Julie Benedicte Brask
- Department of Pathology, Centre of Diagnostic Investigations, Copenhagen University Hospital, Copenhagen, Denmark
| | - Vera Timmermans-Wielenga
- Department of Pathology, Centre of Diagnostic Investigations, Copenhagen University Hospital, Copenhagen, Denmark
| | - John A Foekens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Arzu Umar
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
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Abstract
Artificially modified nucleotides, in the form of nucleoside analogues, are widely used in the treatment of cancers and various other diseases, and have become important tools in the laboratory to characterise DNA repair pathways. In contrast, the role of endogenously occurring nucleotide modifications in genome stability is little understood. This is despite the demonstration over three decades ago that the cellular DNA precursor pool is orders of magnitude more susceptible to modification than the DNA molecule itself. More recently, underscoring the importance of this topic, oxidation of the cellular nucleotide pool achieved through targeting the sanitation enzyme MTH1, appears to be a promising anti-cancer strategy. This article reviews our current understanding of modified DNA precursors in genome stability, with a particular focus upon oxidised nucleotides, and outlines some important outstanding questions.
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Affiliation(s)
- Sean G Rudd
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
| | - Nicholas C K Valerie
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Thomas Helleday
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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72
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Bapiro TE, Richards FM, Jodrell DI. Understanding the Complexity of Porous Graphitic Carbon (PGC) Chromatography: Modulation of Mobile-Stationary Phase Interactions Overcomes Loss of Retention and Reduces Variability. Anal Chem 2016; 88:6190-4. [PMID: 27228284 PMCID: PMC5362737 DOI: 10.1021/acs.analchem.6b01167] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 05/26/2016] [Indexed: 01/24/2023]
Abstract
Porous graphitic carbon (PGC) is an important tool in a chromatographer's armory that retains polar compounds with mass spectrometry (MS)-compatible solvents. However, its applicability is severely limited by an unpredictable loss of retention, which can be attributed to contamination. The solutions offered fail to restore the original retention and our observations of retention time shifts of gemcitabine/metabolites on PGC are not consistent with contamination. The mobile phase affects the ionization state of analytes and the polarizable PGC surface that influences the strength of dispersive forces governing retention on the stationary phase. We hypothesized that failure to maintain the same PGC surface before and after running a gradient is a cause of the observed retention loss/variability on PGC. Herein, we optimize the choice of mobile phase solvent in a gradient program with three parts: a preparatory phase, which allows binding of analytes to column; an elution phase, which gives the required separation/peak shape; and a maintenance phase, to preserve the required retention capacity. Via liquid chromatography/tandem mass spectrometry (LC-MS/MS) analysis of gemcitabine and its metabolites extracted from tumor tissue, we demonstrate reproducible chromatography on three PGC columns of different ages. This approach simplifies use of the PGC to the same level as that of a C-18 column, removes the need for column regeneration, and minimizes run times, thus allowing PGC columns to be used to their full potential.
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Affiliation(s)
| | - Frances M. Richards
- Cancer
Research UK Cambridge
Institute, University of Cambridge, Li Ka
Shing Centre, Box 278, Robinson Way, Cambridge, CB2 0RE, United Kingdom
| | - Duncan I. Jodrell
- Cancer
Research UK Cambridge
Institute, University of Cambridge, Li Ka
Shing Centre, Box 278, Robinson Way, Cambridge, CB2 0RE, United Kingdom
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73
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Liu MY, DeNizio JE, Schutsky EK, Kohli RM. The expanding scope and impact of epigenetic cytosine modifications. Curr Opin Chem Biol 2016; 33:67-73. [PMID: 27315338 DOI: 10.1016/j.cbpa.2016.05.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 05/27/2016] [Accepted: 05/31/2016] [Indexed: 12/11/2022]
Abstract
Chemical modifications to genomic DNA can expand and shape its coding potential. Cytosine methylation in particular has well-established roles in regulating gene expression and defining cellular identity. The discovery of TET family enzymes opened a major frontier beyond DNA methylation, revealing three oxidized forms of cytosine that could mediate DNA demethylation or encode independent epigenetic functions. Chemical biology has been instrumental in uncovering TET's intricate reaction mechanisms and scope of reactivity on a surprising variety of substrates. Moreover, innovative chemoenzymatic strategies have enabled sensitive detection of oxidized cytosine products in vitro and in vivo. We highlight key recent developments that demonstrate how chemical biology is advancing our understanding of the extended, dynamic epigenome.
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Affiliation(s)
- Monica Yun Liu
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jamie E DeNizio
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Emily K Schutsky
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rahul M Kohli
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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74
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Chi C, Ronai D, Than MT, Walker CJ, Sewell AK, Han M. Nucleotide levels regulate germline proliferation through modulating GLP-1/Notch signaling in C. elegans. Genes Dev 2016; 30:307-20. [PMID: 26833730 PMCID: PMC4743060 DOI: 10.1101/gad.275107.115] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In this study, Chi et al. researched the link between known nutrient-sensing systems and reproductive programs. Using a model system in C. elegans, they show that a Notch signaling pathway senses the level of uridine/thymidine and controls germline proliferation, delineating a previously unknown nucleotide-sensing mechanism for controlling reproductivity. Animals alter their reproductive programs to accommodate changes in nutrient availability, yet the connections between known nutrient-sensing systems and reproductive programs are underexplored, and whether there is a mechanism that senses nucleotide levels to coordinate germline proliferation is unknown. We established a model system in which nucleotide metabolism is perturbed in both the nematode Caenorhabditis elegans (cytidine deaminases) and its food (Escherichia coli); when fed food with a low uridine/thymidine (U/T) level, germline proliferation is arrested. We provide evidence that this impact of U/T level on the germline is critically mediated by GLP-1/Notch and MPK-1/MAPK, known to regulate germline mitotic proliferation. This germline defect is suppressed by hyperactivation of glp-1 or disruption of genes downstream from glp-1 to promote meiosis but not by activation of the IIS or TORC1 pathways. Moreover, GLP-1 expression is post-transcriptionally modulated by U/T levels. Our results reveal a previously unknown nucleotide-sensing mechanism for controlling reproductivity.
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Affiliation(s)
- Congwu Chi
- Howard Hughes Medical Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| | - Diana Ronai
- Howard Hughes Medical Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| | - Minh T Than
- Howard Hughes Medical Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| | - Cierra J Walker
- Howard Hughes Medical Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| | - Aileen K Sewell
- Howard Hughes Medical Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| | - Min Han
- Howard Hughes Medical Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado at Boulder, Boulder, Colorado 80309, USA
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Abstract
Inhibiting DNA repair can have a positive outcome on therapeutic interventions
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Affiliation(s)
- Stephen P Jackson
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge CB2 1QN, UK. The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.
| | - Thomas Helleday
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 21 Stockholm, Sweden.
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Gemble S, Buhagiar-Labarchède G, Onclercq-Delic R, Biard D, Lambert S, Amor-Guéret M. A balanced pyrimidine pool is required for optimal Chk1 activation to prevent ultrafine anaphase bridge formation. J Cell Sci 2016; 129:3167-77. [DOI: 10.1242/jcs.187781] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 06/27/2016] [Indexed: 01/05/2023] Open
Abstract
Cytidine deaminase (CDA) deficiency induces an excess of cellular dCTP, which reduces basal PARP-1 activity, thereby compromising complete DNA replication, leading to ultrafine anaphase bridge (UFB) formation. CDA dysfunction has pathological implications, notably in cancer and in Bloom syndrome. It remains unknown how reduced levels of PARP-1 activity and pyrimidine pool imbalance lead to the accumulation of unreplicated DNA during mitosis. We report that a decrease in PARP-1 activity in CDA-deficient cells impairs DNA damage-induced Chk1 activation, and, thus, the downstream checkpoints. Chemical inhibition of the ATR-Chk1 pathway leads to UFB accumulation, and we found that this pathway was compromised in CDA-deficient cells. Our data demonstrate that ATR-Chk1 acts downstream from PARP-1, preventing the accumulation of unreplicated DNA in mitosis, and, thus, UFB formation. Finally, delaying entry into mitosis is sufficient to prevent UFB formation in both CDA-deficient and CDA-proficient cells, suggesting that both physiological and pathological UFBs are derived from unreplicated DNA. Our findings demonstrate an unsuspected requirement for a balanced nucleotide pool for optimal Chk1 activation both in unchallenged cells and in response to genotoxic stress.
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Affiliation(s)
- Simon Gemble
- Institut Curie, PSL Research University, UMR 3348, Unité Stress Génotoxiques et Cancer, Centre de Recherche, Orsay, France
- CNRS UMR 3348, Centre Universitaire, Bât. 110. 91405, Orsay, France
- Université Paris Sud, Université Paris Saclay, UMR3348, Centre Universitaire d'Orsay, France
| | - Géraldine Buhagiar-Labarchède
- Institut Curie, PSL Research University, UMR 3348, Unité Stress Génotoxiques et Cancer, Centre de Recherche, Orsay, France
- CNRS UMR 3348, Centre Universitaire, Bât. 110. 91405, Orsay, France
- Université Paris Sud, Université Paris Saclay, UMR3348, Centre Universitaire d'Orsay, France
| | - Rosine Onclercq-Delic
- Institut Curie, PSL Research University, UMR 3348, Unité Stress Génotoxiques et Cancer, Centre de Recherche, Orsay, France
- CNRS UMR 3348, Centre Universitaire, Bât. 110. 91405, Orsay, France
- Université Paris Sud, Université Paris Saclay, UMR3348, Centre Universitaire d'Orsay, France
| | - Denis Biard
- CEA, DSV, iMETI, SEPIA, 18, route du Panorama. Bât. 60, BP6, 92265 Fontenay-aux-Roses Cedex, France
| | - Sarah Lambert
- Institut Curie, PSL Research University, UMR 3348, Unité Stress Génotoxiques et Cancer, Centre de Recherche, Orsay, France
- CNRS UMR 3348, Centre Universitaire, Bât. 110. 91405, Orsay, France
- Université Paris Sud, Université Paris Saclay, UMR3348, Centre Universitaire d'Orsay, France
| | - Mounira Amor-Guéret
- Institut Curie, PSL Research University, UMR 3348, Unité Stress Génotoxiques et Cancer, Centre de Recherche, Orsay, France
- CNRS UMR 3348, Centre Universitaire, Bât. 110. 91405, Orsay, France
- Université Paris Sud, Université Paris Saclay, UMR3348, Centre Universitaire d'Orsay, France
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78
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Salvaging chemotherapy. Nat Chem Biol 2015. [DOI: 10.1038/nchembio.1921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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