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Conrad JW, Sowers ML, Yap DY, Cherryhomes E, Pettitt BM, Khanipov K, Sowers LC. Transition Mutations in the hTERT Promoter Are Unrelated to Potential i-motif Formation in the C-Rich Strand. Biomolecules 2023; 13:1308. [PMID: 37759708 PMCID: PMC10526324 DOI: 10.3390/biom13091308] [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] [Received: 07/03/2023] [Revised: 08/14/2023] [Accepted: 08/18/2023] [Indexed: 09/29/2023] Open
Abstract
Increased expression of the human telomere reverse transcriptase (hTERT) in tumors promotes tumor cell survival and diminishes the survival of patients. Cytosine-to-thymine (C-to-T) transition mutations (C250T or C228T) in the hTERT promoter create binding sites for transcription factors, which enhance transcription. The G-rich strand of the hTERT promoter can form G-quadruplex structures, whereas the C-rich strand can form an i-motif in which multiple cytosine residues are protonated. We considered the possibility that i-motif formation might promote cytosine deamination to uracil and C-to-T mutations. We computationally probed the accessibility of cytosine residues in an i-motif to attack by water. We experimentally examined regions of the C-rich strand to form i-motifs using pH-dependent UV and CD spectra. We then incubated the C-rich strand with and without the G-rich complementary strand DNA under various conditions, followed by deep sequencing. Surprisingly, deamination rates did not vary substantially across the 46 cytosines examined, and the two mutation hotspots were not deamination hotspots. The appearance of mutational hotspots in tumors is more likely the result of the selection of sequences with increased promoter binding affinity and hTERT expression.
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Affiliation(s)
- James W. Conrad
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Mark L. Sowers
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, TX 77555, USA
- MD-PhD Combined Degree Program, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Dianne Y. Yap
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Ellie Cherryhomes
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - B. Montgomery Pettitt
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Kamil Khanipov
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Lawrence C. Sowers
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Internal Medicine, The University of Texas Medical Branch, Galveston, TX 77555, USA
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2
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Baljinnyam T, Conrad JW, Sowers ML, Chang-Gu B, Herring JL, Hackfeld LC, Zhang K, Sowers LC. Characterization of a Novel Thermostable DNA Lyase Used To Prepare DNA for Next-Generation Sequencing. Chem Res Toxicol 2023; 36:162-176. [PMID: 36647573 PMCID: PMC9945173 DOI: 10.1021/acs.chemrestox.2c00172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Recently, we constructed a hybrid thymine DNA glycosylase (hyTDG) by linking a 29-amino acid sequence from the human thymine DNA glycosylase with the catalytic domain of DNA mismatch glycosylase (MIG) from M. thermoautotrophicum, increasing the overall activity of the glycosylase. Previously, it was shown that a tyrosine to lysine (Y126K) mutation in the catalytic site of MIG could convert the glycosylase activity to a lyase activity. We made the corresponding mutation to our hyTDG to create a hyTDG-lyase (Y163K). Here, we report that the hybrid mutant has robust lyase activity, has activity over a broad temperature range, and is active under multiple buffer conditions. The hyTDG-lyase cleaves an abasic site similar to endonuclease III (Endo III). In the presence of β-mercaptoethanol (β-ME), the abasic site unsaturated aldehyde forms a β-ME adduct. The hyTDG-lyase maintains its preference for cleaving opposite G, as with the hyTDG glycosylase, and the hyTDG-lyase and hyTDG glycosylase can function in tandem to cleave T:G mismatches. The hyTDG-lyase described here should be a valuable tool in studies examining DNA damage and repair. Future studies will utilize these enzymes to quantify T:G mispairs in cells, tissues, and genomic DNA using next-generation sequencing.
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Affiliation(s)
- Tuvshintugs Baljinnyam
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States
| | - James W Conrad
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States
| | - Mark L Sowers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States.,MD-PhD Combined Degree Program University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States
| | - Bruce Chang-Gu
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States.,MD-PhD Combined Degree Program University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States
| | - Jason L Herring
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States
| | - Linda C Hackfeld
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States
| | - Kangling Zhang
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States
| | - Lawrence C Sowers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States.,Department of Internal Medicine, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas77555, United States
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3
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Baljinnyam T, Sowers ML, Hsu CW, Conrad JW, Herring JL, Hackfeld LC, Sowers LC. Chemical and enzymatic modifications of 5-methylcytosine at the intersection of DNA damage, repair, and epigenetic reprogramming. PLoS One 2022; 17:e0273509. [PMID: 36037209 PMCID: PMC9423628 DOI: 10.1371/journal.pone.0273509] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 08/09/2022] [Indexed: 11/19/2022] Open
Abstract
The DNA of all living organisms is persistently damaged by endogenous reactions including deamination and oxidation. Such damage, if not repaired correctly, can result in mutations that drive tumor development. In addition to chemical damage, recent studies have established that DNA bases can be enzymatically modified, generating many of the same modified bases. Irrespective of the mechanism of formation, modified bases can alter DNA-protein interactions and therefore modulate epigenetic control of gene transcription. The simultaneous presence of both chemically and enzymatically modified bases in DNA suggests a potential intersection, or collision, between DNA repair and epigenetic reprogramming. In this paper, we have prepared defined sequence oligonucleotides containing the complete set of oxidized and deaminated bases that could arise from 5-methylcytosine. We have probed these substrates with human glycosylases implicated in DNA repair and epigenetic reprogramming. New observations reported here include: SMUG1 excises 5-carboxyuracil (5caU) when paired with A or G. Both TDG and MBD4 cleave 5-formyluracil and 5caU when mispaired with G. Further, TDG not only removes 5-formylcytosine and 5-carboxycytosine when paired with G, but also when mispaired with A. Surprisingly, 5caU is one of the best substrates for human TDG, SMUG1 and MBD4, and a much better substrate than T. The data presented here introduces some unexpected findings that pose new questions on the interactions between endogenous DNA damage, repair, and epigenetic reprogramming pathways.
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Affiliation(s)
- Tuvshintugs Baljinnyam
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Mark L. Sowers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
- MD-PhD Combined Degree Program, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Chia Wei Hsu
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
- MD-PhD Combined Degree Program, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - James W. Conrad
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Jason L. Herring
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Linda C. Hackfeld
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Lawrence C. Sowers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
- * E-mail:
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Hsu CW, Conrad JW, Sowers ML, Baljinnyam T, Herring JL, Hackfeld LC, Hatch SS, Sowers LC. A combinatorial system to examine the enzymatic repair of multiply damaged DNA substrates. Nucleic Acids Res 2022; 50:7406-7419. [PMID: 35776119 PMCID: PMC9303388 DOI: 10.1093/nar/gkac530] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 05/18/2022] [Accepted: 06/07/2022] [Indexed: 12/03/2022] Open
Abstract
DNA damage drives genetic mutations that underlie the development of cancer in humans. Multiple pathways have been described in mammalian cells which can repair this damage. However, most work to date has focused upon single lesions in DNA. We present here a combinatorial system which allows assembly of duplexes containing single or multiple types of damage by ligating together six oligonucleotides containing damaged or modified bases. The combinatorial system has dual fluorescent labels allowing examination of both strands simultaneously, in order to study interactions or competition between different DNA repair pathways. Using this system, we demonstrate how repair of oxidative damage in one DNA strand can convert a mispaired T:G deamination intermediate into a T:A mutation. We also demonstrate that slow repair of a T:G mispair, relative to a U:G mispair, by the human methyl-binding domain 4 DNA glycosylase provides a competitive advantage to competing repair pathways, and could explain why CpG dinucleotides are hotspots for C to T mutations in human tumors. Data is also presented that suggests repair of closely spaced lesions in opposing strands can be repaired by a combination of short and long-patch base excision repair and simultaneous repair of multiply damage sites can potentially lead to lethal double strand breaks.
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Affiliation(s)
- Chia Wei Hsu
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA.,MD-PhD Combined Degree Program, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - James W Conrad
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - Mark L Sowers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA.,MD-PhD Combined Degree Program, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - Tuvshintugs Baljinnyam
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - Jason L Herring
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - Linda C Hackfeld
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
| | - Sandra S Hatch
- Department of Radiation Oncology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA.,Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lawrence C Sowers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA.,Department of Internal Medicine, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555, USA
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5
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Hsu CW, Sowers ML, Baljinnyam T, Herring JL, Hackfeld LC, Tang H, Zhang K, Sowers LC. Measurement of deaminated cytosine adducts in DNA using a novel hybrid thymine DNA glycosylase. J Biol Chem 2022; 298:101638. [PMID: 35085553 PMCID: PMC8861164 DOI: 10.1016/j.jbc.2022.101638] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 01/16/2023] Open
Abstract
The hydrolytic deamination of cytosine and 5-methylcytosine drives many of the transition mutations observed in human cancer. The deamination-induced mutagenic intermediates include either uracil or thymine adducts mispaired with guanine. While a substantial array of methods exist to measure other types of DNA adducts, the cytosine deamination adducts pose unusual analytical problems, and adequate methods to measure them have not yet been developed. We describe here a novel hybrid thymine DNA glycosylase (TDG) that is comprised of a 29-amino acid sequence from human TDG linked to the catalytic domain of a thymine glycosylase found in an archaeal thermophilic bacterium. Using defined-sequence oligonucleotides, we show that hybrid TDG has robust mispair-selective activity against deaminated U:G and T:G mispairs. We have further developed a method for separating glycosylase-released free bases from oligonucleotides and DNA followed by GC-MS/MS quantification. Using this approach, we have measured for the first time the levels of total uracil, U:G, and T:G pairs in calf thymus DNA. The method presented here will allow the measurement of the formation, persistence, and repair of a biologically important class of deaminated cytosine adducts.
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Affiliation(s)
- Chia Wei Hsu
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, USA,MD-PhD Combined Degree Program, University of Texas Medical Branch, Galveston, Texas, USA
| | - Mark L. Sowers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, USA,MD-PhD Combined Degree Program, University of Texas Medical Branch, Galveston, Texas, USA
| | - Tuvshintugs Baljinnyam
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Jason L. Herring
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Linda C. Hackfeld
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Hui Tang
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Kangling Zhang
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Lawrence C. Sowers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, USA,Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, USA,For correspondence: Lawrence C. Sowers
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6
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Sowers LC, Blanton LS, Weaver SC, Urban RJ, Mouton CP. Pharmacological approaches to the treatment of COVID-19 patients. J Transl Sci 2020; 6:394. [PMID: 33042589 PMCID: PMC7543691] [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] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The current COVID-19 pandemic has presented unprecedented challenges to the world community. No effective therapies or vaccines have yet been established. Upon the basis of homologies to similar coronaviruses, several potential drug targets have been identified and are the focus of both laboratory and clinical investigation. The rationale for several of these drug candidates is presented in this review. Emerging clinical data has revealed that severe COVID-19 disease is associated with heightened inflammatory responses and a procoagulant state, suggesting that patient treatment strategies must extend beyond antiviral agents. Effective approaches to the treatment of vulnerable patients with comorbidities will render COVID-19 substantially more manageable.
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Affiliation(s)
- Lawrence C Sowers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas
| | - Lucas S Blanton
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas
| | - Scott C Weaver
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas
- World Reference Center for Emerging Viruses and Arboviruses
| | - Randall J Urban
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas
| | - Charles P Mouton
- Department of Family Medicine, University of Texas Medical Branch, Galveston, Texas
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7
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Zhang K, Xu P, Sowers JL, Machuca DF, Mirfattah B, Herring J, Tang H, Chen Y, Tian B, Brasier AR, Sowers LC. Proteome Analysis of Hypoxic Glioblastoma Cells Reveals Sequential Metabolic Adaptation of One-Carbon Metabolic Pathways. Mol Cell Proteomics 2017; 16:1906-1921. [PMID: 28874504 DOI: 10.1074/mcp.ra117.000154] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Indexed: 02/04/2023] Open
Abstract
Rapidly proliferating tumors are exposed to a hypoxic microenvironment because of their density, high metabolic consumption, and interruptions in blood flow because of immature angiogenesis. Cellular responses to hypoxia promote highly malignant and metastatic behavior, as well as a chemotherapy-resistant state. To better understand the complex relationships between hypoxic adaptations and cancer progression, we studied the dynamic proteome responses of glioblastoma cells exposed to hypoxia via an innovative approach: quantification of newly synthesized proteins using heavy stable-isotope arginine labeling combined with accurate assessment of cell replication by quantification of the light/heavy arginine ratio of peptides in histone H4. We found that hypoxia affects cancer cells in multiple intertwined ways: inflammation, typically with over-expressed glucose transporter (GLUT1), DUSP4/MKP2, and RelA proteins; a metabolic adaptation with overexpression of all glycolytic pathway enzymes for pyruvate/lactate synthesis; and the EMT (epithelial-mesenchymal transition) and cancer stem cell (CSC) renewal with characteristic morphological changes and mesenchymal/CSC protein expression profiles. For the first time, we identified the vitamin B12 transporter protein TCN2, which is essential for one-carbon metabolism, as being significantly downregulated. Further, we found, by knockdown and overexpression experiments, that TCN2 plays an important role in controlling cancer cell transformation toward the highly aggressive mesenchymal/CSC stage; low expression of TCN2 has an effect similar to hypoxia, whereas high expression of TCN2 can reverse it. We conclude that hypoxia induces sequential metabolic responses of one-carbon metabolism in tumor cells. Our mass spectrometry data are available via ProteomeXchange with identifiers PXD005487 (TMT-labeling) and PXD007280 (label-free).
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Affiliation(s)
- Kangling Zhang
- From the ‡Department of Pharmacology, University of Texas Medical Branch, Galveston (UTMB), Texas, 77555; .,¶Sealy Center for Molecular Medicine, UTMB, Galveston, Texas, 77555
| | - Pei Xu
- ‖Department of Neuroscience and Cell Biology, UTMB, Galveston, Texas, 77555
| | - James L Sowers
- ‖Department of Neuroscience and Cell Biology, UTMB, Galveston, Texas, 77555
| | - Daniel F Machuca
- From the ‡Department of Pharmacology, University of Texas Medical Branch, Galveston (UTMB), Texas, 77555
| | - Barsam Mirfattah
- From the ‡Department of Pharmacology, University of Texas Medical Branch, Galveston (UTMB), Texas, 77555
| | - Jason Herring
- From the ‡Department of Pharmacology, University of Texas Medical Branch, Galveston (UTMB), Texas, 77555
| | - Hui Tang
- From the ‡Department of Pharmacology, University of Texas Medical Branch, Galveston (UTMB), Texas, 77555
| | - Yan Chen
- ‖Department of Neuroscience and Cell Biology, UTMB, Galveston, Texas, 77555
| | - Bing Tian
- §Institute for Translational Sciences, UTMB, Galveston, Texas, 77555.,¶Sealy Center for Molecular Medicine, UTMB, Galveston, Texas, 77555
| | - Allan R Brasier
- §Institute for Translational Sciences, UTMB, Galveston, Texas, 77555.,¶Sealy Center for Molecular Medicine, UTMB, Galveston, Texas, 77555
| | - Lawrence C Sowers
- From the ‡Department of Pharmacology, University of Texas Medical Branch, Galveston (UTMB), Texas, 77555.,§Institute for Translational Sciences, UTMB, Galveston, Texas, 77555
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8
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Lagger S, Connelly JC, Schweikert G, Webb S, Selfridge J, Ramsahoye BH, Yu M, He C, Sanguinetti G, Sowers LC, Walkinshaw MD, Bird A. MeCP2 recognizes cytosine methylated tri-nucleotide and di-nucleotide sequences to tune transcription in the mammalian brain. PLoS Genet 2017; 13:e1006793. [PMID: 28498846 PMCID: PMC5446194 DOI: 10.1371/journal.pgen.1006793] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [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: 01/23/2017] [Revised: 05/26/2017] [Accepted: 05/02/2017] [Indexed: 01/10/2023] Open
Abstract
Mutations in the gene encoding the methyl-CG binding protein MeCP2 cause several neurological disorders including Rett syndrome. The di-nucleotide methyl-CG (mCG) is the classical MeCP2 DNA recognition sequence, but additional methylated sequence targets have been reported. Here we show by in vitro and in vivo analyses that MeCP2 binding to non-CG methylated sites in brain is largely confined to the tri-nucleotide sequence mCAC. MeCP2 binding to chromosomal DNA in mouse brain is proportional to mCAC + mCG density and unexpectedly defines large genomic domains within which transcription is sensitive to MeCP2 occupancy. Our results suggest that MeCP2 integrates patterns of mCAC and mCG in the brain to restrain transcription of genes critical for neuronal function. Rett Syndrome is a severe neurological disorder found in approximately 1:10.000 female births. The gene causing most cases of Rett Syndrome has been identified as methyl-CG binding protein 2 (MeCP2) which is an epigenetic reader protein, classically characterized as binding to CpG methylated (mCG) di-nucleotides. Although much research has focused on the binding capacities of MeCP2, its exact mode of action is still controversial. Here we show, that in addition to the classical mCG motif, frequently occurring mCAC tri-nucleotides are also bound by MeCP2. We additionally discover large genomic regions of high mCG + mCAC density that contain neuro-disease relevant genes sensitive to MeCP2 loss or overexpression. Our results re-emphasize MeCP2’s original proposed function as a transcriptional repressor whose purpose is to maintain the delicate balance of neuronal gene expression.
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Affiliation(s)
- Sabine Lagger
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - John C. Connelly
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Gabriele Schweikert
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
- School of Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Shaun Webb
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Jim Selfridge
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Bernard H. Ramsahoye
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Miao Yu
- Department of Chemistry and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, United States of America
- Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois, United States of America
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, United States of America
- Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois, United States of America
| | - Guido Sanguinetti
- School of Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Lawrence C. Sowers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Malcolm D. Walkinshaw
- Centre for Translational and Chemical Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Adrian Bird
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
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9
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Hsu CW, Sowers ML, Hsu W, Eyzaguirre E, Qiu S, Chao C, Mouton CP, Fofanov Y, Singh P, Sowers LC. How does inflammation drive mutagenesis in colorectal cancer? Trends Cancer Res 2017; 12:111-132. [PMID: 30147278 PMCID: PMC6107301] [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] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Colorectal cancer (CRC) is a major health challenge worldwide. Factors thought to be important in CRC etiology include diet, microbiome, exercise, obesity, a history of colon inflammation and family history. Interventions, including the use of non-steroidal anti-Inflammatory drugs (NSAIDs) and anti-inflammatory agents, have been shown to decrease incidence in some settings. However, our current understanding of the mechanistic details that drive CRC are insufficient to sort out the complex and interacting factors responsible for cancer-initiating events. It has been known for some time that the development of CRC involves mutations in key genes such as p53 and APC, and the sequence in which these mutations occur can determine tumor presentation. Observed recurrent mutations are dominated by C to T transitions at CpG sites, implicating the deamination of 5-methylcytosine (5mC) as a key initiating event in cancer-driving mutations. While it has been widely assumed that inflammation-mediated oxidation drives mutations in CRC, oxidative damage to DNA induces primarily G to T transversions, not C to T transitions. In this review, we discuss this unresolved conundrum, and specifically, we elucidate how the known nucleotide excision repair (NER) and base excision repair (BER) pathways, which are partially redundant and potentially competing, might provide a critical link between oxidative DNA damage and C to T mutations. Studies using recently developed next-generation DNA sequencing technologies have revealed the genetic heterogeneity in human tissues including tumors, as well as the presence of DNA damage. The capacity to follow DNA damage, repair and mutagenesis in human tissues using these emerging technologies could provide a mechanistic basis for understanding the role of oxidative damage in CRC tumor initiation. The application of these technologies could identify mechanism-based biomarkers useful in earlier diagnosis and aid in the development of cancer prevention strategies.
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Affiliation(s)
- Chia Wei Hsu
- MD/PhD program, University of Texas Medical Branch, Galveston, Texas
| | - Mark L Sowers
- MD/PhD program, University of Texas Medical Branch, Galveston, Texas
| | - Willie Hsu
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas
| | - Eduardo Eyzaguirre
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas
| | - Suimin Qiu
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas
| | - Celia Chao
- Department of Surgery, University of Texas Medical Branch, Galveston, Texas
| | - Charles P Mouton
- Department of Family Medicine, University of Texas Medical Branch, Galveston, Texas
| | - Yuri Fofanov
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, Texas
| | - Pomila Singh
- Department of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas
| | - Lawrence C Sowers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, Texas
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, USA
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López-García I, Gerő D, Szczesny B, Szoleczky P, Olah G, Módis K, Zhang K, Gao J, Wu P, Sowers LC, DeWitt D, Prough DS, Szabo C. Development of a stretch-induced neurotrauma model for medium-throughput screening in vitro: identification of rifampicin as a neuroprotectant. Br J Pharmacol 2016; 175:284-300. [PMID: 27723079 DOI: 10.1111/bph.13642] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 09/19/2016] [Accepted: 09/26/2016] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND AND PURPOSE We hypothesized that an in vitro, stretch-based model of neural injury may be useful to identify compounds that decrease the cellular damage in neurotrauma. EXPERIMENTAL APPROACH We screened three neural cell lines (B35, RN33B and SH-SY5Y) subjected to two differentiation methods and selected all-trans-retinoic acid-differentiated B35 rat neuroblastoma cells subjected to rapid stretch injury, coupled with a subthreshold concentration of H2 O2 , for the screen. The model induced marked alterations in gene expression and proteomic signature of the cells and culminated in delayed cell death (LDH release) and mitochondrial dysfunction [reduced 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) conversion]. Follow-up studies utilized human stem cell-derived neurons subjected to rapid stretch injury. KEY RESULTS From screening of a composite library of 3500 drugs, five drugs (when applied in a post-treatment regimen relative to stretch injury) improved both LDH and MTT responses. The effects of rifampicin were investigated in further detail. Rifampicin reduced cell necrosis and apoptosis and improved cellular bioenergetics. In a second model (stretch injury in human stem cell-derived neurons), rifampicin pretreatment attenuated LDH release, protected against the loss of neurite length and maintained neuron-specific class III β-tubulin immunoreactivity. CONCLUSIONS AND IMPLICATIONS We conclude that the current model is suitable for medium-throughput screening to identify compounds with neuroprotective potential. Rifampicin, when applied either in pre- or post-treatment, improves the viability of neurons subjected to stretch injury and protects against neurite loss. Rifampicin may be a candidate for repurposing for the therapy of traumatic brain injury. LINKED ARTICLES This article is part of a themed section on Inventing New Therapies Without Reinventing the Wheel: The Power of Drug Repurposing. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v175.2/issuetoc.
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Affiliation(s)
- Isabel López-García
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, TX, USA
| | - Domokos Gerő
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, TX, USA
| | - Bartosz Szczesny
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, TX, USA
| | - Petra Szoleczky
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, TX, USA
| | - Gabor Olah
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, TX, USA
| | - Katalin Módis
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, TX, USA
| | - Kangling Zhang
- Department of Pharmacology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jungling Gao
- Department of Neuroscience & Cell Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Ping Wu
- Department of Neuroscience & Cell Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Lawrence C Sowers
- Department of Pharmacology, University of Texas Medical Branch, Galveston, TX, USA
| | - Doug DeWitt
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, TX, USA
| | - Donald S Prough
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, TX, USA
| | - Csaba Szabo
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, TX, USA
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Ito I, Bhopale KK, Nishiguchi T, Lee JO, Herndon DN, Suzuki S, Sowers LC, Suzuki F, Kobayashi M. The Polarization of M2b Monocytes in Cultures of Burn Patient Peripheral CD14 + Cells Treated with a Selected Human CCL1 Antisense Oligodeoxynucleotide. Nucleic Acid Ther 2016; 26:269-276. [PMID: 27548631 DOI: 10.1089/nat.2016.0617] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
M2b macrophages (Mφ) play a major role in the increased susceptibility of subacutely burned patients, to sepsis stemming from enterococcal translocation. Certain opportunistic infections in severely burned mice have been controlled by murine CCL1 antisense oligodeoxynucleotide (ODN), a specific polarizer of mouse M2bMφ. In the present study, we have screened CCL1 antisense ODN, which is active against human M2bMφ. Among the 20 CCL1 antisense ODNs synthesized in our laboratory, HCA-11 was shown to be the most active polarizer for human CCL1+CD163+CD14+ cells. Burn patient CCL1+CD163+CD14+ cells (3 × 105 cells/mL) switched to quiescent CCL1-CD163-CD14+ cells within 48 h in cultures supplemented with 100 μg/mL of HCA-11. After treatment with a 25 μg/chimera dose of HCA-11, the bacterial growth was not observed in various organs of patient chimeras (γNSG mice inoculated with burn patient WBCs) infected with a lethal dose of Methicillin-resistant Staphylococcus aureus. The host antibacterial defenses against certain opportunistic pathogens should be improved in severely burned patients treated with a human CCL1 antisense ODN, HCA-11.
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Affiliation(s)
- Ichiaki Ito
- 1 Department of Internal Medicine, The University of Texas Medical Branch , Galveston, Texas
| | - Kamlesh K Bhopale
- 1 Department of Internal Medicine, The University of Texas Medical Branch , Galveston, Texas
| | - Tomoki Nishiguchi
- 1 Department of Internal Medicine, The University of Texas Medical Branch , Galveston, Texas
| | - Jong O Lee
- 2 Shriners Hospitals for Children , Galveston, Texas
| | | | - Sumihiro Suzuki
- 3 University of North Texas Health Science Center , Fort Worth, Texas
| | - Lawrence C Sowers
- 4 Department of Pharmacology and Toxicology, The University of Texas Medical Branch , Galveston, Texas
| | - Fujio Suzuki
- 1 Department of Internal Medicine, The University of Texas Medical Branch , Galveston, Texas.,2 Shriners Hospitals for Children , Galveston, Texas
| | - Makiko Kobayashi
- 1 Department of Internal Medicine, The University of Texas Medical Branch , Galveston, Texas.,2 Shriners Hospitals for Children , Galveston, Texas
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12
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Sowers JL, Mirfattah B, Xu P, Tang H, Park IY, Walker C, Wu P, Laezza F, Sowers LC, Zhang K. Quantification of histone modifications by parallel-reaction monitoring: a method validation. Anal Chem 2016; 87:10006-14. [PMID: 26356480 DOI: 10.1021/acs.analchem.5b02615] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abnormal epigenetic reprogramming is one of the major causes leading to irregular gene expression and regulatory pathway perturbations, in the cells, resulting in unhealthy cell development or diseases. Accurate measurements of these changes of epigenetic modifications, especially the complex histone modifications, are very important, and the methods for these measurements are not trivial. By following our previous introduction of PRM to targeting histone modifications (Tang, H.; Fang, H.; Yin, E.; Brasier, A. R.; Sowers, L. C.; Zhang, K. Multiplexed parallel reaction monitoring targeting histone modifications on the QExactive mass spectrometer. Anal. Chem. 2014, 86 (11), 5526-34), herein we validated this method by varying the protein/trypsin ratios via serial dilutions. Our data demonstrated that PRM with SILAC histones as the internal standards allowed reproducible measurements of histone H3/H4 acetylation and methylation in the samples whose histone contents differ at least one-order of magnitude. The method was further validated by histones isolated from histone H3 K36 trimethyltransferase SETD2 knockout mouse embryonic fibroblasts (MEF) cells. Furthermore, histone acetylation and methylation in human neural stem cells (hNSC) treated with ascorbic acid phosphate (AAP) were measured by this method, revealing that H3 K36 trimethylation was significantly down-regulated by 6 days of treatment with vitamin C.
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Affiliation(s)
| | | | | | | | - In Young Park
- Institute of Biosciences and Technology, Texas A&M Health Sciences Center , Houston, Texas 77030, United States
| | - Cheryl Walker
- Institute of Biosciences and Technology, Texas A&M Health Sciences Center , Houston, Texas 77030, United States
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13
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Patel JP, Sowers ML, Herring JL, Theruvathu JA, Emmett MR, Hawkins BE, Zhang K, DeWitt DS, Prough DS, Sowers LC. Measurement of Postreplicative DNA Metabolism and Damage in the Rodent Brain. Chem Res Toxicol 2015; 28:2352-63. [PMID: 26447562 PMCID: PMC7986959 DOI: 10.1021/acs.chemrestox.5b00359] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The DNA of all organisms is metabolically active due to persistent endogenous DNA damage, repair, and enzyme-mediated base modification pathways important for epigenetic reprogramming and antibody diversity. The free bases released from DNA either spontaneously or by base excision repair pathways constitute DNA metabolites in living tissues. In this study, we have synthesized and characterized the stable-isotope standards for a series of pyrimidines derived from the normal DNA bases by oxidation and deamination. We have used these standards to measure free bases in small molecule extracts from rat brain. Free bases are observed in extracts, consistent with both endogenous DNA damage and 5-methylcytosine demethylation pathways. The most abundant free base observed is uracil, and the potential sources of uracil are discussed. The free bases measured in tissue extracts constitute the end product of DNA metabolism and could be used to reveal metabolic disturbances in human disease.
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Affiliation(s)
- Jay P. Patel
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Mark L. Sowers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Jason L. Herring
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Jacob A. Theruvathu
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Mark R. Emmett
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Bridget E. Hawkins
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, Texas 77555, United States
- Moody Project for Translational Traumatic Brain Injury Research, Department of Anesthesiology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Kangling Zhang
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
- Moody Project for Translational Traumatic Brain Injury Research, Department of Anesthesiology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Douglas S. DeWitt
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, Texas 77555, United States
- Moody Project for Translational Traumatic Brain Injury Research, Department of Anesthesiology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Donald S. Prough
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, Texas 77555, United States
- Moody Project for Translational Traumatic Brain Injury Research, Department of Anesthesiology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Lawrence C. Sowers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
- Department of Internal Medicine, Division of Hematology and Oncology, University of Texas Medical Branch, Galveston, Texas 77555, United States
- Moody Project for Translational Traumatic Brain Injury Research, Department of Anesthesiology, University of Texas Medical Branch, Galveston, Texas 77555, United States
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14
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McLean LS, Watkins CN, Campbell P, Zylstra D, Rowland L, Amis LH, Scott L, Babb CE, Livingston WJ, Darwanto A, Davis WL, Senthil M, Sowers LC, Brantley E. Aryl Hydrocarbon Receptor Ligand 5F 203 Induces Oxidative Stress That Triggers DNA Damage in Human Breast Cancer Cells. Chem Res Toxicol 2015; 28:855-71. [PMID: 25781201 DOI: 10.1021/tx500485v] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Breast tumors often show profound sensitivity to exogenous oxidative stress. Investigational agent 2-(4-amino-3-methylphenyl)-5-fluorobenzothiazole (5F 203) induces aryl hydrocarbon receptor (AhR)-mediated DNA damage in certain breast cancer cells. Since AhR agonists often elevate intracellular oxidative stress, we hypothesize that 5F 203 increases reactive oxygen species (ROS) to induce DNA damage, which thwarts breast cancer cell growth. We found that 5F 203 induced single-strand break formation. 5F 203 enhanced oxidative DNA damage that was specific to breast cancer cells sensitive to its cytotoxic actions, as it did not increase oxidative DNA damage or ROS formation in nontumorigenic MCF-10A breast epithelial cells. In contrast, AhR agonist and procarcinogen benzo[a]pyrene and its metabolite, 1,6-benzo[a]pyrene quinone, induced oxidative DNA damage and ROS formation, respectively, in MCF-10A cells. In sensitive breast cancer cells, 5F 203 activated ROS-responsive kinases: c-Jun-N-terminal kinase (JNK) and p38 mitogen activated protein kinase (p38). AhR antagonists (alpha-naphthoflavone, CH223191) or antioxidants (N-acetyl-l-cysteine, EUK-134) attenuated 5F 203-mediated JNK and p38 activation, depending on the cell type. Pharmacological inhibition of AhR, JNK, or p38 attenuated 5F 203-mediated increases in intracellular ROS, apoptosis, and single-strand break formation. 5F 203 induced the expression of cytoglobin, an oxidative stress-responsive gene and a putative tumor suppressor, which was diminished with AhR, JNK, or p38 inhibition. Additionally, 5F 203-mediated increases in ROS production and cytoglobin were suppressed in AHR100 cells (AhR ligand-unresponsive MCF-7 breast cancer cells). Our data demonstrate 5F 203 induces ROS-mediated DNA damage at least in part via AhR, JNK, or p38 activation and modulates the expression of oxidative stress-responsive genes such as cytoglobin to confer its anticancer action.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Lawrence C Sowers
- ⊥Department of Pharmacology and Toxicology, University of Texas Medical Branch at Galveston, Galveston, Texas 77555, United States
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15
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Theruvathu JA, Darwanto A, Hsu CW, Sowers LC. The effect of Pot1 binding on the repair of thymine analogs in a telomeric DNA sequence. Nucleic Acids Res 2014; 42:9063-73. [PMID: 25053838 PMCID: PMC4132724 DOI: 10.1093/nar/gku602] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [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: 03/21/2014] [Revised: 06/05/2014] [Accepted: 06/23/2014] [Indexed: 12/31/2022] Open
Abstract
Telomeric DNA can form duplex regions or single-stranded loops that bind multiple proteins, preventing it from being processed as a DNA repair intermediate. The bases within these regions are susceptible to damage; however, mechanisms for the repair of telomere damage are as yet poorly understood. We have examined the effect of three thymine (T) analogs including uracil (U), 5-fluorouracil (5FU) and 5-hydroxymethyluracil (5hmU) on DNA-protein interactions and DNA repair within the GGTTAC telomeric sequence. The replacement of T with U or 5FU interferes with Pot1 (Pot1pN protein of Schizosaccharomyces pombe) binding. Surprisingly, 5hmU substitution only modestly diminishes Pot1 binding suggesting that hydrophobicity of the T-methyl group likely plays a minor role in protein binding. In the GGTTAC sequence, all three analogs can be cleaved by DNA glycosylases; however, glycosylase activity is blocked if Pot1 binds. An abasic site at the G or T positions is cleaved by the endonuclease APE1 when in a duplex but not when single-stranded. Abasic site formation thermally destabilizes the duplex that could push a damaged DNA segment into a single-stranded loop. The inability to enzymatically cleave abasic sites in single-stranded telomere regions would block completion of the base excision repair cycle potentially causing telomere attrition.
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Affiliation(s)
- Jacob A Theruvathu
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch, 3.330 Basic Science Building, 301 University Blvd, Galveston, TX 77555-0617, USA
| | - Agus Darwanto
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch, 3.330 Basic Science Building, 301 University Blvd, Galveston, TX 77555-0617, USA
| | - Chia Wei Hsu
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch, 3.330 Basic Science Building, 301 University Blvd, Galveston, TX 77555-0617, USA
| | - Lawrence C Sowers
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch, 3.330 Basic Science Building, 301 University Blvd, Galveston, TX 77555-0617, USA
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16
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Tang H, Fang H, Yin E, Brasier AR, Sowers LC, Zhang K. Multiplexed parallel reaction monitoring targeting histone modifications on the QExactive mass spectrometer. Anal Chem 2014; 86:5526-34. [PMID: 24823915 DOI: 10.1021/ac500972x] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Histone acetylation and methylation play an important role in the regulation of gene expression. Irregular patterns of histone global acetylation and methylation have frequently been seen in various diseases. Quantitative analysis of these patterns is of high value for the evaluation of disease development and of outcomes from therapeutic treatment. Targeting histone acetylation and methylation by selected reaction monitoring (SRM) is one of the current quantitative methods. Here, we reported the use of the multiplexed parallel reaction monitoring (PRM) method on the QExactive mass spectrometer to target previously known lysine acetylation and methylation sites of histone H3 and H4 for the purpose of establishing precursor-product pairs for SRM. 55 modified peptides among which 29 were H3 K27/K36 modified peptides were detected from 24 targeted precursor ions included in the inclusion list. The identification was carried out directly from the trypsin digests of core histones that were separated without derivatization on a homemade capillary column packed with Waters YMC ODS-AQ reversed phase materials. Besides documenting the higher-energy c-trap dissociation (HCD) MS(2) spectra of previously known histone H3/H4 acetylated and methylated tryptic peptides, we identified novel H3 K18 methylation, H3 K27 monomethyl/acetyl duel modifications, H2B K23 acetylation, and H4 K20 acetylation in mammalian histones. The information gained from these experiments sets the foundation for quantification of histone modifications by targeted mass spectrometry methods directly from core histone samples.
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Affiliation(s)
- Hui Tang
- Department of Pharmacology, University of Texas Medical Branch , Galveston, Texas 77555, United States
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Abstract
Malignant brain tumors are among the most lethal of human tumors, with limited treatment options currently available. A complex array of recurrent genetic and epigenetic changes has been observed in gliomas that collectively result in derangements of common cell signaling pathways controlling cell survival, proliferation, and invasion. One important determinant of gene expression is DNA methylation status, and emerging studies have revealed the importance of a recently identified demethylation pathway involving 5-hydroxymethylcytosine (5hmC). Diminished levels of the modified base 5hmC is a uniform finding in glioma cell lines and patient samples, suggesting a common defect in epigenetic reprogramming. Within the tumor microenvironment, infiltrating immune cells increase oxidative DNA damage, likely promoting both genetic and epigenetic changes that occur during glioma evolution. In this environment, glioma cells are selected that utilize multiple metabolic changes, including changes in the metabolism of the amino acids glutamate, tryptophan, and arginine. Whereas altered metabolism can promote the destruction of normal tissues, glioma cells exploit these changes to promote tumor cell survival and to suppress adaptive immune responses. Further understanding of these metabolic changes could reveal new strategies that would selectively disadvantage tumor cells and redirect host antitumor responses toward eradication of these lethal tumors.
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Affiliation(s)
- James L Sowers
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch (UTMB), Galveston, TX, USA
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18
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Theruvathu JA, Yin YW, Pettitt BM, Sowers LC. Comparison of the structural and dynamic effects of 5-methylcytosine and 5-chlorocytosine in a CpG dinucleotide sequence. Biochemistry 2013; 52:8590-8. [PMID: 24147911 DOI: 10.1021/bi400980c] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Inflammation-mediated reactive molecules can result in an array of oxidized and halogenated DNA-damage products, including 5-chlorocytosine ((Cl)C). Previous studies have shown that (Cl)C can mimic 5-methylcytosine ((m)C) and act as a fraudulent epigenetic signal, promoting the methylation of previously unmethylated DNA sequences. Although the 5-halouracils are good substrates for base-excision repair, no repair activity has yet been identified for (Cl)C. Because of the apparent biochemical similarities of (m)C and (Cl)C, we have investigated the effects of (m)C and (Cl)C substitution on oligonucleotide structure and dynamics. In this study, we have constructed oligonucleotide duplexes containing C, (Cl)C, and (m)C within a CpG dinucleotide. The thermal and thermodynamic stability of these duplexes were found to be experimentally indistinguishable. Crystallographic structures of duplex oligonucleotides containing (m)C or (Cl)C were determined to 1.2 and 1.9 Å resolution, respectively. Both duplexes are B-form and are superimposable on a previously determined structure of a cytosine-containing duplex with a rmsd of approximately 0.25 Å. NMR solution studies indicate that all duplexes containing cytosine or the cytosine analogues are normal B-form and that no structural perturbations are observed surrounding the site of each substitution. The magnitude of the base-stacking-induced upfield shifts for nonexchangeable base proton resonances are similar for each of the duplexes examined, indicating that neither (m)C nor (Cl)C significantly alter base-stacking interactions. The (Cl)C analogue is paired with G in an apparently normal geometry; however, the G-imino proton of the (Cl)C-G base pair resonates to higher field relative to (m)C-G or C-G, indicating a weaker imino hydrogen bond. Using selective ¹⁵N-enrichment and isotope-edited NMR, we observe that the amino group of (Cl)C rotates at roughly half of the rate of the corresponding amino groups of the C-G and (m)C-G base pairs. The altered chemical shifts of hydrogen-bonding proton resonances for the (Cl)C-G base pair as well as the slower rotation of the (Cl)C amino group can be attributed to the electron-withdrawing inductive property of the 5-chloro substituent. The apparent similarity of duplexes containing (m)C and (Cl)C demonstrated here is in accord with results of previous biochemical studies and further suggests that (Cl)C is likely to be an unusually persistent form of DNA damage.
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Affiliation(s)
- Jacob A Theruvathu
- Department of Pharmacology & Toxicology, The University of Texas Medical Branch , 3.330 Basic Science Building, 301 University Boulevard, Galveston, Texas 77555, United States
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Carter M, Voth AR, Scholfield MR, Rummel B, Sowers LC, Ho PS. Enthalpy–Entropy Compensation in Biomolecular Halogen Bonds Measured in DNA Junctions. Biochemistry 2013; 52:4891-903. [DOI: 10.1021/bi400590h] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Megan Carter
- Department of Biochemistry and
Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Andrea Regier Voth
- Department of Biochemistry and
Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Matthew R. Scholfield
- Department of Biochemistry and
Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Brittany Rummel
- Department of Biochemistry and
Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Lawrence C. Sowers
- Department of Pharmacology and
Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - P. Shing Ho
- Department of Biochemistry and
Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, United States
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Ibrahim YI, Ninnis JR, Hopper AO, Deming DD, Zhang AX, Herring JL, Sowers LC, McMahon TJ, Power GG, Blood AB. Inhaled nitric oxide therapy increases blood nitrite, nitrate, and s-nitrosohemoglobin concentrations in infants with pulmonary hypertension. J Pediatr 2012; 160:245-51. [PMID: 21907348 PMCID: PMC3237823 DOI: 10.1016/j.jpeds.2011.07.040] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2010] [Revised: 06/30/2011] [Accepted: 07/25/2011] [Indexed: 01/07/2023]
Abstract
OBJECTIVE To measure the circulating concentrations of nitric oxide (NO) adducts with NO bioactivity after inhaled NO (iNO) therapy in infants with pulmonary hypertension. STUDY DESIGN In this single center study, 5 sequential blood samples were collected from infants with pulmonary hypertension before, during, and after therapy with iNO (n = 17). Samples were collected from a control group of hospitalized infants without pulmonary hypertension (n = 16) and from healthy adults for comparison (n = 12). RESULTS After beginning iNO (20 ppm) whole blood nitrite levels increased approximately two-fold within 2 hours (P<.01). Whole blood nitrate levels increased to 4-fold higher than baseline during treatment with 20 ppm iNO (P<.01). S-nitrosohemoglobin increased measurably after beginning iNO (P<.01), whereas iron nitrosyl hemoglobin and total hemoglobin-bound NO-species compounds did not change. CONCLUSION Treatment of pulmonary hypertensive infants with iNO results in increases in levels of nitrite, nitrate, and S-nitrosohemoglobin in circulating blood. We speculate that these compounds may be carriers of NO bioactivity throughout the body and account for peripheral effects of iNO in the brain, heart, and other organs.
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Affiliation(s)
- Yomna I. Ibrahim
- Department of Pediatrics, Division of Neonatology, School of Medicine, Loma Linda University, Loma Linda, California, USA 92354
| | - Janet R. Ninnis
- Department of Pediatrics, Division of Neonatology, School of Medicine, Loma Linda University, Loma Linda, California, USA 92354
| | - Andrew O. Hopper
- Department of Pediatrics, Division of Neonatology, School of Medicine, Loma Linda University, Loma Linda, California, USA 92354
| | - Douglas D. Deming
- Department of Pediatrics, Division of Neonatology, School of Medicine, Loma Linda University, Loma Linda, California, USA 92354
| | - Amy X. Zhang
- Department of Medicine, Duke University, Durham NC 27710
| | - Jason L. Herring
- Department of Biochemistry School of Medicine, Loma Linda University, Loma Linda, California, USA 92354
| | - Lawrence C. Sowers
- Department of Biochemistry School of Medicine, Loma Linda University, Loma Linda, California, USA 92354
| | | | - Gordon G. Power
- Center for Perinatal Biology and School of Medicine, Loma Linda University, Loma Linda, California, USA 92354
| | - Arlin B. Blood
- Center for Perinatal Biology and School of Medicine, Loma Linda University, Loma Linda, California, USA 92354,Department of Pediatrics, Division of Neonatology, School of Medicine, Loma Linda University, Loma Linda, California, USA 92354,Correspondence to: Arlin B. Blood, PhD Department of Pediatrics, Division of Neonatology School of Medicine, Loma Linda University, Loma Linda, California, USA 92354 Phone: 909-558-4800 Fax: 909-558-0298
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Seiberling KA, Church CA, Herring JL, Sowers LC. Epigenetics of chronic rhinosinusitis and the role of the eosinophil. Int Forum Allergy Rhinol 2011; 2:80-4. [PMID: 22311846 DOI: 10.1002/alr.20090] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 06/20/2011] [Accepted: 06/22/2011] [Indexed: 01/11/2023]
Abstract
BACKGROUND One theory for the pathogenesis of chronic rhinosinusitis with nasal polyps (CRSwNP) involves aberration in the expression of genes that maintain the sinonasal innate immune system. We propose that the alteration in gene expression seen in CRSwNP is a result of oxidative byproducts of eosinophils. Activated eosinophils and neutrophils may lead to the production of hypobromous acid (HOBr) and hypochlorous acid (HOCL) and the posttranslational modification products 5-bromocytosine (5BrC) and 5-chlorocytosine (5ClC), respectively. 5BrC and 5ClC may cause aberrant methylation of cytosine during DNA replication and mimic the endogenous methylation signal associated with gene silencing. We propose to use gas chromatography-mass spectrometry (GC-MS) to identify the presence of 5BrC and 5ClC in CRSwNP patients. METHODS Patients with CRSwNP undergoing endoscopic sinus surgery were prospectively recruited into this study. Using GC-MS, tissue specimens were analyzed for the presence of 5BrC, 5ClC, and methylated cytosine. RESULTS Tissue specimens from 14 patients with CRSwNP and 3 normal controls were processed using GC-MS. CRSwNP specimens demonstrate elevated levels of 5BrC and 5ClC compared to normal controls. CONCLUSION Eosinophils, which are predominantly found in CRSwNP, may lead to DNA modification and gene silencing via 5BrC and aberrant methylation patterns and may help explain the pathogenesis of CRSwNP.
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Affiliation(s)
- Kristin A Seiberling
- Department of Otolaryngology-Head and Neck Surgery, Loma Linda University, Loma Linda, CA 92354, USA.
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22
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Xiong L, Darwanto A, Sharma S, Herring J, Hu S, Filippova M, Filippov V, Wang Y, Chen CS, Duerksen-Hughes PJ, Sowers LC, Zhang K. Mass spectrometric studies on epigenetic interaction networks in cell differentiation. J Biol Chem 2011; 286:13657-68. [PMID: 21335548 DOI: 10.1074/jbc.m110.204800] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Arrest of cell differentiation is one of the leading causes of leukemia and other cancers. Induction of cell differentiation using pharmaceutical agents has been clinically attempted for the treatment of these cancers. Epigenetic regulation may be one of the underlying molecular mechanisms controlling cell proliferation or differentiation. Here, we report on the use of proteomics-based differential protein expression analysis in conjunction with quantification of histone modifications to decipher the interconnections among epigenetic modifications, their modifying enzymes or mediators, and changes in the associated pathways/networks that occur during cell differentiation. During phorbol-12-myristate 13-acetate-induced differentiation of U937 cells, fatty acid synthesis and its metabolic processing, the clathrin-coated pit endocytosis pathway, and the ubiquitin/26 S proteasome degradation pathways were up-regulated. In addition, global histone H3/H4 acetylation and H2B ubiquitination were down-regulated concomitantly with impaired chromatin remodeling machinery, RNA polymerase II complexes, and DNA replication. Differential protein expression analysis established the networks linking histone hypoacetylation to the down-regulated expression/activity of p300 and linking histone H2B ubiquitination to the RNA polymerase II-associated FACT-RTF1-PAF1 complex. Collectively, our approach has provided an unprecedentedly systemic set of insights into the role of epigenetic regulation in leukemia cell differentiation.
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Affiliation(s)
- Lei Xiong
- Department of Chemistry, University of California, Riverside, California 92521, USA
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23
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Blood AB, Schroeder HJ, Terry MH, Merrill-Henry J, Bragg SL, Vrancken K, Liu T, Herring JL, Sowers LC, Wilson SM, Power GG. Inhaled nitrite reverses hemolysis-induced pulmonary vasoconstriction in newborn lambs without blood participation. Circulation 2011; 123:605-12. [PMID: 21282501 DOI: 10.1161/circulationaha.110.001073] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
BACKGROUND Nitrite can be converted to nitric oxide (NO) by a number of different biochemical pathways. In newborn lambs, an aerosol of inhaled nitrite has been found to reduce pulmonary blood pressure, possibly acting via conversion to NO by reaction with intraerythrocytic deoxyhemoglobin. If so, the vasodilating effects of nitrite would be attenuated by free hemoglobin in plasma that would rapidly scavenge NO. METHODS AND RESULTS Pulmonary vascular pressures and resistances to flow were measured in anesthetized newborn lambs. Plasma hemoglobin concentrations were then elevated, resulting in marked pulmonary hypertension. This effect was attenuated if infused hemoglobin was first oxidized to methemoglobin, which does not scavenge NO. These results further implicate NO as a tonic pulmonary vasodilator. Next, while free hemoglobin continued to be infused, the lambs were given inhaled NO gas (20 ppm), inhaled sodium nitrite aerosol (0.87 mol/L), or an intravascular nitrite infusion (3 mg/h bolus, 5 mg · kg⁻¹ · h⁻¹ infusion). Inhaled NO and inhaled nitrite aerosol both resulted in pulmonary vasodilation. Intravascular infusion of nitrite, however, did not. Increases in exhaled NO gas were observed in lambs while breathing the nitrite aerosol (≈ 20 ppb NO) but not during intravascular infusion of nitrite. CONCLUSIONS We conclude that the pulmonary vasodilating effect of inhaled nitrite results from its conversion to NO in airway and parenchymal lung tissue and is not dependent on reactions with deoxyhemoglobin in the pulmonary circulation. Inhaled nitrite aerosol remains a promising candidate to reduce pulmonary hypertension in clinical application.
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Affiliation(s)
- Arlin B Blood
- Department of Pediatrics, Division of Neonatology, Center for Perinatal Biology, Loma Linda University School of Medicine, Loma Linda, CA, USA.
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24
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Lao VV, Darwanto A, Sowers LC. Impact of base analogues within a CpG dinucleotide on the binding of DNA by the methyl-binding domain of MeCP2 and methylation by DNMT1. Biochemistry 2010; 49:10228-36. [PMID: 20979427 DOI: 10.1021/bi1011942] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The epigenetic control of transcription requires the selective recognition of methylated CpG dinucleotides by methylation-sensitive sequence-specific DNA binding proteins. In order to probe the mechanism of selective interaction of the methyl-binding protein with methylated DNA, we have prepared a series of oligonucleotides containing modified purines and pyrimidines at the recognition site, and we have examined the binding of these oligonucleotides to the methyl-binding domain (MBD) of the methyl-CpG-binding protein 2 (MeCP2). Our results suggest that pyrimidine 5-substituents similar in size to a methyl group facilitate protein binding; however, binding affinity does not correlate with the hydrophobicity of the substituent, and neither the 4-amino group of 5-methylcytosine (mC) nor Watson-Crick base pair geometry is essential for MBD binding. However, 5-substituted uracil analogues in one strand do not direct human DNA methyltransferase 1 (DNMT1) methylation of the opposing strand, as does mC. Important recognition elements do include the guanine O6 and N7 atoms present in the major groove. Unexpectedly, removal of the guanine 2-amino group from the minor groove substantially enhances MBD binding, likely resulting from DNA bending at the substitution site. The enhanced binding of the MBD to oligonucleotides containing several cytosine analogues observed here is better explained by a DNA-protein interface mediated by structured water as opposed to hydrophobic interactions.
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Affiliation(s)
- Victoria Valinluck Lao
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350, United States
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25
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Ito S, D'Alessio AC, Taranova OV, Hong K, Sowers LC, Zhang Y. Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature 2010; 466:1129-33. [PMID: 20639862 PMCID: PMC3491567 DOI: 10.1038/nature09303] [Citation(s) in RCA: 1871] [Impact Index Per Article: 133.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Revised: 08/26/2010] [Accepted: 06/28/2010] [Indexed: 12/13/2022]
Abstract
DNA methylation is one of the best-characterized epigenetic modifications. Although the enzymes that catalyse DNA methylation have been characterized, enzymes responsible for demethylation have been elusive. A recent study indicates that the human TET1 protein could catalyse the conversion of 5-methylcytosine (5mC) of DNA to 5-hydroxymethylcytosine (5hmC), raising the possibility that DNA demethylation may be a Tet1-mediated process. Here we extend this study by demonstrating that all three mouse Tet proteins (Tet1, Tet2 and Tet3) can also catalyse a similar reaction. Tet1 has an important role in mouse embryonic stem (ES) cell maintenance through maintaining the expression of Nanog in ES cells. Downregulation of Nanog via Tet1 knockdown correlates with methylation of the Nanog promoter, supporting a role for Tet1 in regulating DNA methylation status. Furthermore, knockdown of Tet1 in pre-implantation embryos results in a bias towards trophectoderm differentiation. Thus, our studies not only uncover the enzymatic activity of the Tet proteins, but also demonstrate a role for Tet1 in ES cell maintenance and inner cell mass cell specification.
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Abstract
Inflammation-mediated hypochlorous acid (HOCl) can damage DNA, DNA precursors, and other biological molecules, thereby producing an array of damage products such as 5-chlorouracil (ClU). In this study, we prepared and studied 5-chloro-2'-deoxyuridine (CldU) and ClU-containing oligonucleotide templates. We demonstrate that human K-562 cells grown in culture with 10 muM CldU incorporate substantial amounts of CldU without significant toxicity. When in the template, ClU residues pair with dATP but also with dGTP, in a pH-dependent manner with incorporation by human polymerase beta, avian myeloblastosis virus reverse transcriptase (AMV-RT), and Escherichia coli Klenow fragment (exo(-)) polymerase. The enhanced miscoding of ClU is attributed to the electron-withdrawing 5-chlorine substituent that promotes the formation of an ionized ClU-G mispair. When mispaired with G, ClU is targeted for removal by human glycosylases. The formation, incorporation, and repair of ClU could promote transition mutations and other forms of heritable DNA damage.
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Affiliation(s)
- Cherine H Kim
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350, USA
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27
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Abstract
The selection of nucleoside triphosphates by a polymerase is controlled by several energetic and structural features, including base pairing geometry as well as sugar structure and conformation. Whereas base pairing has been considered exhaustively, substantially less is known about the role of sugar modifications for both nucleotide incorporation and primer extension. In this study, we synthesized oligonucleotides containing 2'-fluoro-modified nucleosides with constrained sugar pucker in an internucleotide position and, for the first time, at a primer 3'-end. The thermodynamic stability of these duplexes was examined. The nucleoside 2'-deoxy-2'-fluoroarabinofuranosyluracil [U(2'F(ara))] favors the 2'-endo conformation (DNA-like), while 2'-deoxy-2'-fluororibofuranosyluracil [U(2'F(ribo))] favors the 3'-endo conformation (RNA-like). Oligonucleotides containing U(2'F(ara)) have slightly higher melting temperatures (T(m)) than those containing U(2'F(ribo)) when located in internucleotide positions or at the 3'-end and when correctly paired with adenine or mispaired with guanine. However, both modifications decrease the magnitude of DeltaH degrees and DeltaS degrees for duplex formation in all sequence contexts. In examining the thermodynamic properties for this set of oligonucleotides, we find entropy-enthalpy compensation is apparent. Our thermodynamic findings led to a series of experiments with DNA ligase that reveal, contrary to expectation based upon observed T(m) values, that the duplex containing the U(2'F(ribo)) analogue is more easily ligated. The 2'-fluoro-2'-deoxynucleosides examined here are valuable probes of the impact of sugar constraint and are also members of an important class of antitumor and antiviral agents. The data reported here may facilitate an understanding of the biological properties of these agents, as well as the contribution of sugar conformation to replication fidelity.
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Affiliation(s)
- Adides A. Williams
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350
| | - Agus Darwanto
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350
| | - Jacob A. Theruvathu
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350
| | - Artur Burdzy
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350
| | - Jonathan W. Neidigh
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350
| | - Lawrence C. Sowers
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350
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28
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Abstract
Hypochlorous acid (HOCl) from activated neutrophils at sites of inflammation can react with and damage biological molecules, including nucleic acids. The reaction of HOCl with cytosine analogues can generate multiple products, including 5-chlorouracil (ClU). In this paper, we have constructed oligonucleotides containing ClU paired opposite guanine (ClU-G). Melting studies indicate that oligonucleotide duplexes containing the ClU-G mispair are substantially less stable than those containing a ClU-A base pair. The melting temperature of the ClU-G mispair is not experimentally distinguishable from that of a T-G pair. NMR studies indicate that the ClU-G base pair adopts a wobble geometry at neutral pH, similar to a T-G mispair. The exchangeable protons of the ClU-G mispair broaden rapidly with an increase in temperature, indicating that the ClU-G mispair is less stable and opens more easily than the surrounding adjacent base pairs. Unlike the ClU-A base pair studied previously [Theruvathu, J. A., et al. (2009) Biochemistry 48, 7539-7546], the ClU-G mispair undergoes a pH-dependent structural change, assuming an ionized base pair configuration that approximates a Watson-Crick base pair at higher pH. Ionization of ClU in a DNA template could promote mispair formation and mutation, in accord with previous studies on other 5-halouracil analogues. The electron-withdrawing 5-chloro substituent facilitates ionization of the ClU N3 proton, promoting mispair formation, but it also renders the glycosidic bond susceptible to base cleavage by DNA repair glycosylases.
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Affiliation(s)
- Jacob A Theruvathu
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350, USA
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29
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Chan N, Obenaus A, Tan A, Sakata N, Mace J, Peverini R, Chinnock R, Sowers LC, Hathout E. Monitoring neovascularization of intraportal islet grafts by dynamic contrast enhanced magnetic resonance imaging. Islets 2009; 1:249-55. [PMID: 21099279 DOI: 10.4161/isl.1.3.9862] [Citation(s) in RCA: 12] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Fifteen thousand youths are diagnosed yearly with type 1 diabetes mellitus. Pancreatic islet transplantation has been shown clinically to provide short-term (~1 year) insulin independence. However, challenges associated with early vascularization of transplanted islet grafts and long-term islet survival remain. We utilized dynamic contrast enhanced magnetic resonance imaging (DCE MRI) to monitor neovascularization of islets transplanted into the right lobe of the liver in a syngeneic mouse model system. The left lobe received no islets and served as a control. DCE data were analyzed for temporal dynamics of contrast (gadolinium) extravasation and the results were fit to a Tofts two-compartment exchange model. We observed maximal right lobe enhancement at seven days post-transplantation. Histological examination up to 28 days was used to confirm imaging results. DCE-derived enhancement strongly correlated with immunohistochemical measures of neovascularization. To our knowledge, these results are the first to demonstrate using a FDA approved contrast agent that DCE MRI can effectively and non-invasively monitor the progression of angiogenesis in intraportal islet grafts.
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Affiliation(s)
- Nathaniel Chan
- Islet Transplant Laboratory, Department of Pediatrics, Loma Linda University School of Medicine, Loma Linda, CA, USA
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30
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Chan NK, Obenaus A, Tan A, Sakata N, Mace J, Peverini R, Chinnock R, Sowers LC, Hathout E. Monitoring neovascularization of intraportal islet grafts by dynamic contrast enhanced magnetic resonance imaging. Islets 2009; 1:249-255. [PMID: 20428485 PMCID: PMC2860316] [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] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/08/2023] Open
Abstract
Fifteen thousand youths are diagnosed yearly with type 1 diabetes mellitus. Pancreatic islet transplantation has been shown clinically to provide short-term (~1 year) insulin independence. However, challenges associated with early vascularization of transplanted islet grafts and long-term islet survival remain. We utilized dynamic contrast enhanced magnetic resonance imaging (DCE MRI) to monitor neovascularization of islets transplanted into the right lobe of the liver in a syngeneic mouse model. The left lobe received no islets and served as a control. DCE data were analyzed for temporal dynamics of contrast (gadolinium) extravasation and the results were fit to a Tofts two-compartment exchange model. We observed maximal right lobe enhancement at seven days post-transplantation. Histological examination up to 28 days was used to confirm imaging results. DCE-derived enhancement strongly correlated with immunohistochemical measures of neovascularization. To our knowledge these results are the first to demonstrate, using a FDA approved contrast agent, that DCE MRI can effectively and non-invasively monitor the progression of angiogenesis in intraportal islet grafts.
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Affiliation(s)
- Nathaniel K Chan
- Islet Transplant Laboratory; Department of Pediatrics; Loma Linda University School of Medicine; Loma Linda, CA USA
| | - Andre Obenaus
- Department of Radiation Medicine; Loma Linda University School of Medicine; Loma Linda, CA USA
| | - Annie Tan
- Islet Transplant Laboratory; Department of Pediatrics; Loma Linda University School of Medicine; Loma Linda, CA USA
| | - Naoaki Sakata
- Islet Transplant Laboratory; Department of Pediatrics; Loma Linda University School of Medicine; Loma Linda, CA USA
- Division of Hepato-Biliary Pancreatic Surgery; Department of Surgery; Tohoku University Graduate School of Medicine; Sendai, Japan
| | - John Mace
- Islet Transplant Laboratory; Department of Pediatrics; Loma Linda University School of Medicine; Loma Linda, CA USA
| | - Ricardo Peverini
- Islet Transplant Laboratory; Department of Pediatrics; Loma Linda University School of Medicine; Loma Linda, CA USA
| | - Richard Chinnock
- Islet Transplant Laboratory; Department of Pediatrics; Loma Linda University School of Medicine; Loma Linda, CA USA
| | - Lawrence C. Sowers
- Islet Transplant Laboratory; Department of Pediatrics; Loma Linda University School of Medicine; Loma Linda, CA USA
| | - Eba Hathout
- Islet Transplant Laboratory; Department of Pediatrics; Loma Linda University School of Medicine; Loma Linda, CA USA
- Correspondence to: Eba Hathout;
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31
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Darwanto A, Farrel A, Rogstad DK, Sowers LC. Characterization of DNA glycosylase activity by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Anal Biochem 2009; 394:13-23. [PMID: 19607800 PMCID: PMC3990469 DOI: 10.1016/j.ab.2009.07.015] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [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: 04/02/2009] [Revised: 07/07/2009] [Accepted: 07/09/2009] [Indexed: 11/25/2022]
Abstract
The DNA of all organisms is persistently damaged by endogenous reactive molecules. Most of the single-base endogenous damage is repaired through the base excision repair (BER) pathway that is initiated by members of the DNA glycosylase family. Although the BER pathway is often considered to proceed through a common abasic site intermediate, emerging evidence indicates that there are likely distinct branches reflected by the multitude of chemically different 3' and 5' ends generated at the repair site. In this study, we have applied matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) to the analysis of model DNA substrates acted on by recombinant glycosylases. We examine the chemical identity of several possible abasic site and nicked intermediates generated by monofunctional and bifunctional glycosylases. Our results suggest that the intermediate from endoIII/Nth might not be a simple beta-elimination product as described previously. On the basis of (18)O incorporation experiments, we propose a new mechanism for the endoIII/Nth family of glycosylases that may resolve several of the previous controversies. We further demonstrate that the use of an array of lesion-containing oligonucleotides can be used to rapidly examine the substrate preferences of a given glycosylase. Some of the lesions examined here can be acted on by more than one glycosylase, resulting in a spectrum of damaged intermediates for each lesion, suggesting that the sequence and coordination of repair activities that act on these lesions may influence the biological outcome of damage repair.
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Affiliation(s)
- Agus Darwanto
- Department of Basic Science, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA
| | - Alvin Farrel
- Department of Basic Science, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA
| | - Daniel K. Rogstad
- Department of Basic Science, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA
| | - Lawrence C. Sowers
- Department of Basic Science, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA
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32
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Theruvathu JA, Kim CH, Rogstad DK, Neidigh JW, Sowers LC. Base pairing configuration and stability of an oligonucleotide duplex containing a 5-chlorouracil-adenine base pair. Biochemistry 2009; 48:7539-46. [PMID: 19618901 DOI: 10.1021/bi9007947] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Inflammation-mediated reactive molecules can damage DNA by oxidation and chlorination. The biological consequences of this damage are as yet incompletely understood. In this paper, we have constructed oligonucleotides containing 5-chlorouracil (ClU), one of the known inflammation damage products. The thermodynamic stability, base pairing configuration, and duplex conformation of oligonucleotides containing ClU paired opposite adenine have been examined. NMR spectra reveal that the ClU-A base pair adopts a geometry similar to that of the T-A base pair, and the ClU-A base pair-containing duplex adopts a normal B-form conformation. The line width of the imino proton of the ClU residue is substantially greater than that of the corresponding T imino proton; however, this difference is not attributed to a reduced thermal or thermodynamic stability or to an increased level of proton exchange with solvent. While the NMR studies reveal an increased level of chemical exchange for the ClU imino proton of the ClU-A base pair, the ClU residue is not a target for removal by the Escherichia coli mispaired uracil glycosylase, which senses damage-related helix instability. The results of this study are consistent with previous reports indicating that the DNA of replicating cells can tolerate substantial substitution with ClU. The fraudulent, pseudo-Watson-Crick ClU-A base pair is sufficiently stable to avoid glycosylase removal and, therefore, might constitute a persistent form of cellular DNA damage.
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Affiliation(s)
- Jacob A Theruvathu
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350, USA
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33
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Herring JL, Rogstad DK, Sowers LC. Enzymatic methylation of DNA in cultured human cells studied by stable isotope incorporation and mass spectrometry. Chem Res Toxicol 2009; 22:1060-8. [PMID: 19449810 DOI: 10.1021/tx900027w] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enzymatic methylation of cytosine residues in DNA, in conjunction with covalent histone modifications, establishes an epigenetic code essential for the proper control of gene expression in higher organisms. Once established during cellular differentiation, the epigenetic code must be faithfully transmitted to progeny cells. However, epigenetic perturbations can be found in most if not all cancer cells, and the mechanisms leading to these changes are not well understood. In this paper, we describe a series of experiments aimed at understanding the dynamic process of DNA methylation that follows DNA replication. Cells in culture can be propagated in the presence of (15)N-enriched uridine, which labels the pyrimidine precursor pool as well as newly replicated DNA. Simultaneous culture in the presence of (2)H-enriched methionine results in labeling of newly methylated cytosine residues. An ensemble of 5-methylcytosine residues differing in the degree of isotopic enrichment is generated, which can be examined by mass spectrometry. Using this method, we demonstrate that the kinetics of both DNA replication and methylation of newly replicated DNA are indistinguishable. The majority of methylation following DNA replication is shown to occur on the newly synthesized DNA. The method reported here does, however, suggest an unexpected methylation of parental DNA during DNA replication, which might indicate a previously undescribed chromatin remodeling process. The method presented here will be useful in monitoring the dynamic process of DNA methylation and will allow a more detailed understanding of the mechanisms of clinically used methylation inhibitors and environmental toxicants.
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Affiliation(s)
- Jason L Herring
- Department of Basic Sciences, Loma Linda University School of Medicine, Alumni Hall for Basic Science, Room 101, 11021 Campus Street, Loma Linda, California 92350, USA
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Rogstad DK, Herring JL, Theruvathu JA, Burdzy A, Perry CC, Neidigh JW, Sowers LC. Chemical decomposition of 5-aza-2'-deoxycytidine (Decitabine): kinetic analyses and identification of products by NMR, HPLC, and mass spectrometry. Chem Res Toxicol 2009; 22:1194-204. [PMID: 19480391 DOI: 10.1021/tx900131u] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The nucleoside analogue 5-aza-2'-deoxycytidine (Decitabine, DAC) is one of several drugs in clinical use that inhibit DNA methyltransferases, leading to a decrease of 5-methylcytosine in newly replicated DNA and subsequent transcriptional activation of genes silenced by cytosine methylation. In addition to methyltransferase inhibition, DAC has demonstrated toxicity and potential mutagenicity, and can induce a DNA-repair response. The mechanisms accounting for these events are not well understood. DAC is chemically unstable in aqueous solutions, but there is little consensus between previous reports as to its half-life and corresponding products of decomposition at physiological temperature and pH, potentially confounding studies on its mechanism of action and long-term use in humans. Here, we have employed a battery of analytical methods to estimate kinetic rates and to characterize DAC decomposition products under conditions of physiological temperature and pH. Our results indicate that DAC decomposes into a plethora of products, formed by hydrolytic opening and deformylation of the triazine ring, in addition to anomerization and possibly other changes in the sugar ring structure. We also discuss the advantages and problems associated with each analytical method used. The results reported here will facilitate ongoing studies and clinical trials aimed at understanding the mechanisms of action, toxicity, and possible mutagenicity of DAC and related analogues.
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Affiliation(s)
- Daniel K Rogstad
- Department of Basic Sciences, Loma Linda University School of Medicine, Alumni Hall for Basic Science, Room 101, 11021 Campus Street, Loma Linda, California 92350, USA
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35
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Neidigh JW, Darwanto A, Williams AA, Wall NR, Sowers LC. Cloning and characterization of Rhodotorula glutinis thymine hydroxylase. Chem Res Toxicol 2009; 22:885-93. [PMID: 19341313 DOI: 10.1021/tx8004482] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thymine hydroxylase (TH) is a member of the alpha-ketoglutarate-dependent nonheme iron dioxygenase family that includes a series of DNA repair proteins including alkB. Substantial interest in this family of enzymes derives from their capacity to modify DNA bases and precursors by oxidation. Previously, a sequence has been published for cloned Rhodotorula glutinis TH. However, the minimal reported activity of this enzyme, coupled with inconsistencies with previously published mass spectrometry data, compelled us to reexamine TH. The sequence reported here differs from the previously reported sequence at two amino acid positions and is consistent with previously reported mass spectrometry data. The cloned enzyme characterized in this report displayed substantial activity, indicating that the sequence differences are critical for activity. The substrate selectivity of TH against a series of pyrimidine analogues is consistent with that reported for the wild-type enzyme and, in part, explains the mode of selection of uracil analogues. A preliminary model of the active site has been constructed for the purposes of comparing TH with other members of this family. TH and alkB share in common the capacity to oxidize N-methyl groups. However, TH has the added capacity to oxidize the 5-methyl group of thymine, a property that is potentially important for enzymes that could act on DNA and modify DNA-protein interactions.
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Affiliation(s)
- Jonathan W Neidigh
- Department of Basic Sciences, Loma Linda University School of Medicine, Alumni Hall for Basic Science, Room 101, 11021 Campus Street, Loma Linda, California 92350, USA
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Darwanto A, Theruvathu JA, Sowers JL, Rogstad DK, Pascal T, Goddard W, Sowers LC. Mechanisms of base selection by human single-stranded selective monofunctional uracil-DNA glycosylase. J Biol Chem 2009; 284:15835-46. [PMID: 19324873 PMCID: PMC2708880 DOI: 10.1074/jbc.m807846200] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [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: 10/10/2008] [Revised: 03/10/2009] [Indexed: 12/11/2022] Open
Abstract
hSMUG1 (human single-stranded selective monofunctional uracil-DNA glyscosylase) is one of three glycosylases encoded within a small region of human chromosome 12. Those three glycosylases, UNG (uracil-DNA glycosylase), TDG (thymine-DNA glyscosylase), and hSMUG1, have in common the capacity to remove uracil from DNA. However, these glycosylases also repair other lesions and have distinct substrate preferences, indicating that they have potentially redundant but not overlapping physiological roles. The mechanisms by which these glycosylases locate and selectively remove target lesions are not well understood. In addition to uracil, hSMUG1 has been shown to remove some oxidized pyrimidines, suggesting a role in the repair of DNA oxidation damage. In this paper, we describe experiments in which a series of oligonucleotides containing purine and pyrimidine analogs have been used to probe mechanisms by which hSMUG1 distinguishes potential substrates. Our results indicate that the preference of hSMUG1 for mispaired uracil over uracil paired with adenine is best explained by the reduced stability of a duplex containing a mispair, consistent with previous reports with Escherichia coli mispaired uracil-DNA glycosylase. We have also extended the substrate range of hSMUG1 to include 5-carboxyuracil, the last in the series of damage products from thymine methyl group oxidation. The properties used by hSMUG1 to select damaged pyrimidines include the size and free energy of solvation of the 5-substituent but not electronic inductive properties. The observed distinct mechanisms of base selection demonstrated for members of the uracil glycosylase family help explain how considerable diversity in chemical lesion repair can be achieved.
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Affiliation(s)
- Agus Darwanto
- From the Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, California 92350 and
| | - Jacob A. Theruvathu
- From the Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, California 92350 and
| | - James L. Sowers
- From the Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, California 92350 and
| | - Daniel K. Rogstad
- From the Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, California 92350 and
| | - Tod Pascal
- the Department of Chemistry, California Institute of Technology, Pasadena, California 91125
| | - William Goddard
- the Department of Chemistry, California Institute of Technology, Pasadena, California 91125
| | - Lawrence C. Sowers
- From the Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, California 92350 and
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Lao VV, Herring JL, Kim CH, Darwanto A, Soto U, Sowers LC. Incorporation of 5-chlorocytosine into mammalian DNA results in heritable gene silencing and altered cytosine methylation patterns. Carcinogenesis 2009; 30:886-93. [PMID: 19279184 DOI: 10.1093/carcin/bgp060] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Cytosine methylation patterns are essential for the proper control of gene expression in higher vertebrates. Although alterations in methylation patterns are frequently observed in human tumors, neither the mechanisms for establishing methylation patterns during normal development nor the mechanisms leading to pathological alterations of methylation patterns are currently known. While epidemiological studies have implicated inflammation in cancer etiology, a mechanistic link has yet to be established. Investigations of inflammation-mediated DNA damage may have provided important new insights. Our in vitro studies revealed that the inflammation-mediated DNA damage product, 5-chlorocytosine, could direct fraudulent methylation of previously unmethylated CpG sites. The purpose of this study was to recapitulate our in vitro findings by introducing 5-chlorocytosine residues into the DNA of replicating mammalian cells and to examine its impact on gene expression and cytosine methylation patterns. CHO-K1 cells hemizygous for the hprt gene were electroporated with the triphosphates of cytosine [2'-deoxycytidine-5'-triphosphate (dCTP)], 5-methylcytosine [5-methyl-2'-deoxycytidine-5'-triphosphate (MedCTP)] and 5'-chloro-2'-deoxycytidine-5'-triphosphate (CldCTP), and then selected with 6-thioguanine for silencing the hprt gene. Both modified nucleotides, MedCTP and CldCTP, but not unmodified dCTP, silenced hprt gene expression. Subsequent bisulfite pyrosequencing of CpG sites within the hprt promoter region of the selected cells confirmed hypermethylation, although global methylation levels as measured by gas chromatography-mass spectrometry did not change. Modified nucleotide-induced gene silencing could be reversed with 5-aza-2'-deoxycytidine indicating an epigenetic rather than mutagenic alteration. These results provide further evidence that the inflammation damage product 5-chlorocytosine could be a link between inflammation and cancer development.
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Affiliation(s)
- Victoria Valinluck Lao
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
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Titova E, Ostrowski RP, Kevil CG, Tong W, Rojas H, Sowers LC, Zhang JH, Tang J. Reduced brain injury in CD18-deficient mice after experimental intracerebral hemorrhage. J Neurosci Res 2009; 86:3240-5. [PMID: 18615643 DOI: 10.1002/jnr.21762] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Many studies have indicated leukocytes are a major contributor to brain injuries caused by intracerebral hemorrhage (ICH). Leukocyte-expressed CD18 is important for neutrophil-endothelial interactions in the vasculature, and CD18 deficiency protects against ischemia-reperfusion injury. We investigated whether CD18 deficiency provides protection against ICH-induced brain injury. Male wild-type (WT) CD18(+/+) mice and CD18(-/-) -knockout mice were used in this study. ICH was induced by a collagenase injection. Mortality, neurological function, brain edema, and myeloperoxidase (MPO) activity as well as tissue expression of nitrotyrosine and MPO were evaluated 24 hr after ICH. We discovered significantly reduced brain edema and diminished mortality with a concomitant decrease in MPO and nitrotyrosine immunoreactivity in brains of CD18-knockout mice.
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Affiliation(s)
- Elena Titova
- Department of Physiology and Pharmacology, Loma Linda University, Loma Linda, CA 92354, USA
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Abstract
Inflammation-mediated, neutrophil-derived hypochlorous acid can damage DNA and result in the chlorination damage products 5-chlorocytosine and 5-chlorouracil as well as the oxidation damage products 5-hydroxycytosine and 5-hydroxyuracil. While 5-chlorocytosine could potentially perturb epigenetic signals if formed at a CpG dinucleotide, the remaining products are miscoding and could result in transition mutations. In this article, we have investigated the reaction of hypochlorous acid with an oligonucleotide site-specifically enriched with 15N to probe the reactivity of cytosine at CpG. These experiments demonstrate directly the formation of 5-chlorocytosine at a CpG dinucleotide in duplex DNA. We observe that chlorination relative to oxidation damage is greater at CpG by a factor of approximately two, whereas similar amounts of 5-chlorocytosine and 5-hydroxycytosine are formed at two non-CpG sites examined. The relative amounts of deamination of the cytosine to uracil derivatives are similar at CpG and non-CpG sites. Overall, we observe that the reactivity of cytosine at CpG and non-CpG sites toward hypochlorous acid induced damage is similar (5-chlorocytosine > 5-hydroxycytosine > 5-hydroxyuracil > 5-chlorouracil), with a greater proportion of chlorination damage at CpG sites. These results are in accord with the potential of inflammation-mediated DNA damage to both induce transition mutations and to perturb epigenetic signals.
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Affiliation(s)
- Joseph I Kang
- Department of Basic Science, Loma Linda University School of Medicine, Loma Linda, California 92350, USA
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Cui Z, Theruvathu JA, Farrel A, Burdzy A, Sowers LC. Characterization of synthetic oligonucleotides containing biologically important modified bases by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Anal Biochem 2008; 379:196-207. [PMID: 18485883 PMCID: PMC3985270 DOI: 10.1016/j.ab.2008.04.031] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [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: 01/23/2008] [Revised: 04/11/2008] [Accepted: 04/18/2008] [Indexed: 11/16/2022]
Abstract
Oligonucleotides containing modified bases are commonly used for biochemical and biophysical studies to assess the impact of specific types of chemical damage on DNA structure and function. In contrast to the synthesis of oligonucleotides with normal DNA bases, oligonucleotide synthesis with modified bases often requires modified synthetic or deprotection conditions. Furthermore, several modified bases of biological interest are prone to further damage during synthesis and oligonucleotide isolation. In this article, we describe the application of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) to the characterization of a series of modified synthetic oligonucleotides. The potential for and limits in obtaining high mass accuracy for confirming oligonucleotide composition are discussed. Examination of the isotope cluster is also proposed as a method for confirming oligonucleotide elemental composition. MALDI-TOF-MS analysis of the unpurified reaction mixture can be used to confirm synthetic sequence and to reveal potential problems during synthesis. Analysis during and after purification can yield important information on depurination and base oxidation. It can also reveal unexpected problems that can occur with nonstandard synthesis, deprotection, or purification strategies. Proper characterization of modified oligonucleotides is essential for the correct interpretation of experiments performed with these substrates, and MALDI-TOF-MS analysis provides a simple yet extensive method of characterization that can be used at multiple stages of oligonucleotide production and use.
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Affiliation(s)
- Zhengfang Cui
- Department of Basic Science, Loma Linda University School of Medicine, Loma Linda, California
| | - Jacob A. Theruvathu
- Department of Basic Science, Loma Linda University School of Medicine, Loma Linda, California
| | - Alvin Farrel
- Department of Basic Science, Loma Linda University School of Medicine, Loma Linda, California
| | - Artur Burdzy
- Department of Basic Science, Loma Linda University School of Medicine, Loma Linda, California
| | - Lawrence C. Sowers
- Department of Basic Science, Loma Linda University School of Medicine, Loma Linda, California
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Calderon TC, Wu W, Rawson RA, Sakala EP, Sowers LC, Boskovic DS, Angeles DM. Effect of mode of birth on purine and malondialdehyde in umbilical arterial plasma in normal term newborns. J Perinatol 2008; 28:475-81. [PMID: 18368062 PMCID: PMC4158434 DOI: 10.1038/jp.2008.29] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
OBJECTIVE To examine the effect of mode of birth on plasma purine and malondialdehyde levels in normal term infants. STUDY DESIGN Umbilical arterial cord blood was obtained immediately after birth from a convenience sample of 119 normal term newborns born by vaginal delivery, with or without oxytocin augmentation or by elective cesarean delivery. Plasma was analyzed for purine and/or malondialdehyde levels. Numeric data were analyzed utilizing independent samples t-test and ordinal data were analyzed using Mann-Whitney test. Correlation coefficients were obtained using Spearman's rho. RESULT Uric acid levels were significantly elevated (P<0.001) in neonates undergoing vaginal birth, compared to neonates born by elective cesarean delivery. When the effect of oxytocin and length of labor was analyzed, neonates born to mothers on oxytocin had lower hypoxanthine, significantly lower xanthine (P=0.05) and higher uric acid levels. In addition, malondialdehyde levels were significantly higher (P<0.006) in neonates born to mothers who received oxytocin compared to neonates born to mothers without oxytocin augmentation. We also found significant correlations between malondialdehyde (MDA) and hypoxanthine (r=-0.465, P<0.039) and between MDA and xanthine (r=-0.753, P=0.003) in neonates born via oxytocin-augmented birth. Mode of birth had no statistically significant effect on clinical outcomes, although infants born by elective cesarean had higher incidence of acute respiratory distress and transient tachypnea of the newborn compared to those born vaginally. CONCLUSION Neonates born by elective cesarean had the lowest purine levels in cord blood compared to neonates born vaginally. Oxytocin augmentation is associated with some degree of uterine hyperstimulation which may enhance the ATP degradation pathway resulting in the rapid conversion of hypoxanthine to xanthine and xanthine to uric acid. Significantly higher MDA levels in neonates whose mothers received oxytocin as well as significant correlation between MDA and the purines hypoxanthine and xanthine, suggest free-radical production, most likely due to xanthine oxidase activation. However, despite differences in plasma purine and malondialdehyde levels, no significant differences were seen in neonatal outcome. Further studies are required to fully characterize the effect of mode of birth on purine metabolism and free-radical production.
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Affiliation(s)
- TC Calderon
- Department of Biochemistry, Loma Linda University, Loma Linda, CA, USA
| | - W Wu
- Department of Biochemistry, Loma Linda University, Loma Linda, CA, USA
| | - RA Rawson
- Department of Biochemistry, Loma Linda University, Loma Linda, CA, USA
| | - EP Sakala
- Department of Obstetrics and Gynecology, Loma Linda University, Loma Linda, CA, USA
| | - LC Sowers
- Department of Biochemistry, Loma Linda University, Loma Linda, CA, USA
| | - DS Boskovic
- Department of Biochemistry, Loma Linda University, Loma Linda, CA, USA
| | - DM Angeles
- Department of Physiology and Pharmacology, Loma Linda University, Loma Linda, CA, USA
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Liu P, Theruvathu JA, Darwanto A, Lao VV, Pascal T, Goddard W, Sowers LC. Mechanisms of base selection by the Escherichia coli mispaired uracil glycosylase. J Biol Chem 2008; 283:8829-36. [PMID: 18208817 DOI: 10.1074/jbc.m707174200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The repair of the multitude of single-base lesions formed daily in cells of all living organisms is accomplished primarily by the base excision repair pathway that initiates repair through a series of lesion-selective glycosylases. In this article, single-turnover kinetics have been measured on a series of oligonucleotide substrates containing both uracil and purine analogs for the Escherichia coli mispaired uracil glycosylase (MUG). The relative rates of glycosylase cleavage have been correlated with the free energy of helix formation and with the size and electronic inductive properties of a series of uracil 5-substituents. Data are presented that MUG can exploit the reduced thermodynamic stability of mispairs to distinguish U:A from U:G pairs. Discrimination against the removal of thymine results primarily from the electron-donating property of the thymine 5-methyl substituent, whereas the size of the methyl group relative to a hydrogen atom is a secondary factor. A series of parameters have been obtained that allow prediction of relative MUG cleavage rates that correlate well with observed relative rates that vary over 5 orders of magnitude for the series of base analogs examined. We propose that these parameters may be common among DNA glycosylases; however, specific glycosylases may focus more or less on each of the parameters identified. The presence of a series of glycosylases that focus on different lesion properties, all coexisting within the same cell, would provide a robust and partially redundant repair system necessary for the maintenance of the genome.
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Affiliation(s)
- Pingfang Liu
- Department of Basic Science, Loma Linda University School of Medicine, Loma Linda, CA 92354, USA
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43
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Rogstad DK, Darwanto A, Herring JL, Rogstad KN, Burdzy A, Hadley S, Neidigh JW, Sowers LC. Measurement of the incorporation and repair of exogenous 5-hydroxymethyl-2'-deoxyuridine in human cells in culture using gas chromatography-negative chemical ionization-mass spectrometry. Chem Res Toxicol 2007; 20:1787-96. [PMID: 17914883 PMCID: PMC2532841 DOI: 10.1021/tx700221x] [Citation(s) in RCA: 6] [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] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The DNA of all organisms is constantly damaged by oxidation. Among the array of damage products is 5-hydroxymethyluracil, derived from oxidation of the thymine methyl group. Previous studies have established that HmU can be a sensitive and valuable marker of DNA damage. More recently, the corresponding deoxynucleoside, 5-hydroxymethyl-2'-deoxyuridine (HmdU), has proven to be valuable for the introduction of controlled amounts of a single type of damage lesion into the DNA of replicating cells, which is subsequently repaired by the base excision repair pathway. Complicating the study of HmU formation and repair, however, is the known chemical reactivity of the hydroxymethyl group of HmU under conditions used to hydrolyze DNA. In the work reported here, this chemical property has been exploited by creating conditions that convert HmU to the corresponding methoxymethyluracil (MmU) derivative that can be further derivatized to the 3,5-bis-(trifluoromethyl)benzyl analogue. This derivatized compound can be detected by gas chromatography-negative chemical ionization-mass spectrometry (GC-NCI-MS) with good sensitivity. Using isotopically enriched exogenous HmdU and human osteosarcoma cells (U2OS) in culture, we demonstrate that this method allows for the measurement of HmU in DNA formed from the incorporation of exogenous HmdU. We further demonstrate that the addition of isotopically enriched uridine to the culture medium allows for the simultaneous measurement of DNA replication and repair kinetics. This sensitive and facile method should prove valuable for studies on DNA oxidation damage and repair in living cells.
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Affiliation(s)
| | | | | | | | | | | | | | - Lawrence C. Sowers
- *To whom correspondence should be addressed. Tel: 909-558-4480. Fax: 909-558-4035 E-mail:
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Abstract
1. In the present study, we investigated whether the administration of apocynin, an NADPH oxidase inhibitor, provided brain protection in a rat model of intracerebral haemorrhage (ICH). 2. Rats were divided into sham, ICH untreated, ICH treated with vehicle (ethanol) and ICH treated with apocynin groups. Intracerebral haemorrhage was induced by collagenase injection. Neurological function, haemorrhage volume and brain oedema were measured 24 h after ICH. 3. Intracerebral haemorrhage caused significant neurological deficit associated with brain oedema. Apocynin (3, 10 and 30 mg/kg) failed to reduce brain injury after ICH. Low dose ethanol (0.2 g/kg) improved neurological function and reduced brain oedema (ICH-vehicle vs ICH-untreated, P < 0.05). 4. In conclusion, apocynin has no neuroprotective effect when administered intraperitoneally after ICH.
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Affiliation(s)
- Elena Titova
- Department of Physiology and Pharmacology, Loma Linda University, Loma Linda, California 92354, USA
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Valinluck V, Sowers LC. Inflammation-Mediated Cytosine Damage: A Mechanistic Link between Inflammation and the Epigenetic Alterations in Human Cancers: Figure 1. Cancer Res 2007; 67:5583-6. [PMID: 17575120 DOI: 10.1158/0008-5472.can-07-0846] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.6] [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: 11/16/2022]
Abstract
Aberrant methylation patterns have long been known to exist in the promoter regions of key regulatory genes in the DNA of tumor cells. However, the mechanisms by which these methylation patterns become altered during the transformation of normal cells to tumor cells have remained elusive. We have recently shown in in vitro studies that inflammation-mediated halogenated cytosine damage products can mimic 5-methylcytosine in directing enzymatic DNA methylation and in enhancing the binding of methyl-binding proteins whereas certain oxidative damage products inhibit both. We have therefore proposed that cytosine damage products could potentially interfere with normal epigenetic control by altering DNA-protein interactions critical for gene regulation and the heritable transmission of methylation patterns. These inflammation-mediated cytosine damage products may provide, in some cases, a mechanistic link between inflammation and cancer.
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Affiliation(s)
- Victoria Valinluck
- Department of Biochemistry and Microbiology, School of Medicine, Loma Linda University, Loma Linda, California 92354, USA
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Morkos AA, Hopper AO, Deming DD, Yellon SM, Wycliffe N, Ashwal S, Sowers LC, Peverini RL, Angeles DM. Elevated total peripheral leukocyte count may identify risk for neurological disability in asphyxiated term neonates. J Perinatol 2007; 27:365-70. [PMID: 17443199 DOI: 10.1038/sj.jp.7211750] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [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: 11/09/2022]
Abstract
OBJECTIVE The present study investigated the relationship between neurologic outcome and total circulating white blood cell (WBC) and absolute neutrophil counts (ANCs) in the first week of life in term infants with hypoxic-ischemic encephalopathy (HIE). STUDY DESIGN Long-term neurologic outcome at 18 months was measured retrospectively in 30 term neonates with HIE using the Pediatric Cerebral Performance Category Scale (PCPCS) score with outcomes dichotomized as either good or poor. We then compared white blood cell and ANC levels during the first 4 days of life and magnetic resonance imaging (MRI) obtained within the first month life between the two PCPCS groups. MRI was quantified using a validated scoring system. RESULTS Neonates with good long-term outcomes had significantly lower MRI scores (indicating lesser injury) than neonates with poor outcomes. More importantly, neonates with poor outcomes had significantly higher WBC and ANC levels as early as12 h after birth and up to 96 h after birth compared to those with good outcomes. These data suggest that elevated peripheral neutrophil counts in the first 96 h of life may signal or predict adverse long-term outcome. CONCLUSIONS Our findings suggest that elevated peripheral neutrophil counts in the first 96 h of life in term infants with HIE may contribute to abnormal neurodevelopmental outcome.
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Affiliation(s)
- A A Morkos
- Department of Pediatrics, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA
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Abstract
Alterations in cytosine methylation patterns are usually observed in human tumors. The consequences of altered cytosine methylation patterns include both inappropriate activation of transforming genes and silencing of tumor suppressor genes. Despite the biological effect of methylation changes, little is known about how such changes are caused. The heritability of cytosine methylation patterns from parent to progeny cells is attributed to the fidelity of the methylation-sensitive human maintenance methyltransferase DNMT1, which methylates with high specificity the unmethylated strand of a hemimethylated CpG sequence following DNA replication. We have been studying DNA damage that might alter the specificity of DNMT1, either inhibiting the methylation of hemimethylated sites or triggering the inappropriate methylation of previously unmethylated sites. Here, we show that known forms of endogenous DNA damage can cause either hypermethylation or hypomethylation. Inflammation-induced 5-halogenated cytosine damage products, including 5-chlorocytosine, mimic 5-methylcytosine and induce inappropriate DNMT1 methylation within a CpG sequence. In contrast, oxidation damage of the methyl group of 5-methylcytosine, with the formation of 5-hydroxymethylcytosine, prevents DNMT1 methylation of the target cytosine. We propose that reduced DNMT1 selectivity resulting from DNA damage could cause heritable changes in cytosine methylation patterns, resulting in human tumor formation. These data may provide a mechanistic link for the associations documented between inflammation and cancer.
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Affiliation(s)
- Victoria Valinluck
- Department of Biochemistry and Microbiology, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
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48
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Zhang H, Darwanto A, Linkhart TA, Sowers LC, Zhang L. Maternal cocaine administration causes an epigenetic modification of protein kinase Cepsilon gene expression in fetal rat heart. Mol Pharmacol 2007; 71:1319-28. [PMID: 17202284 DOI: 10.1124/mol.106.032011] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [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] [Indexed: 01/24/2023] Open
Abstract
Protein kinase Cepsilon (PKCepsilon) plays a pivotal role in cardioprotection during cardiac ischemia and reperfusion injury. Recent studies demonstrated that prenatal cocaine exposure caused a decrease in PKCepsilon expression and increased heart susceptibility to ischemic injury in adult offspring, suggesting an in utero programming of PKCepsilon gene expression pattern in the heart. The present investigation aimed to elucidate whether an epigenetic mechanism, DNA methylation, accounts for cocaine-mediated repression of the PKCepsilon gene in the heart. Pregnant rats were administered either saline or cocaine intraperitoneally (15 mg/kg) twice daily from days 15 to 20 of gestational age, and term fetal hearts were studied. Cocaine treatment significantly decreased PKCepsilon mRNA and protein levels in the heart. CpG dinucleotides found in cAMP response element-binding protein (CREB), CREB/c-Jun1, and CREB/c-Jun2 binding sites at the proximal promoter region of the PKCepsilon gene were densely methylated and were not affected by cocaine. In contrast, methylation of CpGs in the activator protein 1 (AP-1) binding sites was low but was significantly increased by cocaine. Reporter gene assays showed that the AP-1 binding site played a strong stimulatory role of PKCepsilon gene transcription. Methylation of the AP-1 binding sites significantly decreased AP-1 binding to the PKCepsilon promoter. Supershift analyses implicated c-Jun homodimers binding to the AP-1 binding sites. Cocaine did not affect nuclear c-Jun levels or the binding of c-Jun to the unmethylated AP-1 binding sites. The results indicate a role for DNA methylation in cocaine-mediated PKCepsilon gene repression in the developing heart and suggest an epigenetic mechanism affecting this gene linked with vulnerability of ischemic injury in the heart of adult offspring.
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Affiliation(s)
- Haitao Zhang
- Center for Perinatal Biology, Department of Pharmacology and Physiology, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA
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49
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Patrick T, Wu W, Rawson RA, Sowers LC, Boskovic DS, Angeles DM. Effect of the mode of birth on purine and malondialdehyde levels in umbilical arterial plasma. FASEB J 2007. [DOI: 10.1096/fasebj.21.6.a1287-c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | | | | | - Danilyn M Angeles
- Physiology and Pharmacology
- NursingLoma Linda UniversityLoma LindaCA92350
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50
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