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Zhang T, Huang J, Zhang Z, Lv J, Zhang D, Qing R, Lan L. Flow cytometry and 5-ethynyl-2'-deoxyuridine (EdU) labeling to detect the cell cycle dynamics of Phaeodactylum tricornutum under light. J Phycol 2022; 58:555-567. [PMID: 35352350 DOI: 10.1111/jpy.13250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 02/28/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Cell cycle studies in plants and algae are highly dependent on reliable methods for detecting cellular DNA replication. With its short growth cycle and ease of genetic transformation, Phaeodactylum tricornutum is an important model organism for the study of pennate diatoms. Here we explored two different methods to detect the cell cycle of P. tricornutum, one using SYBR-green I to via flow cytometry, and the other using EdU labeling to observe cell cycle changes under fluorescence microscopy. Both EdU labeling fluorescence microscopy and SYBR-green I staining flow cytometry accurately indicated that the cells of P. tricornutum enter the G2/M phase after 12 h of light exposure. The results indicate that SYBR Green I was an adequate detection method for nuclear DNA quantitation in cells of P. tricornutum using a flow cytometer and without RNase A treatment. In addition, EdU can be applied to P. tricornutum to reliably detect cell proliferation. Besides, Mg-ProtoIX was able to reverse the cell cycle division inhibition of P. tricornutum and allow the nuclear DNA replication to proceed normally. Taken together, the photoperiodic division time point was clearly identified, which sheds light on the regulation of cell division mechanism in P. tricornutum.
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Affiliation(s)
- Ting Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of the Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Jingyi Huang
- Key Laboratory of Bio-Resource and Eco-Environment of the Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Zhixia Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of the Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Jie Lv
- Key Laboratory of Bio-Resource and Eco-Environment of the Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Dongqun Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of the Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Renwei Qing
- Key Laboratory of Bio-Resource and Eco-Environment of the Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610065, China
| | - Liqiong Lan
- Key Laboratory of Bio-Resource and Eco-Environment of the Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610065, China
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2
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Lesslich HM, Klapal L, Wilke J, Haak A, Dietzel ID. Adjusting the neuron to astrocyte ratio with cytostatics in hippocampal cell cultures from postnatal rats: A comparison of cytarabino furanoside (AraC) and 5-fluoro-2'-deoxyuridine (FUdR). PLoS One 2022; 17:e0265084. [PMID: 35263366 PMCID: PMC8906639 DOI: 10.1371/journal.pone.0265084] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 02/22/2022] [Indexed: 01/29/2023] Open
Abstract
Cell culture studies offer the unique possibility to investigate the influence of pharmacological treatments with quantified dosages applied for defined time durations on survival, morphological maturation, protein expression and function as well as the mutual interaction of various cell types. Cultures obtained from postnatal rat brain contain a substantial number of glial cells that further proliferate with time in culture leading to an overgrowth of neurons with glia, especially astrocytes and microglia. A well-established method to decrease glial proliferation in vitro is to apply low concentrations of cytosine arabinoside (AraC). While AraC primarily effects dividing cells, it has been reported repeatedly that it is also neurotoxic, which is the reason why most protocols limit its application to concentrations of up to 5 μM for a duration of 24 h. Here, we investigated 5-fluoro-2'-deoxyuridine (FUdR) as a possible substitute for AraC. We applied concentrations of both cytostatics ranging from 4 μM to 75 μM and compared cell composition and cell viability in cultures prepared from 0-2- and 3-4-day old rat pups. Using FUdR as proliferation inhibitor, higher ratios of neurons to glia cells were obtained with a maximal neuron to astrocyte ratio of up to 10:1, which could not be obtained using AraC in postnatal cultures. Patch-clamp recordings revealed no difference in the amplitudes of voltage-gated Na+ currents in neurons treated with FUdR compared with untreated control cells suggesting replacement of AraC by FUdR as glia proliferation inhibitor if highly neuron-enriched postnatal cultures are desired.
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Affiliation(s)
- Heiko M. Lesslich
- Department of Biochemistry II, Ruhr-Universität Bochum, Bochum, Germany
- * E-mail:
| | - Lars Klapal
- Department of Biochemistry II, Ruhr-Universität Bochum, Bochum, Germany
| | - Justus Wilke
- Department of Biochemistry II, Ruhr-Universität Bochum, Bochum, Germany
| | - Annika Haak
- Nanoscopy Group, RUBION, Ruhr-Universität Bochum, Bochum, Germany
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3
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Birdwhistell KE, Hurley DJ, Heins B, Peroni JF. Evaluation of equine xenogeneic mixed lymphocyte reactions using 5-ethynyl-2'-deoxyuridine (EdU). Vet Immunol Immunopathol 2022; 249:110430. [PMID: 35525064 DOI: 10.1016/j.vetimm.2022.110430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 04/29/2022] [Accepted: 05/01/2022] [Indexed: 11/19/2022]
Abstract
Allogeneic solid organ transplantation is currently the only treatment option for end stage organ disease. The shortage of available donor organs has driven efforts to utilize xenogeneic organs for transplantation. In vitro methods for evaluating immune-compatibility are a quick and low cost means of screening novel tissue products prior to more involved, expensive, and invasive live animal studies. Recently, a new analog of the DNA base thymidine, 5-ethynyl-2'-deoxyuridine (EdU), was developed. It may be used in a fast, efficient and specific means of evaluating cell proliferation via flow cytometry. This study was designed to test and optimize this platform for assessing equine xenogeneic one-way mixed lymphocyte reaction (MLR) to porcine stimulator cells. Furthermore, it was hypothesized that an enriched T-lymphocyte (T-cell) population would generate a stronger proliferative response to stimulation, and higher levels of cytokine production when compared to unfractionated peripheral blood mononuclear cells (PBMCs). PBMCs and T-cells were isolated from 3 horses and 4 pigs. Equine xenogeneic MLRs were set up using porcine allogeneic MLRs as a reference for clinically acceptable levels of cell proliferation. Equine T-cells showed significantly greater EdU incorporation in one-way xenogeneic MLRs than equine PBMCs. However, there was no significant difference in cell proliferation between porcine T-cell and PBMC as responders in allogenic one-way MLRs. Given the results of this study, we consider that enriched equine T-cells should be used in preference to unfractionated PBMCs when attempting to evaluate the equine xenogeneic response using the EdU assay as an indicator of suitability for transplant in vivo.
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Affiliation(s)
- Kate E Birdwhistell
- Department of Large Animal Medicine and Surgery, University of Georgia College of Veterinary Medicine, 2200 College Station Rd, Athens, GA 30602, USA.
| | - David J Hurley
- Department of Population Health, University of Georgia College of Veterinary Medicine, 2200 College Station Rd, Athens, GA 30602, USA
| | - Bradley Heins
- Department of Population Health, University of Georgia College of Veterinary Medicine, 2200 College Station Rd, Athens, GA 30602, USA
| | - John F Peroni
- Department of Large Animal Medicine and Surgery, University of Georgia College of Veterinary Medicine, 2200 College Station Rd, Athens, GA 30602, USA
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4
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Maltsev DI, Mellanson KA, Belousov VV, Enikolopov GN, Podgorny OV. The bioavailability time of commonly used thymidine analogues after intraperitoneal delivery in mice: labeling kinetics in vivo and clearance from blood serum. Histochem Cell Biol 2022; 157:239-250. [PMID: 34757474 PMCID: PMC10411052 DOI: 10.1007/s00418-021-02048-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2021] [Indexed: 10/19/2022]
Abstract
Detection of synthetic thymidine analogues after their incorporation into replicating DNA during the S-phase of the cell cycle is a widely exploited methodology for evaluating proliferative activity, tracing dividing and post-mitotic cells, and determining cell-cycle parameters both in vitro and in vivo. To produce valid quantitative readouts for in vivo experiments with single intraperitoneal delivery of a particular nucleotide, it is necessary to determine the time interval during which a synthetic thymidine analogue can be incorporated into newly synthesized DNA, and the time by which the nucleotide is cleared from the blood serum. To date, using a variety of methods, only the bioavailability time of tritiated thymidine and 5-bromo-2'-deoxyuridine (BrdU) have been evaluated. Recent advances in double- and triple-S-phase labeling using 5-iodo-2'-deoxyuridine (IdU), 5-chloro-2'-deoxyuridine (CldU), and 5-ethynyl-2'-deoxyuridine (EdU) have raised the question of the bioavailability time of these modified nucleotides. Here, we examined their labeling kinetics in vivo and evaluated label clearance from blood serum after single intraperitoneal delivery to mice at doses equimolar to the saturation dose of BrdU (150 mg/kg). We found that under these conditions, all the examined thymidine analogues exhibit similar labeling kinetics and clearance rates from the blood serum. Our results indicate that all thymidine analogues delivered at the indicated doses have similar bioavailability times (approximately 1 h). Our findings are significant for the practical use of multiple S-phase labeling with any combinations of BrdU, IdU, CldU, and EdU and for obtaining valid labeling readouts.
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Affiliation(s)
- Dmitry I Maltsev
- Federal Center of Brain Research and Neurotechnologies, Federal Medical Biological Agency, Moscow, Russia, 117997
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia, 117997
| | - Kennelia A Mellanson
- Molecular and Cellular Pharmacology Graduate Program and Center for Developmental Genetics, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Vsevolod V Belousov
- Federal Center of Brain Research and Neurotechnologies, Federal Medical Biological Agency, Moscow, Russia, 117997
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia, 117997
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia, 117997
| | - Grigori N Enikolopov
- Center for Developmental Genetics and Department of Anesthesiology, Stony Brook University, Stony Brook, NY, 11794, USA
- Institute for Advanced Brain Studies, Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Oleg V Podgorny
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia, 117997.
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia, 117997.
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia, 119334.
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5
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Waters MD, Warren S, Hughes C, Lewis P, Zhang F. Human genetic risk of treatment with antiviral nucleoside analog drugs that induce lethal mutagenesis: The special case of molnupiravir. Environ Mol Mutagen 2022; 63:37-63. [PMID: 35023215 DOI: 10.1002/em.22471] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/28/2021] [Accepted: 01/08/2022] [Indexed: 06/14/2023]
Abstract
This review considers antiviral nucleoside analog drugs, including ribavirin, favipiravir, and molnupiravir, which induce genome error catastrophe in SARS-CoV or SARS-CoV-2 via lethal mutagenesis as a mode of action. In vitro data indicate that molnupiravir may be 100 times more potent as an antiviral agent than ribavirin or favipiravir. Molnupiravir has recently demonstrated efficacy in a phase 3 clinical trial. Because of its anticipated global use, its relative potency, and the reported in vitro "host" cell mutagenicity of its active principle, β-d-N4-hydroxycytidine, we have reviewed the development of molnupiravir and its genotoxicity safety evaluation, as well as the genotoxicity profiles of three congeners, that is, ribavirin, favipiravir, and 5-(2-chloroethyl)-2'-deoxyuridine. We consider the potential genetic risks of molnupiravir on the basis of all available information and focus on the need for additional human genotoxicity data and follow-up in patients treated with molnupiravir and similar drugs. Such human data are especially relevant for antiviral NAs that have the potential of permanently modifying the genomes of treated patients and/or causing human teratogenicity or embryotoxicity. We conclude that the results of preclinical genotoxicity studies and phase 1 human clinical safety, tolerability, and pharmacokinetics are critical components of drug safety assessments and sentinels of unanticipated adverse health effects. We provide our rationale for performing more thorough genotoxicity testing prior to and within phase 1 clinical trials, including human PIG-A and error corrected next generation sequencing (duplex sequencing) studies in DNA and mitochondrial DNA of patients treated with antiviral NAs that induce genome error catastrophe via lethal mutagenesis.
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Affiliation(s)
- Michael D Waters
- Michael Waters Consulting USA, Hillsborough, North Carolina, USA
| | | | - Claude Hughes
- Duke University Medical Center, Durham, North Carolina, USA
| | | | - Fengyu Zhang
- Global Clinical and Translational Research Institute, Bethesda, Maryland, USA
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6
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Chen X, Emerson MM. Notch signaling represses cone photoreceptor formation through the regulation of retinal progenitor cell states. Sci Rep 2021; 11:14525. [PMID: 34267251 PMCID: PMC8282820 DOI: 10.1038/s41598-021-93692-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/25/2021] [Indexed: 11/29/2022] Open
Abstract
Notch signaling is required to repress the formation of vertebrate cone photoreceptors and to maintain the proliferative potential of multipotent retinal progenitor cells. However, the mechanism by which Notch signaling controls these processes is unknown. Recently, restricted retinal progenitor cells with limited proliferation capacity and that preferentially generate cone photoreceptors have been identified. Thus, there are several potential steps during cone genesis that Notch signaling could act. Here we use cell type specific cis-regulatory elements to localize the primary role of Notch signaling in cone genesis to the formation of restricted retinal progenitor cells from multipotent retinal progenitor cells. Localized inhibition of Notch signaling in restricted progenitor cells does not alter the number of cones derived from these cells. Cell cycle promotion is not a primary effect of Notch signaling but an indirect effect on progenitor cell state transitions that leads to depletion of the multipotent progenitor cell population. Taken together, this suggests that the role of Notch signaling in cone photoreceptor formation and proliferation are both mediated by a localized function of Notch in multipotent retinal progenitor cells to repress the formation of restricted progenitor cells.
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Affiliation(s)
- Xueqing Chen
- Biology PhD Program, The Graduate Center, The City University of New York, New York, NY, 10016, USA
- Department of Biology, The City College of New York, The City University of New York, New York, NY, 10031, USA
| | - Mark M Emerson
- Biology PhD Program, The Graduate Center, The City University of New York, New York, NY, 10016, USA.
- Department of Biology, The City College of New York, The City University of New York, New York, NY, 10031, USA.
- Biochemistry PhD Program, The Graduate Center, The City University of New York, New York, NY, 10016, USA.
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7
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Clua A, Fàbrega C, García-Chica J, Grijalvo S, Eritja R. Parallel G-quadruplex Structures Increase Cellular Uptake and Cytotoxicity of 5-Fluoro-2'-deoxyuridine Oligomers in 5-Fluorouracil Resistant Cells. Molecules 2021; 26:molecules26061741. [PMID: 33804620 PMCID: PMC8003610 DOI: 10.3390/molecules26061741] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/17/2021] [Accepted: 03/19/2021] [Indexed: 12/13/2022] Open
Abstract
Fluoropyrimidines, such as 5-fluorouracil (5-FU) and related prodrugs have been considered first-line chemotherapy agents for the treatment of colorectal cancer. However, poor specificity and tumor cell resistance remain major limiting bottlenecks. G-quadruplexes, have been suggested as preferred nanostructures for enhancing cellular uptake mediated by G-quadruplex binding proteins which are abundant at the membranes of some tumor cells. In the current study, we propose a new strategy to deliver 5-fluoro-2′-deoxyuridine (5-FdU) monophosphate, the main active drug from 5-FU derivatives that may circumvent the cellular mechanisms of FU-resistant cancer cells. Two G-quadruplexes delivery systems containing four and six G-tetrads ((TG4T) and (TG6T)) linked to a FdU oligonucleotide were synthesized. Biophysical studies show that the G-quadruplex parallel structures are not affected by the incorporation of the 5 units of FdU at the 5’-end. Internalization studies confirmed the ability of such G-quadruplex nanostructures to facilitate the transport of the FdU pentamer and increase its cytotoxic effect relative to conventional FU drug in FU-resistant colorectal cancer cells. These results suggest that FdU oligomers linked to G-quadruplex parallel sequences may be a promising strategy to deliver fluoropyrimidines to cancer cells.
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Affiliation(s)
- Anna Clua
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), ) Jordi Girona 18-26, E-08034 Barcelona, Spain; (A.C.); (C.F.); (J.G.-C.); (S.G.)
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, E-08034 Barcelona, Spain
| | - Carme Fàbrega
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), ) Jordi Girona 18-26, E-08034 Barcelona, Spain; (A.C.); (C.F.); (J.G.-C.); (S.G.)
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, E-08034 Barcelona, Spain
| | - Jesús García-Chica
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), ) Jordi Girona 18-26, E-08034 Barcelona, Spain; (A.C.); (C.F.); (J.G.-C.); (S.G.)
| | - Santiago Grijalvo
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), ) Jordi Girona 18-26, E-08034 Barcelona, Spain; (A.C.); (C.F.); (J.G.-C.); (S.G.)
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, E-08034 Barcelona, Spain
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC-CSIC), ) Jordi Girona 18-26, E-08034 Barcelona, Spain; (A.C.); (C.F.); (J.G.-C.); (S.G.)
- Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26, E-08034 Barcelona, Spain
- Correspondence: ; Tel.: +34-934-006-145
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8
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Wear EE, Song J, Zynda GJ, Mickelson-Young L, LeBlanc C, Lee TJ, Deppong DO, Allen GC, Martienssen RA, Vaughn MW, Hanley-Bowdoin L, Thompson WF. Comparing DNA replication programs reveals large timing shifts at centromeres of endocycling cells in maize roots. PLoS Genet 2020; 16:e1008623. [PMID: 33052904 PMCID: PMC7588055 DOI: 10.1371/journal.pgen.1008623] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 10/26/2020] [Accepted: 08/28/2020] [Indexed: 12/20/2022] Open
Abstract
Plant cells undergo two types of cell cycles–the mitotic cycle in which DNA replication is coupled to mitosis, and the endocycle in which DNA replication occurs in the absence of cell division. To investigate DNA replication programs in these two types of cell cycles, we pulse labeled intact root tips of maize (Zea mays) with 5-ethynyl-2’-deoxyuridine (EdU) and used flow sorting of nuclei to examine DNA replication timing (RT) during the transition from a mitotic cycle to an endocycle. Comparison of the sequence-based RT profiles showed that most regions of the maize genome replicate at the same time during S phase in mitotic and endocycling cells, despite the need to replicate twice as much DNA in the endocycle and the fact that endocycling is typically associated with cell differentiation. However, regions collectively corresponding to 2% of the genome displayed significant changes in timing between the two types of cell cycles. The majority of these regions are small with a median size of 135 kb, shift to a later RT in the endocycle, and are enriched for genes expressed in the root tip. We found larger regions that shifted RT in centromeres of seven of the ten maize chromosomes. These regions covered the majority of the previously defined functional centromere, which ranged between 1 and 2 Mb in size in the reference genome. They replicate mainly during mid S phase in mitotic cells but primarily in late S phase of the endocycle. In contrast, the immediately adjacent pericentromere sequences are primarily late replicating in both cell cycles. Analysis of CENH3 enrichment levels in 8C vs 2C nuclei suggested that there is only a partial replacement of CENH3 nucleosomes after endocycle replication is complete. The shift to later replication of centromeres and possible reduction in CENH3 enrichment after endocycle replication is consistent with a hypothesis that centromeres are inactivated when their function is no longer needed. In traditional cell division, or mitosis, a cell’s genetic material is duplicated and then split between two daughter cells. In contrast, in some specialized cell types, the DNA is duplicated a second time without an intervening division step, resulting in cells that carry twice as much DNA. This phenomenon, which is called the endocycle, is common during plant development. At each step, DNA replication follows an ordered program in which highly compacted DNA is unraveled and replicated in sections at different times during the synthesis (S) phase. In plants, it is unclear whether traditional and endocycle programs are the same, especially since endocycling cells are typically in the process of differentiation. Using root tips of maize, we found that in comparison to replication in the mitotic cell cycle, there is a small portion of the genome whose replication in the endocycle is shifted in time, usually to later in S phase. Some of these regions are scattered around the genome and mostly coincide with active genes. However, the most prominent shifts occur in centromeres. The shift to later replication in centromeres is noteworthy because they orchestrate the process of separating duplicated chromosomes into daughter cells, a function that is not needed in the endocycle.
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Affiliation(s)
- Emily E. Wear
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail:
| | - Jawon Song
- Texas Advanced Computing Center, University of Texas, Austin, Texas, United States of America
| | - Gregory J. Zynda
- Texas Advanced Computing Center, University of Texas, Austin, Texas, United States of America
| | - Leigh Mickelson-Young
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Chantal LeBlanc
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Tae-Jin Lee
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - David O. Deppong
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - George C. Allen
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Robert A. Martienssen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Matthew W. Vaughn
- Texas Advanced Computing Center, University of Texas, Austin, Texas, United States of America
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - William F. Thompson
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, United States of America
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Haskins JS, Su C, Maeda J, Walsh KD, Haskins AH, Allum AJ, Froning CE, Kato TA. Evaluating the Genotoxic and Cytotoxic Effects of Thymidine Analogs, 5-Ethynyl-2'-Deoxyuridine and 5-Bromo-2'-Deoxyurdine to Mammalian Cells. Int J Mol Sci 2020; 21:E6631. [PMID: 32927807 PMCID: PMC7555307 DOI: 10.3390/ijms21186631] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/02/2020] [Accepted: 09/08/2020] [Indexed: 12/23/2022] Open
Abstract
BrdU (bromodeoxyuridine) and EdU (ethynyldeoxyuridine) have been largely utilized as the means of monitoring DNA replication and cellular division. Although BrdU induces gene and chromosomal mutations and induces sensitization to photons, EdU's effects have not been extensively studied yet. Therefore, we investigated EdU's potential cytotoxic and mutagenic effects and its related underlying mechanisms when administered to Chinese hamster ovary (CHO) wild type and DNA repair-deficient cells. EdU treatment displayed a higher cytotoxicity and genotoxicity than BrdU treatment. Cells with defective homologous recombination repair displayed a greater growth delay and severe inhibition of clonogenicity with EdU compared to wild type and other DNA repair-deficient cells. Inductions of sister chromatid exchange and hypoxanthine phosphorybosyl transferase (HPRT) mutation were observed in EdU-incorporated cells as well. Interestingly, on the other hand, EdU did not induce sensitization to photons to the same degree as BrdU. Our results demonstrate that elevated concentrations (similar to manufacturers suggested concentration; >5-10 μM) of EdU treatment were toxic to the cell cultures, particularly in cells with a defect in homologous recombination repair. Therefore, EdU should be administered with additional precautions.
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Affiliation(s)
| | | | | | | | | | | | | | - Takamitsu A. Kato
- Department of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, CO 80526, USA; (J.S.H.); (C.S.); (J.M.); (K.D.W.); (A.H.H.); (A.J.A.); (C.E.F.)
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10
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Manska S, Octaviano R, Rossetto CC. 5-Ethynyl-2'-deoxycytidine and 5-ethynyl-2'-deoxyuridine are differentially incorporated in cells infected with HSV-1, HCMV, and KSHV viruses. J Biol Chem 2020; 295:5871-5890. [PMID: 32205447 PMCID: PMC7196651 DOI: 10.1074/jbc.ra119.012378] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 03/18/2020] [Indexed: 11/06/2022] Open
Abstract
Nucleoside analogues are a valuable experimental tool. Incorporation of these molecules into newly synthesized DNA (i.e. pulse-labeling) is used to monitor cell proliferation or to isolate nascent DNA. Some of the most common nucleoside analogues used for pulse-labeling of DNA in cells are the deoxypyrimidine analogues 5-ethynyl-2'-deoxyuridine (EdU) and 5-ethynyl-2'-deoxycytidine (EdC). Click chemistry enables conjugation of an azide molecule tagged with a fluorescent dye or biotin to the alkyne of the analog, which can then be used to detect incorporation of EdU and EdC into DNA. The use of EdC is often recommended because of the potential cytotoxicity associated with EdU during longer incubations. Here, by comparing the relative incorporation efficiencies of EdU and EdC during short 30-min pulses, we demonstrate significantly lower incorporation of EdC than of EdU in noninfected human fibroblast cells or in cells infected with either human cytomegalovirus or Kaposi's sarcoma-associated herpesvirus. Interestingly, cells infected with herpes simplex virus type-1 (HSV-1) incorporated EdC and EdU at similar levels during short pulses. Of note, exogenous expression of HSV-1 thymidine kinase increased the incorporation efficiency of EdC. These results highlight the limitations when using substituted pyrimidine analogues in pulse-labeling and suggest that EdU is the preferable nucleoside analogue for short pulse-labeling experiments, resulting in increased recovery and sensitivity for downstream applications. This is an important discovery that may help to better characterize the biochemical properties of different nucleoside analogues with a given kinase, ultimately leading to significant differences in labeling efficiency of nascent DNA.
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Affiliation(s)
- Salomé Manska
- Department of Microbiology and Immunology, University of Nevada, Reno, School of Medicine, Reno, Nevada 89557
| | - Rionna Octaviano
- Department of Microbiology and Immunology, University of Nevada, Reno, School of Medicine, Reno, Nevada 89557
| | - Cyprian C Rossetto
- Department of Microbiology and Immunology, University of Nevada, Reno, School of Medicine, Reno, Nevada 89557.
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11
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Zhang X, Ruan Y, Wu AK, Zaid U, Villalta JD, Wang G, Banie L, Reed-Maldonado AB, Lin G, Lue TF. Delayed Treatment With Low-intensity Extracorporeal Shock Wave Therapy in an Irreversible Rat Model of Stress Urinary Incontinence. Urology 2020; 141:187.e1-187.e7. [PMID: 32283169 DOI: 10.1016/j.urology.2020.03.035] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 03/22/2020] [Accepted: 03/25/2020] [Indexed: 12/13/2022]
Abstract
OBJECTIVE To determine the outcomes and mechanisms of delayed low-intensity extracorporeal shock wave therapy (Li-ESWT) in a rat model of irreversible stress urinary incontinence (SUI). MATERIALS AND METHODS Twenty-four female Sprague-Dawley rats were randomly assigned into 3 groups: sham control, vaginal balloon dilation + β-aminopropionitrile (BAPN; SUI group), and vaginal balloon dilation + BAPN + treatment with Li-ESWT (SUI-Li-ESWT group). An irreversible SUI model was developed by inhibiting the urethral structural recovery with BAPN daily for 5 weeks. Thereafter, in the SUI-Li-ESWT group, Li-ESWT was administered twice per week for 2 weeks. After a 1-week washout, all 24 rats were evaluated with functional and histologic studies at 17 weeks of age. Endogenous progenitor cells were detected via the EdU-labeling method. RESULTS Functional analysis with leak point pressure testing showed that the SUI-Li-ESWT group had significantly higher leak point pressures compared with untreated rats. Increased urethral and vaginal smooth and striated muscle content and increased thickness of the vaginal wall were noted in the SUI-Li-ESWT group. The SUI group had significantly decreased neuronal nitric oxide /tyrosine hydroxylase positive nerves ratio in the smooth muscle layers of the urethra, while the SUI-Li-ESWT group had neuronal nitric oxide/tyrosine hydroxylase+ nerves ratio similar to that of the control group. The continuality of urothelial cell lining was also improved in the SUI-Li-ESWT group. In addition, there were significantly increased EdU-positive cells in the SUI-Li-ESWT group. CONCLUSION Li-ESWT appears to increase smooth muscle content in the urethra and the vagina, increase the thickness of urethral wall, improve striated muscle content and neuromuscular junctions, restore the integrity of the urothelium, and increase the number of EdU-retaining progenitor cells in the urethral wall.
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Affiliation(s)
- Xiaoyu Zhang
- Department of Urology, Knuppe Molecular Urology Laboratory, School of Medicine, University of California, San Francisco, CA
| | - Yajun Ruan
- Department of Urology, Knuppe Molecular Urology Laboratory, School of Medicine, University of California, San Francisco, CA
| | - Alex K Wu
- Department of Urology, Knuppe Molecular Urology Laboratory, School of Medicine, University of California, San Francisco, CA
| | - Uwais Zaid
- Department of Urology, Knuppe Molecular Urology Laboratory, School of Medicine, University of California, San Francisco, CA
| | - Jaqueline D Villalta
- Department of Urology, Knuppe Molecular Urology Laboratory, School of Medicine, University of California, San Francisco, CA
| | - Guifang Wang
- Department of Urology, Knuppe Molecular Urology Laboratory, School of Medicine, University of California, San Francisco, CA
| | - Lia Banie
- Department of Urology, Knuppe Molecular Urology Laboratory, School of Medicine, University of California, San Francisco, CA
| | - Amanda B Reed-Maldonado
- Department of Urology, Knuppe Molecular Urology Laboratory, School of Medicine, University of California, San Francisco, CA
| | - Guiting Lin
- Department of Urology, Knuppe Molecular Urology Laboratory, School of Medicine, University of California, San Francisco, CA
| | - Tom F Lue
- Department of Urology, Knuppe Molecular Urology Laboratory, School of Medicine, University of California, San Francisco, CA.
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12
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Croce S, Serdjukow S, Carell T, Frischmuth T. Chemoenzymatic Preparation of Functional Click-Labeled Messenger RNA. Chembiochem 2020; 21:1641-1646. [PMID: 31943671 DOI: 10.1002/cbic.201900718] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Indexed: 12/23/2022]
Abstract
Synthetic mRNAs are promising candidates for a new class of transformative drugs that provide genetic information for patients' cells to develop their own cure. One key advancement to develop so-called druggable mRNAs was the preparation of chemically modified mRNAs, by replacing standard bases with modified bases, such as uridine with pseudouridine, which can ameliorate the immunogenic profile and translation efficiency of the mRNA. Thus the introduction of modified nucleobases was the foundation for the clinical use of such mRNAs. Herein we describe modular and simple methods to chemoenzymatically modify mRNA. Alkyne- and/or azide-modified nucleotides are enzymatically incorporated into mRNA and subsequently conjugated to fluorescent dyes using click chemistry. This allows visualization of the labeled mRNA inside cells. mRNA coding for the enhanced green fluorescent protein (eGFP) was chosen as a model system and the successful expression of eGFP demonstrated that our modified mRNA is accepted by the translation machinery.
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Affiliation(s)
- Stefano Croce
- baseclick GmbH, Floriansbogen 2-4, 82061, Neuried (bei München), Germany
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377, München, Germany
| | - Sascha Serdjukow
- baseclick GmbH, Floriansbogen 2-4, 82061, Neuried (bei München), Germany
| | - Thomas Carell
- Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377, München, Germany
| | - Thomas Frischmuth
- baseclick GmbH, Floriansbogen 2-4, 82061, Neuried (bei München), Germany
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13
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Nuthanakanti A, Ahmed I, Khatik SY, Saikrishnan K, Srivatsan SG. Probing G-quadruplex topologies and recognition concurrently in real time and 3D using a dual-app nucleoside probe. Nucleic Acids Res 2020; 47:6059-6072. [PMID: 31106340 PMCID: PMC6614846 DOI: 10.1093/nar/gkz419] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 04/30/2019] [Accepted: 05/06/2019] [Indexed: 12/30/2022] Open
Abstract
Comprehensive understanding of structure and recognition properties of regulatory nucleic acid elements in real time and atomic level is highly important to devise efficient therapeutic strategies. Here, we report the establishment of an innovative biophysical platform using a dual-app nucleoside analog, which serves as a common probe to detect and correlate different GQ structures and ligand binding under equilibrium conditions and in 3D by fluorescence and X-ray crystallography techniques. The probe (SedU) is composed of a microenvironment-sensitive fluorophore and an excellent anomalous X-ray scatterer (Se), which is assembled by attaching a selenophene ring at 5-position of 2'-deoxyuridine. SedU incorporated into the loop region of human telomeric DNA repeat fluorescently distinguished subtle differences in GQ topologies and enabled quantify ligand binding to different topologies. Importantly, anomalous X-ray dispersion signal from Se could be used to determine the structure of GQs. As the probe is minimally perturbing, a direct comparison of fluorescence data and crystal structures provided structural insights on how the probe senses different GQ conformations without affecting the native fold. Taken together, our dual-app probe represents a new class of tool that opens up new experimental strategies to concurrently investigate nucleic acid structure and recognition in real time and 3D.
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Affiliation(s)
- Ashok Nuthanakanti
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Ishtiyaq Ahmed
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Saddam Y Khatik
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Kayarat Saikrishnan
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
- Correspondence may also be addressed to Kayarat Saikrishnan.
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
- To whom correspondence should be addressed. Tel: +91 2025908086;
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14
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Zeng X, Hernandez-Sanchez W, Xu M, Whited TL, Baus D, Zhang J, Berdis AJ, Taylor DJ. Administration of a Nucleoside Analog Promotes Cancer Cell Death in a Telomerase-Dependent Manner. Cell Rep 2019; 23:3031-3041. [PMID: 29874588 DOI: 10.1016/j.celrep.2018.05.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 04/02/2018] [Accepted: 05/04/2018] [Indexed: 12/21/2022] Open
Abstract
Telomerase, the end-replication enzyme, is reactivated in malignant cancers to drive cellular immortality. While this distinction makes telomerase an attractive target for anti-cancer therapies, most approaches for inhibiting its activity have been clinically ineffective. As opposed to inhibiting telomerase, we use its activity to selectively promote cytotoxicity in cancer cells. We show that several nucleotide analogs, including 5-fluoro-2'-deoxyuridine (5-FdU) triphosphate, are effectively incorporated by telomerase into a telomere DNA product. Administration of 5-FdU results in an increased number of telomere-induced foci, impedes binding of telomere proteins, activates the ATR-related DNA-damage response, and promotes cell death in a telomerase-dependent manner. Collectively, our data indicate that telomerase activity can be exploited as a putative anti-cancer strategy.
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Affiliation(s)
- Xuehuo Zeng
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA
| | | | - Mengyuan Xu
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Tawna L Whited
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Diane Baus
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Junran Zhang
- Department of Radiation Oncology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Anthony J Berdis
- Department of Chemistry, Cleveland State University, Cleveland, OH 44115, USA
| | - Derek J Taylor
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA; Department of Biochemistry, Case Western Reserve University, Cleveland, OH 44106, USA.
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15
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Nobis D, Fisher RS, Simmermacher M, Hopkins PA, Tor Y, Jones AC, Magennis SW. Single-Molecule Detection of a Fluorescent Nucleobase Analogue via Multiphoton Excitation. J Phys Chem Lett 2019; 10:5008-5012. [PMID: 31397575 PMCID: PMC7024020 DOI: 10.1021/acs.jpclett.9b02108] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The ability to routinely detect fluorescent nucleobase analogues at the single-molecule level would create a wealth of opportunities to study nucleic acids. We report the multiphoton-induced fluorescence and single-molecule detection of a dimethylamine-substituted extended-6-aza-uridine (DMAthaU). We show that DMAthaU can exist in a highly fluorescent form, emitting strongly in the visible region (470-560 nm). Using pulse-shaped broadband Ti:sapphire laser excitation, DMAthaU undergoes two-photon (2P) absorption at low excitation powers, switching to three-photon (3P) absorption at high incident intensity. The assignment of a 3P process is supported by cubic response calculations. Under both 2P and 3P excitation, the single-molecule brightness was over an order of magnitude higher than reported previously for any fluorescent base analogue, which facilitated the first single-molecule detection of an emissive nucleoside with multiphoton excitation.
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Affiliation(s)
- David Nobis
- WestCHEM School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow G12 8QQ, U.K
| | - Rachel S. Fisher
- EaStCHEM School of Chemistry, The University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, U.K
| | - Mats Simmermacher
- EaStCHEM School of Chemistry, The University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, U.K
| | - Patrycja A. Hopkins
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Anita C. Jones
- EaStCHEM School of Chemistry, The University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, U.K
- Corresponding Authors (A.C.J.)., (S.W.M.)
| | - Steven W. Magennis
- WestCHEM School of Chemistry, University of Glasgow, Joseph Black Building, University Avenue, Glasgow G12 8QQ, U.K
- Corresponding Authors (A.C.J.)., (S.W.M.)
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16
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Seelam Prabhakar P, A Manderville R, D Wetmore S. Impact of the Position of the Chemically Modified 5-Furyl-2'-Deoxyuridine Nucleoside on the Thrombin DNA Aptamer-Protein Complex: Structural Insights into Aptamer Response from MD Simulations. Molecules 2019; 24:molecules24162908. [PMID: 31405145 PMCID: PMC6720718 DOI: 10.3390/molecules24162908] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/06/2019] [Accepted: 08/07/2019] [Indexed: 02/07/2023] Open
Abstract
Aptamers are functional nucleic acids that bind to a range of targets (small molecules, proteins or cells) with a high affinity and specificity. Chemically-modified aptamers are of interest because the incorporation of novel nucleobase components can enhance aptamer binding to target proteins, while fluorescent base analogues permit the design of functional aptasensors that signal target binding. However, since optimally modified nucleoside designs have yet to be identified, information about how to fine tune aptamer stability and target binding affinity is required. The present work uses molecular dynamics (MD) simulations to investigate modifications to the prototypical thrombin-binding aptamer (TBA), which is a 15-mer DNA sequence that folds into a G-quadruplex structure connected by two TT loops and one TGT loop. Specifically, we modeled a previously synthesized thymine (T) analog, namely 5-furyl-2′-deoxyuridine (5FurU), into each of the six aptamer locations occupied by a thymine base in the TT or TGT loops of unbound and thrombin bound TBA. This modification and aptamer combination were chosen as a proof-of-principle because previous experimental studies have shown that TBA displays emissive sensitivity to target binding based on the local environment polarity at different 5FurU modification sites. Our simulations reveal that the chemically-modified base imparts noticeable structural changes to the aptamer without affecting the global conformation. Depending on the modification site, 5FurU performance is altered due to changes in the local environment, including the modification site structural dynamics, degree of solvent exposure, stacking with neighboring bases, and interactions with thrombin. Most importantly, these changes directly correlate with the experimentally-observed differences in the stability, binding affinity and emissive response of the modified aptamers. Therefore, the computational protocols implemented in the present work can be used in subsequent studies in a predictive way to aid the fine tuning of aptamer target recognition for use as biosensors (aptasensors) and/or therapeutics.
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Affiliation(s)
- Preethi Seelam Prabhakar
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AL T1K 3M4, Canada
| | - Richard A Manderville
- Department of Chemistry and Toxicology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AL T1K 3M4, Canada.
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Abstract
The ability to analyze individual DNA fibers undergoing active DNA synthesis has emerged as a powerful technique in the field of DNA replication. Much of the initial analysis has focused on replication throughout the genome. However, more recent advancements in this technique have allowed for the visualization of replication patterns at distinct loci or regions within the genome. This type of locus-specific resolution will greatly enhance our understanding of the dynamics of DNA replication in regions that provide a challenge to the replication machinery. Here, we describe a protocol that will allow for the visualization of DNA replication through one of the most structurally complex regions in the human genome, the telomeric DNA.
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Affiliation(s)
- Himabindu Gali
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
- Department of Medicine, Cancer Center, Boston University School of Medicine, Boston, MA, USA
| | - Emily Mason-Osann
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
- Department of Medicine, Cancer Center, Boston University School of Medicine, Boston, MA, USA
| | - Rachel Litman Flynn
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA.
- Department of Medicine, Cancer Center, Boston University School of Medicine, Boston, MA, USA.
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18
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Jorge AF, Aviñó A, Pais AACC, Eritja R, Fàbrega C. DNA-based nanoscaffolds as vehicles for 5-fluoro-2'-deoxyuridine oligomers in colorectal cancer therapy. Nanoscale 2018; 10:7238-7249. [PMID: 29632908 DOI: 10.1039/c7nr08442k] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Fluoropyrimidines, such as 5-fluorouracil (5-FU) and related prodrugs, are considered one of the most successful agents in the treatment of colorectal cancer, yet poor specificity and tumor cell resistance remain the major limiting bottlenecks. Here, we exploited for the first time the ability of two DNA nanoscaffolds, a DNA tetrahedron (Td) and rectangle DNA origami, to incorporate 5-fluoro-2'-deoxyuridine (FdUn) oligomers. In addition, cholesterol moieties were synthetically attached to Td and DNA origami staples to enhance cellular uptake. DNA nanostructures functionalized with FdUn exhibited an enhanced cytotoxicity and higher ability to trigger apoptosis in colorectal cancer cells relative to conventional 5-FU and FdU, especially having cholesterol as an internalization helper. The cholesterol content mostly correlates with the increase of the FdUn nanostructure cytotoxicity. DNA nanoscaffolds bearing FdUn were able to circumvent the low sensitivity of colorectal cancer cells towards 5-FU. Both DNA nanostructures attained a comparable cytotoxic effect yet Td displays higher antiproliferative action. The ability to reduce the proliferation of cancer cells is mainly related to the concentration of DNA nanostructures. The present work suggests that self-assembled DNA nanoparticles are privileged vehicles for delivering fluoropyrimidines, opening new avenues to the development of promising therapeutics for cancer treatment.
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Affiliation(s)
- A F Jorge
- Coimbra Chemistry Centre (CQC), Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal.
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19
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Yan Y, Qing Y, Pink JJ, Gerson SL. Loss of Uracil DNA Glycosylase Selectively Resensitizes p53-Mutant and -Deficient Cells to 5-FdU. Mol Cancer Res 2018; 16:212-221. [PMID: 29117941 DOI: 10.1158/1541-7786.mcr-17-0215] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 08/02/2017] [Accepted: 10/26/2017] [Indexed: 11/16/2022]
Abstract
Thymidylate synthase (TS) inhibitors including fluoropyrimidines [e.g., 5-Fluorouracil (5-FU) and 5-Fluorodeoxyuridine (5-FdU, floxuridine)] and antifolates (e.g., pemetrexed) are widely used against solid tumors. Previously, we reported that shRNA-mediated knockdown (KD) of uracil DNA glycosylase (UDG) sensitized cancer cells to 5-FdU. Because p53 has also been shown as a critical determinant of the sensitivity to TS inhibitors, we further interrogated 5-FdU cytotoxicity after UDG depletion with regard to p53 status. By analyzing a panel of human cancer cells with known p53 status, it was determined that p53-mutated or -deficient cells are highly resistant to 5-FdU. UDG depletion resensitizes 5-FdU in p53-mutant and -deficient cells, whereas p53 wild-type (WT) cells are not affected under similar conditions. Utilizing paired HCT116 p53 WT and p53 knockout (KO) cells, it was shown that loss of p53 improves cell survival after 5-FdU, and UDG depletion only significantly sensitizes p53 KO cells. This sensitization can also be recapitulated by UDG depletion in cells with p53 KD by shRNAs. In addition, sensitization is also observed with pemetrexed in p53 KO cells, but not with 5-FU, most likely due to RNA incorporation. Importantly, in p53 WT cells, the apoptosis pathway induced by 5-FdU is activated independent of UDG status. However, in p53 KO cells, apoptosis is compromised in UDG-expressing cells, but dramatically elevated in UDG-depleted cells. Collectively, these results provide evidence that loss of UDG catalyzes significant cell death signals only in cancer cells mutant or deficient in p53.Implications: This study reveals that UDG depletion restores sensitivity to TS inhibitors and has chemotherapeutic potential in the context of mutant or deficient p53. Mol Cancer Res; 16(2); 212-21. ©2017 AACR.
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Affiliation(s)
- Yan Yan
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio
| | - Yulan Qing
- Case Comprehensive Cancer Center, Division of General Medical Sciences-Oncology, Case Western Reserve University, Cleveland, Ohio
| | - John J Pink
- Case Comprehensive Cancer Center, Division of General Medical Sciences-Oncology, Case Western Reserve University, Cleveland, Ohio
| | - Stanton L Gerson
- Case Comprehensive Cancer Center, Division of General Medical Sciences-Oncology, Case Western Reserve University, Cleveland, Ohio.
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20
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Flygt J, Clausen F, Marklund N. Diffuse traumatic brain injury in the mouse induces a transient proliferation of oligodendrocyte progenitor cells in injured white matter tracts. Restor Neurol Neurosci 2018; 35:251-263. [PMID: 27768001 DOI: 10.3233/rnn-160675] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND Injury to the white matter may lead to impaired neuronal signaling and is commonly observed following traumatic brain injury (TBI). Although endogenous repair of TBI-induced white matter pathology is limited, oligodendrocyte progenitor cells (OPCs) may be stimulated to proliferate and regenerate functionally myelinating oligodendrocytes. Even though OPCs are present throughout the adult brain, little is known about their proliferative activity following axonal injury caused by TBI. OBJECTIVE We hypothesized that central fluid percussion injury (cFPI) in mice, a TBI model causing wide-spread axonal injury, results in OPC proliferation. METHODS Proliferation of OPCs was evaluated in 27 cFPI mice using 5-ethynyl-2'-deoxyuridine (EdU) labeling and a cell proliferation assay at 2 (n = 9), 7 (n = 8) and 21 (n = 10) days post injury (dpi). Sham-injured mice (n = 14) were used as controls. OPC proliferation was quantified by immunohistochemistry using the OPC markers NG2 and Olig2 in several white matter loci including the corpus callosum, external capsule, fimbriae, the internal capsule and cerebral peduncle. RESULTS The number of EdU/DAPI/Olig2-positive cells were increased in the cFPI group compared to sham-injured animals at 7 days post-injury (dpi; p≤0.05) in the majority of white matter regions. The OPC proliferation had subsided by 21 dpi. The number of EdU/DAPI/NG2 cells was also increase at 7 dpi in the external capsule and fimbriae. CONCLUSION These results suggest that traumatic axonal injury in the mouse induces a transient proliferative response of residing OPCs. These proliferating OPCs may replace dead oligodendrocytes and contribute to remyelination, which needs evaluation in future studies.
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Abstract
Understanding the efficacy of and creating delivery mechanisms for therapeutic nucleic acids requires understanding structural and kinetic properties which allow these polymers to promote the death of cancerous cells. One molecule of interest is a 10 mer of FdUMP (5-fluoro-2'-deoxyuridine-5'-O-monophosphate) - also called F10. Here we investigate the structural and kinetic behavior of F10 in intracellular and extracellular solvent conditions along with non-biological conditions that may be efficacious in in vitro preparations of F10 delivery systems. From our all-atom molecular dynamics simulations totaling 80 microseconds, we predict that F10's phosphate groups form close-range interactions with calcium and zinc ions, with calcium having the highest affinity of the five ions investigated. We also predict that F10's interactions with magnesium, potassium and sodium are almost exclusively long-range interactions. In terms of intramolecular interactions, we find that F10 is least structured (in terms of hydrogen bonds among bases) in the 150 mM NaCl (extracellular-like solvent conditions) and most structured in 150 mM ZnCl2. Kinetically, we see that F10 is unstable in the presence of magnesium, sodium or potassium, finding stable kinetic traps in the presence of calcium or zinc.
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Affiliation(s)
- Ryan L Melvin
- Department of Physics, Wake Forest University, Winston Salem, NC, USA.
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Fu Q, Lyu D, Zhang L, Qin Z, Tang Q, Yin H, Lou X, Chen Z, Yao K. Airborne particulate matter (PM2.5) triggers autophagy in human corneal epithelial cell line. Environ Pollut 2017; 227:314-322. [PMID: 28477555 DOI: 10.1016/j.envpol.2017.04.078] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 04/24/2017] [Accepted: 04/26/2017] [Indexed: 06/07/2023]
Abstract
PURPOSE To investigate particulate matter (PM2.5)-induced damage to human corneal epithelial cells (HCECs) and to determine the underlying mechanisms. METHODS HCECs were exposed to PM2.5 at a series of concentrations for various periods. Cell viability was measured by using a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Cell proliferation was evaluated via 5-ethynyl-2'-deoxyuridine (EdU) analysis, while autophagy was determined by immunofluorescence and Western blot. RESULTS PM2.5-induced cell damage of HCECs occurred in a time- and dose-dependent manner. Decreased cell viability and proliferation as well as increased apoptosis were observed in HCECs after PM2.5 exposure for 24 h. Autophagy in HCECs was slightly inhibited in the early stage (before 4 h) of exposure but significantly activated in the late stage (after 24 h), as evidenced by a decrease in the former and increase in the latter of the expression of the autophagy-associated markers LC3B, ATG5, and BECN1. Interestingly, rapamycin, an autophagy activator, attenuated early-stage but aggravated late-stage PM2.5-induced cell damage, suggesting that the role of autophagy in HCECs may change over time during PM2.5 exposure. In addition, in the early stage, the expression of LC3B and ATG5 increased in cells co-treated with rapamycin and PM2.5 compared to rapamycin-only or PM2.5-only treated cells, suggesting that autophagy may benefit cell viability after PM2.5 exposure. CONCLUSIONS The results indicate the potential role of autophagy in the treatment of PM2.5-induced ocular corneal diseases and provide direct evidence for the cytotoxicity, possibly involving an autophagic process, of PM2.5 in HCECs.
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Affiliation(s)
- Qiuli Fu
- Eye Center of the 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, Zhejiang Province, China
| | - Danni Lyu
- Eye Center of the 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, Zhejiang Province, China
| | - Lifang Zhang
- Eye Center of the 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, Zhejiang Province, China
| | - Zhenwei Qin
- Eye Center of the 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, Zhejiang Province, China
| | - Qiaomei Tang
- Eye Center of the 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, Zhejiang Province, China
| | - Houfa Yin
- Eye Center of the 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, Zhejiang Province, China
| | - Xiaoming Lou
- Department of Environmental and Occupational Health, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang Province, China
| | - Zhijian Chen
- Department of Environmental and Occupational Health, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, Zhejiang Province, China.
| | - Ke Yao
- Eye Center of the 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, China; Zhejiang Provincial Key Lab of Ophthalmology, Hangzhou, Zhejiang Province, China.
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Lin G, Reed-Maldonado AB, Wang B, Lee YC, Zhou J, Lu Z, Wang G, Banie L, Lue TF. In Situ Activation of Penile Progenitor Cells With Low-Intensity Extracorporeal Shockwave Therapy. J Sex Med 2017; 14:493-501. [PMID: 28258952 DOI: 10.1016/j.jsxm.2017.02.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 01/28/2017] [Accepted: 02/03/2017] [Indexed: 01/02/2023]
Abstract
BACKGROUND We previously reported that progenitor cells, or stem cells, exist within penile tissue. We hypothesized that acoustic wave stimulation by low-intensity extracorporeal shockwave therapy (Li-ESWT) would activate local stem or progenitor cells within the penis, producing regenerative effects. AIMS To study the feasibility of in situ penile progenitor cell activation by Li-ESWT. METHODS We performed a cohort analysis of young and middle-age male Sprague-Dawley rats treated with 5-ethynyl-2'-deoxyuridine (EdU) pulse followed by Li-ESWT. In addition, Li-ESWT was applied to cultured Schwann cells and endothelial cells to study the molecular mechanism involved in cell proliferation. Thirty minutes before Li-ESWT, each rat received an intraperitoneal injection of EdU. Li-ESWT was applied to the penis at very low (0.02 mJ/mm2 at 3 Hz for 300 pulses) or low (0.057 mJ/mm2 at 3 Hz for 500 pulses) energy levels. The endothelial and Schwann cells were treated with very low energy (0.02 mJ/mm2 at 3 Hz for 300 pulses) in vitro. OUTCOMES At 48 hours or 1 week after Li-ESWT, penile tissues were harvested for histologic study to assess EdU+ and Ki-67+ cells, and cell proliferation, Ki-67 expression, Erk1/2 phosphorylation, translocation, and angiogenesis were examined in cultured Schwann and endothelial cells after Li-ESWT. RESULTS Li-ESWT significantly increased EdU+ cells within penile erectile tissues (P < .01) at 48 hours and 1 week. There were more cells activated in young animals than in middle-age animals, and the effect depended on dosage. Most activated cells were localized within subtunical spaces. In vitro studies indicated that Li-ESWT stimulated cell proliferation through increased phosphorylation of Erk1/2. CLINICAL TRANSLATION The present results provide a possible explanation for the clinical benefits seen with Li-ESWT. STRENGTHS AND LIMITATIONS The main limitation of the present project was the short period of study and the animal model used. Li-ESWT could be less effective in improving erectile function in old animals because of the decreased number and quality of penile stem or progenitor cells associated with aging. CONCLUSION Li-ESWT activation of local penile progenitor cells might be one of the mechanisms that contribute to the beneficial effects of shockwave treatment for erectile dysfunction, which represents a non-invasive alternative to exogenous stem cell therapy. Lin G, Reed-Maldonado AB, Wang B, et al. In Situ Activation of Penile Progenitor Cells With Low-Intensity Extracorporeal Shockwave Therapy. J Sex Med 2017;14:493-501.
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Affiliation(s)
- Guiting Lin
- Knuppe Molecular Urology Laboratory, Department of Urology, School of Medicine, University of California-San Francisco, San Francisco, CA, USA
| | - Amanda B Reed-Maldonado
- Knuppe Molecular Urology Laboratory, Department of Urology, School of Medicine, University of California-San Francisco, San Francisco, CA, USA
| | - Bohan Wang
- Knuppe Molecular Urology Laboratory, Department of Urology, School of Medicine, University of California-San Francisco, San Francisco, CA, USA; Department of Urology, The Second Hospital, Zhejiang University, Zhejiang, China
| | - Yung-Chin Lee
- Knuppe Molecular Urology Laboratory, Department of Urology, School of Medicine, University of California-San Francisco, San Francisco, CA, USA; Department of Urology, Kaohsiung Medical University Hospital, and Department of Urology, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Jun Zhou
- Knuppe Molecular Urology Laboratory, Department of Urology, School of Medicine, University of California-San Francisco, San Francisco, CA, USA; Department of Urology, The Third XiangYa Hospital, Central South University, Changsha, China
| | - Zhihua Lu
- Knuppe Molecular Urology Laboratory, Department of Urology, School of Medicine, University of California-San Francisco, San Francisco, CA, USA; Department of Urology, The First Hospital of Jilin University, Changchun, China
| | - Guifang Wang
- Knuppe Molecular Urology Laboratory, Department of Urology, School of Medicine, University of California-San Francisco, San Francisco, CA, USA
| | - Lia Banie
- Knuppe Molecular Urology Laboratory, Department of Urology, School of Medicine, University of California-San Francisco, San Francisco, CA, USA
| | - Tom F Lue
- Knuppe Molecular Urology Laboratory, Department of Urology, School of Medicine, University of California-San Francisco, San Francisco, CA, USA.
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Higaki S, Shimada M, Kawamoto K, Todo T, Kawasaki T, Tooyama I, Fujioka Y, Sakai N, Takada T. In vitro differentiation of fertile sperm from cryopreserved spermatogonia of the endangered endemic cyprinid honmoroko (Gnathopogon caerulescens). Sci Rep 2017; 7:42852. [PMID: 28211534 PMCID: PMC5314417 DOI: 10.1038/srep42852] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 01/18/2017] [Indexed: 01/17/2023] Open
Abstract
Many endemic fish species are threatened with extinction. Conservation strategies and the restoration of endemic fish after extinction must therefore be investigated. Although sperm cryopreservation is indispensable for the conservation of endangered fishes, the limited number of mature fish and limited availability (volume and period) of sperm from small endemic fish hinders the optimization and practical use of this material. In this report, we demonstrate the in vitro differentiation of fertile sperm from cryopreserved spermatogonia of juveniles of the endangered small cyprinid honmoroko (Gnathopogon caerulescens), which is endemic to Lake Biwa in Japan. The entire process of spermatogenesis was recapitulated in vitro using cryopreserved spermatogonia of non-spawning adult and juvenile fish. The differentiation of sperm from spermatogonia was captured as a time-lapse video and confirmed by 5-ethynyl-2'-deoxyuridine (EdU) incorporation into sperm. Fertility was demonstrated by artificial insemination. These results suggest that the combination of cryopreservation of spermatogonia and in vitro sperm differentiation will provide a new and promising strategy for the preservation of paternal genetic materials.
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Affiliation(s)
- Shogo Higaki
- Laboratory of Cell Engineering, Department of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Manami Shimada
- Laboratory of Cell Engineering, Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Kazuaki Kawamoto
- Laboratory of Cell Engineering, Department of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Takaaki Todo
- Laboratory of Cell Engineering, Department of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Toshihiro Kawasaki
- Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Ikuo Tooyama
- Molecular Neuroscience Research Center, Shiga University of Medical Science, Otsu, Shiga, 520-2192, Japan
| | | | - Noriyoshi Sakai
- Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Tatsuyuki Takada
- Laboratory of Cell Engineering, Department of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
- Laboratory of Cell Engineering, Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
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Abstract
BACKGROUND Glioblastomas (GBMs) are a heterogeneous group of primary brain tumors. These tumors are resistant to therapeutic interventions and invariably recur after surgical resection. The multifunctional protein transglutaminase 2 (TG2) has been shown to promote cell survival in a number of different tumors. There is also evidence that TG2 may be a pro-survival factor in GBMs. However, the roles that TG2 plays in facilitating GBM survival and proliferation have not yet been clearly delineated . METHODS The functions of TG2 are often cell- and context-specific. Therefore, in this study we examined the ability of TG2 to facilitate GBM proliferation using colony formation assays and 5-ethynyl-2'-deoxyuridine (EdU) incorporation in several different GBM cell lines as well as neurospheres derived from patient tumors representing the 3 major subtypes of GBM tumors (mesenchymal, proneural, and classical) and maintained in the absence of serum. TG2 knockdown or selective TG2 inhibitors were used to modulate TG2 expression and activity. RESULTS We show that TG2 plays differential roles in the proliferative process depending on the cell type. In most, but not all, GBM models TG2 plays a crucial role in the proliferative process, and some but not all TG2 inhibitors were highly effective at reducing proliferation in a large subset of the GBM models. CONCLUSION Our results show that TG2 plays an important-but notoriously context-specific-role in GBM cell biology. Nonetheless, as future studies unravel the genetic "fingerprints" that make TG2 inhibitors effective, this information could be exploited to develop TG2 inhibitors into personalized GBM therapies.
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Affiliation(s)
- Soner Gundemir
- Department of Anesthesiology, University of Rochester, Rochester, New York; Department of Pharmacology and Physiology, University of Rochester, Rochester, New York; Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Alina Monteagudo
- Department of Anesthesiology, University of Rochester, Rochester, New York; Department of Pharmacology and Physiology, University of Rochester, Rochester, New York; Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Abdullah Akbar
- Department of Anesthesiology, University of Rochester, Rochester, New York; Department of Pharmacology and Physiology, University of Rochester, Rochester, New York; Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Jeffrey W Keillor
- Department of Anesthesiology, University of Rochester, Rochester, New York; Department of Pharmacology and Physiology, University of Rochester, Rochester, New York; Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Gail V W Johnson
- Department of Anesthesiology, University of Rochester, Rochester, New York; Department of Pharmacology and Physiology, University of Rochester, Rochester, New York; Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada
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Kawasaki F, Murat P, Li Z, Santner T, Balasubramanian S. Synthesis and biophysical analysis of modified thymine-containing DNA oligonucleotides. Chem Commun (Camb) 2017; 53:1389-1392. [PMID: 28074944 PMCID: PMC5759927 DOI: 10.1039/c6cc08670e] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We report the synthesis of a 5-formyl-2'-deoxyuridine (5fU) phosphoramidite and the preparation of oligonucleotides comprising all known, naturally observed eukaryotic thymidine modifications. Biophysical characterization of the synthetic oligonucleotides indicates that 5fU, but not the other T-derivatives, can alter DNA structures.
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Affiliation(s)
- F Kawasaki
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - P Murat
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Z Li
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - T Santner
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - S Balasubramanian
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK and School of Clinical Medicine, University of Cambridge, Cambridge CB2 0SP, UK
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27
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Mickelson-Young L, Wear E, Mulvaney P, Lee TJ, Szymanski ES, Allen G, Hanley-Bowdoin L, Thompson W. A flow cytometric method for estimating S-phase duration in plants. J Exp Bot 2016; 67:6077-6087. [PMID: 27697785 PMCID: PMC5100020 DOI: 10.1093/jxb/erw367] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The duration of the DNA synthesis stage (S phase) of the cell cycle is fundamental in our understanding of cell cycle kinetics, cell proliferation, and DNA replication timing programs. Most S-phase duration estimates that exist for plants are based on indirect measurements. We present a method for directly estimating S-phase duration by pulse-labeling root tips or actively dividing suspension cells with the halogenated thymidine analog 5-ethynl-2'-deoxyuridine (EdU) and analyzing the time course of replication with bivariate flow cytometry. The transition between G1 and G2 DNA contents can be followed by measuring the mean DNA content of EdU-labeled S-phase nuclei as a function of time after the labeling pulse. We applied this technique to intact root tips of maize (Zea mays L.), rice (Oryza sativa L.), barley (Hordeum vulgare L.), and wheat (Triticum aestivum L.), and to actively dividing cell cultures of Arabidopsis (Arabidopsis thaliana (L.) Heynh.) and rice. Estimates of S-phase duration in root tips were remarkably consistent, varying only by ~3-fold, although the genome sizes of the species analyzed varied >40-fold.
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Affiliation(s)
- Leigh Mickelson-Young
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Emily Wear
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Patrick Mulvaney
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Tae-Jin Lee
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA
- Present address: Syngenta Crop Protection, LLC, Research Triangle Park, NC 27709, USA
| | - Eric S Szymanski
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
- Present address: Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | - George Allen
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - William Thompson
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
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28
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Berryhill GE, Brust-Mascher I, Huynh JH, Famula TR, Reardon C, Hovey RC. A Convenient Method for Evaluating Epithelial Cell Proliferation in the Whole Mammary Glands of Female Mice. Endocrinology 2016; 157:3742-3748. [PMID: 27571136 PMCID: PMC5045499 DOI: 10.1210/en.2016-1480] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The mammary glands (MG) undergo rapid expansion of the ductal network during puberty in response to endocrine cues including the potent mitogenic effects of estrogen. The proliferation of mammary epithelial cells occurs in a spatially distinctive manner, where terminal end buds located at the ductal termini are the primary site of cell division. Here, we present a relatively high throughput approach to spatially assess epithelial cell proliferation in whole mouse MG using histochemical detection of 5-ethynyl-2'-deoxyuridine in conjunction with a standard curve-based data deconvolution technique to semiquantitatively measure proliferation via wide-field epifluorescent microscopy. This approach was validated against the "gold standard" of counting labeled nuclei from confocal images utilizing computer-assisted image analysis. Our method proved sensitive enough to describe the significant and spatially variable proliferative response to low-dose estrogen after 108 hours. This flexible method presents a timely and economical approach to obtaining spatial information regarding epithelial cell proliferation in the mouse MG.
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Affiliation(s)
- Grace E Berryhill
- Department of Animal Science (G.E.B., J.H.H., T.R.F., R.C.H.) and University of California Davis Health Sciences District Advanced Imaging Facility, School of Veterinary Medicine, (I.B.-M., C.R.), University of California, Davis, California 95616-8521
| | - Ingrid Brust-Mascher
- Department of Animal Science (G.E.B., J.H.H., T.R.F., R.C.H.) and University of California Davis Health Sciences District Advanced Imaging Facility, School of Veterinary Medicine, (I.B.-M., C.R.), University of California, Davis, California 95616-8521
| | - Jill H Huynh
- Department of Animal Science (G.E.B., J.H.H., T.R.F., R.C.H.) and University of California Davis Health Sciences District Advanced Imaging Facility, School of Veterinary Medicine, (I.B.-M., C.R.), University of California, Davis, California 95616-8521
| | - Thomas R Famula
- Department of Animal Science (G.E.B., J.H.H., T.R.F., R.C.H.) and University of California Davis Health Sciences District Advanced Imaging Facility, School of Veterinary Medicine, (I.B.-M., C.R.), University of California, Davis, California 95616-8521
| | - Colin Reardon
- Department of Animal Science (G.E.B., J.H.H., T.R.F., R.C.H.) and University of California Davis Health Sciences District Advanced Imaging Facility, School of Veterinary Medicine, (I.B.-M., C.R.), University of California, Davis, California 95616-8521
| | - Russell C Hovey
- Department of Animal Science (G.E.B., J.H.H., T.R.F., R.C.H.) and University of California Davis Health Sciences District Advanced Imaging Facility, School of Veterinary Medicine, (I.B.-M., C.R.), University of California, Davis, California 95616-8521
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Holleran JL, Eiseman JL, Parise RA, Kummar S, Beumer JH. LC-MS/MS assay for the quantitation of FdCyd and its metabolites FdUrd and FU in human plasma. J Pharm Biomed Anal 2016; 129:359-366. [PMID: 27454087 PMCID: PMC5003709 DOI: 10.1016/j.jpba.2016.07.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 07/13/2016] [Accepted: 07/16/2016] [Indexed: 11/17/2022]
Abstract
The hypomethylating agent 5-fluoro-2'-deoxycytidine (FdCyd, NSC 48006) is being evaluated clinically both via the intravenous route and via the oral route in combination with 3,4,5,6-tetrahydrouridine (THU), a potent inhibitor of FdCyd catabolism. To determine the pharmacokinetics of FdCyd and downstream metabolites, we developed and validated an LC-MS/MS assay for the quantitation of FdCyd, 5-fluoro-2'-deoxyuridine (FdUrd), and 5-fluorouracil (FU) in 0.2mL human plasma. After acetonitrile protein precipitation, the sample was split and separate chromatography was achieved for FdCyd with a Synergi Polar-RP column and for FdUrd and FU with a Shodex Asahipak NH2P-50 2D column. Gradients of 0.1% acetic acid in acetonitrile and water were used. Detection with a Quattromicro quadrupole mass spectrometer with electrospray ionization in positive-ion (FdCyd) or negative-ion (FdUrd and FU) multiple reaction monitoring (MRM) mode. The assay was linear from 5 to 3000ng/mL for all three analytes and proved to be accurate (96.7-105.5%) and precise (<8.1%CV), and fulfilled FDA criteria for bioanalytical method validation. We demonstrated the suitability of this assay for measuring FdCyd and metabolites FdUrd and FU in plasma from a patient who was administered 120mg PO FdCyd 30min after 3000mg THU. Our LC-MS/MS assay will be an essential tool to further define the pharmacology of FdCyd in ongoing and future studies.
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Affiliation(s)
- Julianne L Holleran
- Cancer Therapeutics Drug Discovery Program, University of Pittsburgh Cancer Institute, Pittsburgh, PA, United States
| | - Julie L Eiseman
- Cancer Therapeutics Drug Discovery Program, University of Pittsburgh Cancer Institute, Pittsburgh, PA, United States; Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Robert A Parise
- Cancer Therapeutics Drug Discovery Program, University of Pittsburgh Cancer Institute, Pittsburgh, PA, United States; Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, United States
| | - Shivaani Kummar
- Division of Cancer Treatment and Diagnosis, NCI, Bethesda, MD, United States
| | - Jan H Beumer
- Cancer Therapeutics Drug Discovery Program, University of Pittsburgh Cancer Institute, Pittsburgh, PA, United States; Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, United States; Division of Hematology-Oncology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.
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Yin X, Tsukaya H. A pulse-chase strategy for EdU labelling assay is able to rapidly quantify cell division orientation. New Phytol 2016; 211:1462-1469. [PMID: 27121010 DOI: 10.1111/nph.13980] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 03/19/2016] [Indexed: 06/05/2023]
Abstract
Measurement of the direction of cell division is an important, yet difficult, task to analyse how a plant organ acquires its final shape from an initially small group of cells. We introduce a method that rapidly and easily quantifies cell division direction and is applicable to all plant species. A pulse-chase strategy for 5-ethynyl-2'-deoxyuridine (EdU) labelling assay was established and was shown to be successful for leaves of Arabidopsis thaliana (Arabidopsis) and Juncus prismatocarpus. By optimization of the pulse and chase periods, most of the signals obtained were sets of daughter nuclei. For Arabidopsis, the optimal time was a 45-min pulse and a 7-h chase. For J. prismatocarpus, the optimal time was a 2-h pulse and a 13.5-h chase. The positions of the daughter nuclei were used to quantify cell division direction in the Arabidopsis leaf primordia. Overall, cell division along the proximal-distal axis was more frequent than along the medial-lateral axis. In petiole, major vein, minor vein and margin areas, the major cell division direction seemed to be coincident with the direction of auxin flow. The advantages of our method over the few methods used previously are discussed. We anticipate that it will provide opportunities to study plant development in the near future.
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Affiliation(s)
- Xiaofeng Yin
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hirokazu Tsukaya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Bio-Next Project, Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Yamate Building no. 3, 5-1, Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
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31
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Vasseur P, Tonazzini S, Ziane R, Camasses A, Rando OJ, Radman-Livaja M. Dynamics of Nucleosome Positioning Maturation following Genomic Replication. Cell Rep 2016; 16:2651-2665. [PMID: 27568571 PMCID: PMC5014762 DOI: 10.1016/j.celrep.2016.07.083] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 03/22/2016] [Accepted: 07/28/2016] [Indexed: 12/31/2022] Open
Abstract
Chromatin is thought to carry epigenetic information from one generation to the next, although it is unclear how such information survives the disruptions of nucleosomal architecture occurring during genomic replication. Here, we measure a key aspect of chromatin structure dynamics during replication—how rapidly nucleosome positions are established on the newly replicated daughter genomes. By isolating newly synthesized DNA marked with 5-ethynyl-2′-deoxyuridine (EdU), we characterize nucleosome positions on both daughter genomes of S. cerevisiae during chromatin maturation. We find that nucleosomes rapidly adopt their mid-log positions at highly transcribed genes, which is consistent with a role for transcription in positioning nucleosomes in vivo. Additionally, experiments in hir1Δ mutants reveal a role for HIR in nucleosome spacing. We also characterized nucleosome positions on the leading and lagging strands, uncovering differences in chromatin maturation dynamics at hundreds of genes. Our data define the maturation dynamics of newly replicated chromatin and support a role for transcription in sculpting the chromatin template. Nucleosome positions are determined on newly replicated DNA Transcription reorders nucleosomes in gene bodies after DNA replication The HIR complex tightens nucleosome spacing in gene bodies following replication Nucleosome positions on leading and lagging strands depend on genes’ orientation
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Affiliation(s)
- Pauline Vasseur
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 Route de Mende, 34293 Montpellier Cedex 5, France; Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France
| | - Saphia Tonazzini
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 Route de Mende, 34293 Montpellier Cedex 5, France; Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France
| | - Rahima Ziane
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 Route de Mende, 34293 Montpellier Cedex 5, France; Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France
| | - Alain Camasses
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 Route de Mende, 34293 Montpellier Cedex 5, France; Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Marta Radman-Livaja
- Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 Route de Mende, 34293 Montpellier Cedex 5, France; Université de Montpellier, 163 rue Auguste Broussonnet, 34090 Montpellier, France.
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Poznanski J, Bretner M, Kulikowski T, Balzarini J, Van Aerschot A, De Clercq E. Synthesis, Solution Conformation and Anti-HIV Activity of Novel 3-Substituted-2′,3′-Dideoxy-5-Hydroxymethyl-Uridines and Their 4,5-Substituted Analogues. ACTA ACUST UNITED AC 2016; 14:127-38. [PMID: 14521329 DOI: 10.1177/095632020301400302] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
To decrease the toxicity of potent anti-HIV nucleosides 3-azido-2′,3′-dideoxythymidine (AZT) and 2,3′-dideoxy-3′-fluorothymidine (3-FddThd, FLT), their new analogues, 3-azido-2′,3′-dideoxy-5-hydroxymethyluridine (3-Az5HmddUrd) and 2,3′-dideoxy-3′-fluoro-5-hydroxymethyluridine (3′-F5HmddUrd), were synthesized. The reaction of 3′-azido-2′,3′-dideoxyuridine (3′-AzddUrd) and 2,3′-dideoxy-3′-fluorouridine (3′-FddUrd) with formaldehyde, under strongly alkaline conditions and at elevated temperature, proceeded after 4 days to completion to afford the corresponding 5-hydroxymethyl derivatives 3′-Az5HmddUrd and 3′-F5HmddUrd in good yield. These compounds were also prepared by oxidation of AZT and FLT with the use of K2S2O8. 1H NMR analyses were subjected to the series of 3′,4 and 5-substituted pyrimidine 2′-deoxy- and 2′,3′-dideoxynucleosides involving 3′-Az5HmddUrd and 3′-F5HmddUrd. Analysis of the sugar furanose ring puckering demonstrated that all 3′-fluorine derivatives exhibited strong domination of the S conformation (∼100%) while 3-substitution by electron-donating groups, such as NH2, increased population of the N conformation. Experimentally observed substituent effect on the furanose ring puckering equilibrium was reconstructed in the 100 ps molecular dynamic trajectories obtained for AZT, FLT, dThd, 2′,3′-ddThd and 3′-amino-2′,3′-ddThd. It may be concluded that anti-HIV activity is linked to a direct interaction of the 3′-sub-stituent with reverse transcriptase (RT) binding site. Anti-HIV activities of 3′-Az5HmddUrd and 3′-F5HmddUrd are lower than activity of AZT and FLT; however, 3′-Az5HmddUrd and 3′-F5HmddUrd are less toxic than AZT and FLT.
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Affiliation(s)
- Jaroslaw Poznanski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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Abstract
Determination of cellular proliferation and population turnover is an important tool for research on lymphoid cell function. Historically this has been done using radiolabeled nucleotides or nucleoside analogs, such as BrdU (5-bromo-2-deoxyuridine), that are incorporated into nascent DNA during S-phase. Recently, a new procedure was developed to label nascent DNA using EdU (5-Ethynyl-2-deoxyuridine). This new method overcomes limitations imposed by the procedure used to detect BrdU because EdU detection is based on an easily performed chemical reaction that does not require DNA denaturation, is quick and reproducible, and has a superior signal-to-noise ratio. This technique offers a wide range of opportunities to analyze cellular proliferation, population homeostasis, and cell marking procedures.
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Affiliation(s)
- Francis A Flomerfelt
- Experimental Transplantation and Immunology Branch, National Cancer Institute, Building 10, CRC, Room 3-3330, Bethesda, MD, 20892, USA,
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Sato A, Omi T, Yamamoto A, Satake A, Hiramoto A, Masutani M, Tanuma SI, Wataya Y, Kim HS. MicroRNA-351 Regulates Two-Types of Cell Death, Necrosis and Apoptosis, Induced by 5-fluoro-2'-deoxyuridine. PLoS One 2016; 11:e0153130. [PMID: 27071035 PMCID: PMC4829180 DOI: 10.1371/journal.pone.0153130] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 03/24/2016] [Indexed: 11/18/2022] Open
Abstract
Cell-death can be necrosis and apoptosis. We are investigating the mechanisms regulating the cell death that occurs on treatment of mouse cancer cell-line FM3A with antitumor 5-fluoro-2'-deoxyuridine (FUdR): necrosis occurs for the original clone F28-7, and apoptosis for its variant F28-7-A. Here we report that a microRNA (miR-351) regulates the cell death pattern. The miR-351 is expressed strongly in F28-7-A but only weakly in F28-7. Induction of a higher expression of miR-351 in F28-7 by transfecting an miRNA mimic into F28-7 resulted in a change of the death mode; necrosis to apoptosis. Furthermore, transfection of an miR-351 inhibitor into F28-7-A resulted in the morphology change, apoptosis to necrosis, in this death-by-FUdR. Possible mechanism involving lamin B1 in this miR-351's regulatory action is discussed.
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Affiliation(s)
- Akira Sato
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Yamazaki, Noda, Chiba, Japan
- Division of Genome Stability Research, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, Japan
- Division of Chemotherapy and Clinical Research, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, Japan
- Department of Drug Informatics, Faculty of Pharmaceutical Sciences, Okayama University, Tsushima-naka, Kita-ku, Okayama, Japan
| | - Takuya Omi
- Department of Drug Informatics, Faculty of Pharmaceutical Sciences, Okayama University, Tsushima-naka, Kita-ku, Okayama, Japan
| | - Akihiro Yamamoto
- Department of Drug Informatics, Faculty of Pharmaceutical Sciences, Okayama University, Tsushima-naka, Kita-ku, Okayama, Japan
| | - Akito Satake
- Department of Drug Informatics, Faculty of Pharmaceutical Sciences, Okayama University, Tsushima-naka, Kita-ku, Okayama, Japan
| | - Akiko Hiramoto
- Department of Drug Informatics, Faculty of Pharmaceutical Sciences, Okayama University, Tsushima-naka, Kita-ku, Okayama, Japan
| | - Mitsuko Masutani
- Division of Genome Stability Research, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, Japan
- Division of Chemotherapy and Clinical Research, National Cancer Center Research Institute, Tsukiji, Chuo-ku, Tokyo, Japan
- Department of Frontier Life Sciences, Nagasaki University Graduate School of Biomedical Sciences, Sakamoto, Nagasaki, Japan
| | - Sei-ichi Tanuma
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, Tokyo University of Science, Yamazaki, Noda, Chiba, Japan
| | - Yusuke Wataya
- Department of Drug Informatics, Faculty of Pharmaceutical Sciences, Okayama University, Tsushima-naka, Kita-ku, Okayama, Japan
| | - Hye-Sook Kim
- Department of Drug Informatics, Faculty of Pharmaceutical Sciences, Okayama University, Tsushima-naka, Kita-ku, Okayama, Japan
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Szymańska-Michalak A, Wawrzyniak D, Framski G, Kujda M, Zgoła P, Stawinski J, Barciszewski J, Boryski J, Kraszewski A. New 3'-O-aromatic acyl-5-fluoro-2'-deoxyuridine derivatives as potential anticancer agents. Eur J Med Chem 2016; 115:41-52. [PMID: 26994842 DOI: 10.1016/j.ejmech.2016.03.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 03/02/2016] [Accepted: 03/03/2016] [Indexed: 12/29/2022]
Abstract
New aromatic and aliphatic 3'-O-acyl-5-fluoro-2'-deoxyuridine derivatives were synthesized and evaluated as candidates for prodrugs against various cancer cell lines. As the most promising candidate for antimalignant therapeutics was found a dual-acting acyl derivative 7h, which apparently released not only the known anticancer nucleoside, 5-fluoro-2'-deoxyuridine (FdU), but also an additional active metabolite, acetylsalicylic acid, reinforcing thus therapeutic effect of FdU. Promising therapeutic indices showed also some aromatic dicarboxylic acids derivatives decorated with FdU esters (11 and 12).
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Affiliation(s)
| | - Dariusz Wawrzyniak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznań, Poland
| | - Grzegorz Framski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznań, Poland
| | - Marta Kujda
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239, Cracow, Poland
| | - Paulina Zgoła
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznań, Poland
| | - Jacek Stawinski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznań, Poland
| | - Jan Barciszewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznań, Poland
| | - Jerzy Boryski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznań, Poland
| | - Adam Kraszewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznań, Poland.
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Wear EE, Concia L, Brooks AM, Markham EA, Lee TJ, Allen GC, Thompson WF, Hanley-Bowdoin L. Isolation of Plant Nuclei at Defined Cell Cycle Stages Using EdU Labeling and Flow Cytometry. Methods Mol Biol 2016; 1370:69-86. [PMID: 26659955 DOI: 10.1007/978-1-4939-3142-2_6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
5-Ethynyl-2'-deoxyuridine (EdU) is a nucleoside analog of thymidine that can be rapidly incorporated into replicating DNA in vivo and, subsequently, detected by using "click" chemistry to couple its terminal alkyne group to fluorescent azides such as Alexa Fluor 488. Recently, EdU incorporation followed by coupling with a fluorophore has been used to visualize newly synthesized DNA in a wide range of plant species. One particularly useful application is in flow cytometry, where two-parameter sorting can be employed to analyze different phases of the cell cycle, as defined both by total DNA content and the amount of EdU pulse-labeled DNA. This approach allows analysis of the cell cycle without the need for synchronous cell populations, which can be difficult to obtain in many plant systems. The approach presented here, which was developed for fixed, EdU-labeled nuclei, can be used to prepare analytical profiles as well as to make highly purified preparations of G1, S, or G2/M phase nuclei for molecular or biochemical analysis. We present protocols for EdU pulse labeling, tissue fixation and harvesting, nuclei preparation, and flow sorting. Although developed for Arabidopsis suspension cells and maize root tips, these protocols should be modifiable to many other plant systems.
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Affiliation(s)
- Emily E Wear
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Lorenzo Concia
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Ashley M Brooks
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA
| | - Emily A Markham
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Tae-Jin Lee
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, 27709, USA
| | - George C Allen
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, 27695, USA
| | - William F Thompson
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Linda Hanley-Bowdoin
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, 27695, USA.
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Abstract
The ability to analyze cell division in both spatial and temporal dimensions within an organism is a key requirement in developmental biology. Specialized cell types within individual organs, such as those within shoot and root apical meristems, have often been identified by differences in their rates of proliferation prior to the characterization of distinguishing molecular markers. Replication-dependent labeling of DNA is a widely used method for assaying cell proliferation. The earliest approaches used radioactive labeling with tritiated thymidine, which were later followed by immunodetection of bromodeoxyuridine (BrdU). A major advance in DNA labeling came with the use of 5-ethynyl-2'deoxyuridine (EdU) which has proven to have multiple advantages over BrdU. Here we describe the methodology for analyzing EdU labeling and retention in whole plants and histological sections of Arabidopsis.
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Affiliation(s)
- Anita Kazda
- Gregor Mendel Institute of Plant Molecular Biology, Vienna Biocenter, Dr. Bohr-Gasse 3, Vienna, 1030, Austria
| | - Svetlana Akimcheva
- Gregor Mendel Institute of Plant Molecular Biology, Vienna Biocenter, Dr. Bohr-Gasse 3, Vienna, 1030, Austria
| | - J Matthew Watson
- Gregor Mendel Institute of Plant Molecular Biology, Vienna Biocenter, Dr. Bohr-Gasse 3, Vienna, 1030, Austria.
| | - Karel Riha
- Gregor Mendel Institute of Plant Molecular Biology, Vienna Biocenter, Dr. Bohr-Gasse 3, Vienna, 1030, Austria.
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic.
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Sisdelli L, Vidi AC, Moysés-Oliveira M, Di Battista A, Bortolai A, Moretti-Ferreira D, da Silva MRD, Melaragno MI, Carvalheira G. Incorporation of 5-ethynyl-2'-deoxyuridine (EdU) as a novel strategy for identification of the skewed X inactivation pattern in balanced and unbalanced X-rearrangements. Hum Genet 2015; 135:185-92. [PMID: 26670424 DOI: 10.1007/s00439-015-1622-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 11/28/2015] [Indexed: 12/12/2022]
Abstract
X-chromosome inactivation occurs randomly in normal female cells. However, the inactivation can be skewed in patients with alterations in X-chromosome. In balanced X-autosome translocations, normal X is preferentially inactivated, while in unbalanced X alterations, the aberrant X is usually inactivated. Here, we present a novel strategy to verify the skewed X inactivation pattern through the incorporation of 5-ethynyl-2'-deoxyuridine (EdU) into cells, in 11 patients: five carriers of balanced X-autosome translocations and six of unbalanced X-chromosome alterations. Since EdU is a labeled nucleoside analog of thymidine, its incorporation during DNA synthesis can reveal late replication regions and the inactive X-chromosome. All EdU findings were validated by the human androgen receptor gene (HUMARA) assay. The late replication regions were easily and quickly visualized in all cells, where inactive Xs are marked with strong green fluorescence. It was observed that the normal X-chromosome was preferentially inactivated in patients with balanced X-autosome translocations; while the aberrant X-chromosome was inactivated in most cells from patients with unbalanced alterations. By performing the fluorescence-based EdU assay, the differences between the active and inactive X-chromosomes are more easily recognizable than by classic cytogenetic methods. Furthermore, EdU incorporation allows the observation of the late replication regions in autosomal segments present in X derivatives from X-autosome translocations. Therefore, EdU assay permits an accurate and efficient cytogenetic evaluation of the X inactivation pattern with a low-cost, easy to perform and highly reproducible technique.
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Affiliation(s)
- Luiza Sisdelli
- Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, 04023-900, Brazil
| | - Angela Cristina Vidi
- Department of Biochemistry, Universidade Federal de São Paulo, São Paulo, Brazil
- Department of Medicine, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Mariana Moysés-Oliveira
- Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, 04023-900, Brazil
| | - Adriana Di Battista
- Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, 04023-900, Brazil
| | - Adriana Bortolai
- Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, 04023-900, Brazil
| | - Danilo Moretti-Ferreira
- Department of Genetics, Instituto de Biociências de Botucatu, São Paulo State University, São Paulo, 18618-970, Brazil
| | - Magnus R Dias da Silva
- Department of Biochemistry, Universidade Federal de São Paulo, São Paulo, Brazil
- Department of Medicine, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Maria Isabel Melaragno
- Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, 04023-900, Brazil
| | - Gianna Carvalheira
- Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, 04023-900, Brazil.
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Wang J, Lin G, Alwaal A, Zhang X, Wang G, Jia X, Banie L, Villalta J, Lin CS, Lue TF. Kinetics of Label Retaining Cells in the Developing Rat Kidneys. PLoS One 2015; 10:e0144734. [PMID: 26650841 PMCID: PMC4674088 DOI: 10.1371/journal.pone.0144734] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 11/23/2015] [Indexed: 12/23/2022] Open
Abstract
Background The kidney is a specialized low-regenerative organ with several different types of cellular lineages. The BrdU label-retaining cell (LRCs) approach has been used as part of a strategy to identify tissue-specific stem cells in the kidney; however, because the complementary base pairing in double-stranded DNA blocks the access of the anti-BrdU antibody to BrdU subunits, the stem cell marker expression in BrdU-labeled cells are often difficult to detect. In this study, we introduced a new cell labeling and detection method in which BrdU was replaced with 5-ethynyl-2-deoxyuridine (EdU) and examined the time-dependent dynamic changes of EdU-labeled cells and potential stem/progenitor markers in the development of kidney. Methods Newborn rats were intraperitoneally injected with EdU, and their kidneys were harvested respectively at different time points at 1 day, 3 days, 1 week, 2 weeks, and 6 weeks post-injection. The kidney tissues were processed for EdU and cellular markers by immunofluorescence staining. Results At the early stage, LRCs labeled by EdU were 2176.0 ± 355.6 cells at day one in each renal tissue section, but dropped to 168 ± 48.4 cells by week 6. As time increased, the numbers of LRCs were differentially expressed in the renal cortex and papilla. At the postnatal day one, nearly twice as many cells in the cortex were EdU-labeled as compared to the papilla (28.6 ± 3.6% vs. 15.6 ± 3.4%, P<0.05), while there were more LRCs within the renal papilla since the postnatal week one, and at the postnatal week 6, one third as many cells in the cortex were EdU-labeled as compared to the papilla (2.5 ± 0.1% vs. 7.7 ± 2.7%, P<0.05). The long-term LRCs at 6-week time point were associated exclusively with the glomeruli in the cortex and the renal tubules in the papilla. At 6 weeks, the EdU-labeled LRCs combined with expression of CD34, RECA-1, Nestin, and Synaptopodin were discretely but widely distributed within the glomeruli; Stro-1 around the glomeruli; and α-smooth muscle actin (SMA) in arteries. Conversely, co-expression of CD34, RECA-1, and Nestin with the long term EdU-labeled LRCs was significantly lower in renal tubules (P<0.01), while Stro-1 and Synaptopodin were not detected. Conclusion Our data found that at 6-week time point, EdU-labeled LRCs existing in the glomeruli expressed undifferentiated podocyte and endothelial markers at high rates, while those in the renal tubules expressed Nestin and vascular markers at low rates. To understand the characterization and localization of these EdU-LRCs, further studies will be needed to test cell lineage tracing, clonogenicity and differentiation potency, and the contributions to the regeneration of the kidney in response to renal injury/repair.
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Affiliation(s)
- Jianwen Wang
- Department of Urology, Beijing ChaoYang Hospital, Capital Medical University, 8 Gongtinanlu, Beijing, 100020, China
- Knuppe Molecular Urology Laboratory, Department of Urology, School of Medicine, University of California San Francisco, San Francisco, CA, 94143-0738, United States of America
- * E-mail:
| | - Guiting Lin
- Knuppe Molecular Urology Laboratory, Department of Urology, School of Medicine, University of California San Francisco, San Francisco, CA, 94143-0738, United States of America
| | - Amjad Alwaal
- Knuppe Molecular Urology Laboratory, Department of Urology, School of Medicine, University of California San Francisco, San Francisco, CA, 94143-0738, United States of America
| | - Xiaoyu Zhang
- Knuppe Molecular Urology Laboratory, Department of Urology, School of Medicine, University of California San Francisco, San Francisco, CA, 94143-0738, United States of America
| | - Guifang Wang
- Knuppe Molecular Urology Laboratory, Department of Urology, School of Medicine, University of California San Francisco, San Francisco, CA, 94143-0738, United States of America
| | - Xingyuan Jia
- Department of Urology, Beijing ChaoYang Hospital, Capital Medical University, 8 Gongtinanlu, Beijing, 100020, China
| | - Lia Banie
- Knuppe Molecular Urology Laboratory, Department of Urology, School of Medicine, University of California San Francisco, San Francisco, CA, 94143-0738, United States of America
| | - Jacqueline Villalta
- Knuppe Molecular Urology Laboratory, Department of Urology, School of Medicine, University of California San Francisco, San Francisco, CA, 94143-0738, United States of America
| | - Ching-Shwun Lin
- Knuppe Molecular Urology Laboratory, Department of Urology, School of Medicine, University of California San Francisco, San Francisco, CA, 94143-0738, United States of America
| | - Tom F. Lue
- Knuppe Molecular Urology Laboratory, Department of Urology, School of Medicine, University of California San Francisco, San Francisco, CA, 94143-0738, United States of America
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Mukhina TM, Nikolaienko TY. THE EFFECT OF CHLORINATION OF NUCLEOTIDE BASES ON THE CONFORMATIONAL PROPERTIES OF THYMIDINE MONOPHOSPHATE. Ukr Biochem J 2015; 87:141-55. [PMID: 26255348 DOI: 10.15407/ubj87.02.141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Recent studies on Escherichia coli bacteria cultivation, in which DNA thymine was replaced with 5-chlorouracil have refreshed the problem of understanding the changes to physical properties of DNA monomers resultant from chemical modifications. These studies have shown that the replacement did not affect the normal activities and division of the bacteria, but has significantly reduced its life span. In this paper a comparative analysis was carried out by the methods of computational experiment of a set of 687 possible conformers of natural monomeric DNA unit (2'-deoxyribonucleotide thymidine monophosphate) and 660 conformers of 5-chloro-2'-deoxyuridine monophosphate - a similar molecules in which the natural nitrogenous base thymine is substituted with 5-chlorouracil. Structures of stable conformers of the modified deoxyribonucleotide have been obtained and physical factors, which determine their variation from the conformers of the unmodified molecule have been analyzed. A comparative analysis of the elastic properties of conformers of investigated molecules and non-covalent interactions present in them was conducted. The results can be usedfor planning experiments on synthesis of artficial DNA suitable for incorporation into living organisms.
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Zdrowowicz M, Chomicz L, Żyndul M, Wityk P, Rak J, Wiegand TJ, Hanson CG, Adhikary A, Sevilla MD. 5-Thiocyanato-2'-deoxyuridine as a possible radiosensitizer: electron-induced formation of uracil-C5-thiyl radical and its dimerization. Phys Chem Chem Phys 2015; 17:16907-16. [PMID: 26059609 PMCID: PMC4481187 DOI: 10.1039/c5cp02081f] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
In this work, we have synthesized 5-thiocyanato-2'-deoxyuridine (SCNdU) along with the C6-deuterated nucleobase 5-thiocyanatouracil (6-D-SCNU) and studied their reactions with radiation-produced electrons. ESR spectra in γ-irradiated nitrogen-saturated frozen homogeneous solutions (7.5 M LiCl in H2O or D2O) of these compounds show that electron-induced S-CN bond cleavage occurs to form a thiyl radical (dU-5-S˙ or 6-D-U-5-S˙) and CN(-)via the initial π-anion radical (SCNdU˙(-)) intermediate in which the excess electron is on the uracil base. HPLC and LC-MS/MS studies of γ-irradiated N2-saturated aqueous solutions of SCNdU in the presence of sodium formate as a OH-radical scavenger at ambient temperature show the formation of the dU-5S-5S-dU dimer in preference to dU by about 10 to 1 ratio. This shows that both possible routes of electron-induced bond cleavage (dUC5-SCN and S-CN) in SCNdU˙(-) and dU-5-S˙ formation are preferred for the production of the σ-type uracilyl radical (dU˙) by 10 fold. DFT/M06-2x/6-31++G(d,p) calculations employing the polarizable continuum model (PCM) for aqueous solutions show that dU-5-S˙ and CN(-) formation was thermodynamically favored by over 15 kcal mol(-1) (ΔG) compared to dU˙ and SCN(-) production. The activation barriers for C5-S and S-CN bond cleavage in SCNdU˙(-) amount to 8.7 and 4.0 kcal mol(-1), respectively, favoring dU-5-S˙ and CN(-) formation. These results support the experimental observation of S-CN bond cleavage by electron addition to SCNdU that results in the formation of dU-5-S˙ and the subsequent dU-5S-5S-dU dimer. This establishes SCNdU as a potential radiosensitizer that could cause intra- and inter-strand crosslinking as well as DNA-protein crosslinking via S-S dimer formation.
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Affiliation(s)
- Magdalena Zdrowowicz
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland.
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Kitazawa Y, Ueta H, Hünig T, Sawanobori Y, Matsuno K. A novel multicolor immunostaining method using ethynyl deoxyuridine for analysis of in situ immunoproliferative response. Histochem Cell Biol 2015; 144:195-208. [PMID: 25976155 PMCID: PMC4534512 DOI: 10.1007/s00418-015-1329-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2015] [Indexed: 01/08/2023]
Abstract
Immune responses are generally accompanied by antigen presentation and proliferation and differentiation of antigen-specific lymphocytes (immunoproliferation), but analysis of these events in situ on tissue sections is very difficult. We have developed a new method of simultaneous multicolor immunofluorescence staining for immunohistology and flow cytometry using a thymidine analogue, 5-ethynyl-2′-deoxyuridine (EdU). Because of the small size of azide dye using click chemistry and elimination of DNA denaturation steps, EdU staining allowed for immunofluorescence staining of at least four colors including two different markers on a single-cell surface, which is impossible with the standard 5-bromo-2′-deoxyuridine method. By using two rat models, successfully detected parameters were the cluster of differentiation antigens including phenotypic and functional markers of various immune cells, histocompatibility complex antigens, and even some nuclear transcription factors. Proliferating cells could be further sorted and used for RT-PCR analysis. This method thus enables functional in situ time-kinetic analysis of immunoproliferative responses in a distinct domain of the lymphoid organs, which are quantitatively confirmed by flow cytometry.
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Affiliation(s)
- Yusuke Kitazawa
- />Department of Anatomy (Macro), Dokkyo Medical University, 880 Kitakobayashi, Mibu, Tochigi 321-0293 Japan
| | - Hisashi Ueta
- />Department of Anatomy (Macro), Dokkyo Medical University, 880 Kitakobayashi, Mibu, Tochigi 321-0293 Japan
| | - Thomas Hünig
- />Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Yasushi Sawanobori
- />Department of Anatomy (Macro), Dokkyo Medical University, 880 Kitakobayashi, Mibu, Tochigi 321-0293 Japan
| | - Kenjiro Matsuno
- />Department of Anatomy (Macro), Dokkyo Medical University, 880 Kitakobayashi, Mibu, Tochigi 321-0293 Japan
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Ligasová A, Strunin D, Friedecký D, Adam T, Koberna K. A fatal combination: a thymidylate synthase inhibitor with DNA damaging activity. PLoS One 2015; 10:e0117459. [PMID: 25671308 PMCID: PMC4324964 DOI: 10.1371/journal.pone.0117459] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 12/25/2014] [Indexed: 12/28/2022] Open
Abstract
2′-deoxy-5-ethynyluridine (EdU) has been previously shown to be a cell poison whose toxicity depends on the particular cell line. The reason is not known. Our data indicates that different efficiency of EdU incorporation plays an important role. The EdU-mediated toxicity was elevated by the inhibition of 2′-deoxythymidine 5′-monophosphate synthesis. EdU incorporation resulted in abnormalities of the cell cycle including the slowdown of the S phase and a decrease in DNA synthesis. The slowdown but not the cessation of the first cell division after EdU administration was observed in all of the tested cell lines. In HeLa cells, a 10 μM EdU concentration led to the cell death in the 100% of cells probably due to the activation of an intra S phase checkpoint in the subsequent S phase. Our data also indicates that this EdU concentration induces interstrand DNA crosslinks in HeLa cells. We suppose that these crosslinks are the primary DNA damage resulting in cell death. According to our results, the EdU-mediated toxicity is further increased by the inhibition of thymidylate synthase by EdU itself at its higher concentrations.
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Affiliation(s)
- Anna Ligasová
- Institute of Molecular and Translational Medicine, Faculty of Medicine, Palacký University, Olomouc, 779 00, Czech Republic
- * E-mail:
| | - Dmytro Strunin
- Institute of Molecular and Translational Medicine, Faculty of Medicine, Palacký University, Olomouc, 779 00, Czech Republic
| | - David Friedecký
- Institute of Molecular and Translational Medicine, Faculty of Medicine, Palacký University, Olomouc, 779 00, Czech Republic
| | - Tomáš Adam
- Institute of Molecular and Translational Medicine, Faculty of Medicine, Palacký University, Olomouc, 779 00, Czech Republic
| | - Karel Koberna
- Institute of Molecular and Translational Medicine, Faculty of Medicine, Palacký University, Olomouc, 779 00, Czech Republic
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Bourge M, Fort C, Soler MN, Satiat-Jeunemaître B, Brown SC. A pulse-chase strategy combining click-EdU and photoconvertible fluorescent reporter: tracking Golgi protein dynamics during the cell cycle. New Phytol 2015; 205:938-50. [PMID: 25266734 DOI: 10.1111/nph.13069] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 08/13/2014] [Indexed: 05/12/2023]
Abstract
Imaging or quantifying protein synthesis in cellulo through a well-resolved analysis of the cell cycle (also defining G1 subcompartments) is a methodological challenge. Click chemistry is the method of choice to reveal the thymidine analogue 5-ethynyl-2'-deoxyuridine (EdU) and track proliferating nuclei undergoing DNA synthesis. However, the click reaction quenches fluorescent proteins. Our challenge was to reconcile these two tools. A robust protocol based on a high-resolution cytometric cell cycle analysis in tobacco (Nicotiana tabacum) BY2 cells expressing fluorescent Golgi markers has been established. This was broadly applicable to tissues, cell clusters, and other eukaryotic material, and compatible with Scale clearing. EdU was then used with the photoconvertible protein sialyl transferase (ST)-Kaede as a Golgi marker in a photoconversion pulse-chase cytometric configuration resolving, in addition, subcompartments of G1. Quantitative restoration of protein fluorescence was achieved by introducing acidic EDTA washes to strip the copper from these proteins which were then imaged at neutral pH. The rate of synthesis of this Golgi membrane marker was low during early G1, but in the second half of G1 (30% of cycle duration) much of the synthesis occurred. Marker synthesis then persisted during S and G2. These insights into Golgi biology are discussed in terms of the cell's ability to adapt exocytosis to cell growth needs.
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Affiliation(s)
- Mickaël Bourge
- Pôle de Biologie Cellulaire, Imagif, Centre de Recherche de Gif (FRC3115), CNRS, Saclay Plant Sciences, 91198, Gif-sur-Yvette Cedex, France
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45
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Yang G, Li X, Yuan G, Liu P, Fan M. The effects of osterix on the proliferation and odontoblastic differentiation of human dental papilla cells. J Endod 2014; 40:1771-7. [PMID: 25258338 DOI: 10.1016/j.joen.2014.04.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 03/07/2014] [Accepted: 04/25/2014] [Indexed: 12/28/2022]
Abstract
INTRODUCTION Dental papilla cells (DPCs) are precursors of odontoblasts and have the potential to differentiate into odontoblasts. Osteoblasts and odontoblasts have many common characteristics. Osterix (Osx) is essential for osteoblast differentiation. However, no information is available for the effects of Osx on the odontoblastic differentiation of DPCs. The purpose of this study was to investigate the effects of Osx on the proliferation and odontoblastic differentiation of DPCs. METHODS An immortalized human dental papilla cell (hDPC) line was used. Osx was stably overexpressed or knocked down in hDPCs with infection of lentiviral particles to determine its biological effects on hDPCs. The proliferation of cells was measured by the 5-ethynyl-2'-deoxyuridine incorporation assay and direct cell counting. Expressions of dentin sialophosphoprotein, nestin, dentin matrix protein 1, and alkaline phosphatase were detected by real-time polymerase chain reaction to determine the odontoblastic differentiation of cells. The mineralization ability of cells was evaluated by von Kossa staining and alkaline phosphatase activity assay. RESULTS Overexpression of Osx retarded the proliferation of hDPCs, whereas knockdown of Osx increased the cell proliferation. Overexpression of Osx promoted the odontoblastic differentiation of hDPCs by up-regulating odontoblastic differentiation genes and increased the mineralization ability of hDPCs. Knockdown of Osx down-regulated odontoblastic differentiation genes and decreased the mineralization ability of hDPCs. CONCLUSIONS Osx might function as a potential regulator for the proliferation and odontoblastic differentiation of hDPCs.
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Affiliation(s)
- Guobin Yang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan
| | - Xiaoyan Li
- The State Key Laboratory Breeding Base of Basic Science of Stomatology and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan; Department of Endodontics, School and Hospital of Stomatology, Shandong University, Shandong Provincial Key Laboratory of Oral Biomedicine, Shandong, China
| | - Guohua Yuan
- The State Key Laboratory Breeding Base of Basic Science of Stomatology and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan
| | - Pingxian Liu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan
| | - Mingwen Fan
- The State Key Laboratory Breeding Base of Basic Science of Stomatology and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan.
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Yao M, Wang L, Shi Y, Qian Q, Yu D, Shi Y, Lu S, Yao D. [Intervention of glypican-3 genetic transcription on anti-proliferative effect of hepatoma cells with high metastatic potentiality]. Zhonghua Yi Xue Za Zhi 2014; 94:2544-2548. [PMID: 25410930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
OBJECTIVE To explore the silencing glypican-3 (GPC-3) gene transcription by specific small hairpin RNA (shRNA) on the inhibition of hepatoma cells with high metastatic potentiality and hepatoma growth. METHODS After MHCC-97H cells were transfected with higher effective GPC-3-shRNA, GPC-3 mRNA was analyzed by multiple FG-RT-PCR or protein by Western blot. Cell proliferation was detected by 5-ethynyl-2'-deoxyuridine and sulforhodamine B assay, its migratory metastasis and invasiveness by wound healing or transwell chamber system and cell apoptosis was detected by Caspase-Glo(®) 3/7 Luminescence assay. Nude mice were subcutaneously injected with stable MHCC-97H cells for observing the forming time or volume of xenograft tumors. And the expressions of GPC-3, β-catenin, p-GSK3β and CyclinD1 were analyzed by immunohistochemistry. RESULTS After shRNA1 transfection with high efficiency (>80%), the expression of GPC-3 was down-regulated to 75.6% (t = 15.473, P < 0.001) at mRNA level in accordance with its protein, inhibiting cell proliferation (71.1%, t = 10.468, P < 0.001) notably, decreasing its migration (80.1%, t = 32.697, P < 0.001) and invasiveness (69.1%, t = 39.647, P < 0.001). β-catenin was down-regulated (67.7%, t = 18.4, P < 0.001) and Gli1 increased (53.5%, t = -4.824, P = 0.008) with its protein. The average forming time of subcutaneous tumors was 11.2 days (d) in the shRNA group and it was significantly longer (P < 0.01) than that in the control (5.3 d) or shRNA-neg (5.5 d) group. And the average volume (65.5 mm(3)) of tumors with decreased GPC-3, β-catenin, p-GSK3β, and cyclinD1 expressions in the shRNA group was significantly smaller (P < 0.01) than that in the shRNA-neg (365.7 mm(3)) or control (404.8 mm(3)) group, respectively. CONCLUSION Specific shRNA might intervene effectively the GPC-3 gene transcription and inhibit invasion and tumor growth. Thus GPC-3 may become a potential molecular target for hepatoma gene therapy.
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Affiliation(s)
- Min Yao
- Research Center of Clinical Medicine, Nantong University, Nantong 226001, China
| | - Li Wang
- Research Center of Clinical Medicine, Nantong University, Nantong 226001, China
| | - Yun Shi
- Research Center of Clinical Medicine, Nantong University, Nantong 226001, China
| | - Qi Qian
- Research Center of Clinical Medicine, Nantong University, Nantong 226001, China
| | - Dandan Yu
- Research Center of Clinical Medicine, Nantong University, Nantong 226001, China
| | - Yang Shi
- Research Center of Clinical Medicine, Nantong University, Nantong 226001, China
| | - Shaolin Lu
- Research Center of Clinical Medicine, Nantong University, Nantong 226001, China
| | - Dengfu Yao
- Research Center of Clinical Medicine, Nantong University, Nantong 226001, China.
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Mori S, Morihiro K, Obika S. C5-azobenzene-substituted 2'-deoxyuridine-containing oligodeoxynucleotides for photo-switching hybridization. Molecules 2014; 19:5109-18. [PMID: 24759071 PMCID: PMC6271114 DOI: 10.3390/molecules19045109] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 04/15/2014] [Accepted: 04/17/2014] [Indexed: 11/17/2022] Open
Abstract
A new photoisomeric nucleoside dUAz bearing an azobenzene group at the C5-position of 2'-deoxyuridine was designed and synthesized. Photoisomerization of dUAz in oligodeoxynucleotides can be achieved rapidly and selectively with 365 nm (forward) and 450 nm (backward) irradiation. Thermal denaturation experiments revealed that dUAz stabilized the duplex in the cis-form and destabilized it in the trans-form with mismatch discrimination ability comparable to thymidine. These results indicate that dUAz could be a powerful material for reversibly manipulating nucleic acid hybridization with spatiotemporal control.
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Affiliation(s)
- Shohei Mori
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Kunihiko Morihiro
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
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Wiebusch L, Hagemeier C. Use of 5-ethynyl-2'-deoxyuridine labelling and flow cytometry to study cell cycle-dependent regulation of human cytomegalovirus gene expression. Methods Mol Biol 2014; 1119:123-32. [PMID: 24639222 DOI: 10.1007/978-1-62703-788-4_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
The cell cycle position at the time of infection has a profound influence on human cytomegalovirus (HCMV) gene expression and therefore needs consideration in the design and control of HCMV experiments. While G0/G1 cells support the immediate onset of viral transcription, cells progressing through the S and G2 cell cycle phases prevent HCMV from entering the lytic replication cycle. Here, we provide two fast and reliable protocols that allow one to determine the cell cycle distribution of the designated host cells and monitor viral protein expression as a function of the cell cycle state. Both protocols make use of the thymidine analogue 5-ethynyl-2'-deoxyuridine and "click" chemistry to label HCMV-non-permissive S phase cells in a gentle and sensitive way.
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Affiliation(s)
- Lüder Wiebusch
- Labor für Pädiatrische Molekularbiologie, Charité Universitätsmedizin, Augustenburger Platz 1, 13353, Berlin, Germany,
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Abstract
Thymidine analogues are powerful tools when studying DNA synthesis including DNA replication, repair and recombination. However, these analogues have been reported to have severe effects on cell-cycle progression and growth, the very processes being investigated in most of these studies. Here, we have analyzed the effects of 5-ethynyl-2′-deoxyuridine (EdU) and 5-Chloro-2′-deoxyuridine (CldU) using fission yeast cells and optimized the labelling procedure. We find that both analogues affect the cell cycle, but that the effects can be mitigated by using the appropriate analogue, short pulses of labelling and low concentrations. In addition, we report sequential labelling of two consecutive S phases using EdU and 5-bromo-2′-deoxyuridine (BrdU). Furthermore, we show that detection of replicative DNA synthesis is much more sensitive than DNA-measurements by flow cytometry.
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Affiliation(s)
- Silje Anda
- Department of Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Montebello, Norway
| | - Erik Boye
- Department of Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Montebello, Norway
| | - Beata Grallert
- Department of Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Montebello, Norway
- * E-mail:
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Gonda Y, Andrews WD, Tabata H, Namba T, Parnavelas JG, Nakajima K, Kohsaka S, Hanashima C, Uchino S. Robo1 regulates the migration and laminar distribution of upper-layer pyramidal neurons of the cerebral cortex. Cereb Cortex 2013; 23:1495-508. [PMID: 22661412 PMCID: PMC3643720 DOI: 10.1093/cercor/bhs141] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Laminar organization is a key feature of the mammalian cerebral cortex, but the mechanisms by which final positioning and "inside-out" distribution of neurons are determined remain largely unknown. Here, we demonstrate that Robo1, a member of the family of Roundabout receptors, regulates the correct positioning of layers II/III pyramidal neurons in the neocortex. Specifically, we used RNA interference in mice to suppress the expression of Robo1 in a subset of layers II/III neurons, and observed the positions of these cells at distinct developmental stages. In contrast to control neurons that migrated toward the pial surface by P1, Robo1-suppressed neurons exhibited a delay in entering the cortical plate at respective stages. Unexpectedly, after the first postnatal week, these neurons were predominantly located in the upper part of layers II/III, in contrast to control cells that were distributed throughout these layers. Sequential electroporation studies revealed that Robo1-suppressed cells failed to establish the characteristic inside-out neuronal distribution and, instead, they accumulated beneath the marginal zone regardless of their birthdate. These results demonstrate that Robo receptors play a crucial role in neocortical lamination and particularly in the positioning of layers II/III pyramidal neurons.
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Affiliation(s)
- Yuko Gonda
- Laboratory for Neocortical Development, RIKEN Center for Developmental Biology, Kobe 650-0047, Japan
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