Charles Brenner

University of Iowa, Iowa City, Iowa, United States

Are you Charles Brenner?

Claim your profile

Publications (77)484.61 Total impact

  • Charles Brenner
    [Show abstract] [Hide abstract]
    ABSTRACT: Ex vivo experiments have strangely shown that inhibition or stimulation of NAD metabolism can be neuroprotective. In this issue of Cell Metabolism, Brown et al. (2014) demonstrate that cochlear NAD is diminished by deafening noise but protected by nicotinamide riboside or WldS mutation. Hearing protection by nicotinamide riboside depends on Sirt3. Copyright © 2014 Elsevier Inc. All rights reserved.
    Cell metabolism. 12/2014; 20(6):926-7.
  • Bo-Kuan Wu, Charles Brenner
    [Show abstract] [Hide abstract]
    ABSTRACT: Hypermethylation-mediated tumor suppressor gene (TSG) silencing is a central epigenetic alteration in RAS-dependent tumorigenesis. Ten-eleven translocation (TET) enzymes can depress DNA methylation by hydroxylation of 5-methylcytosine (5mC) bases to 5-hydroxymethylcytosine (5hmC). Here, we report that suppression of TET1 is required for KRAS-induced DNA hypermethylation and cellular transformation. In distinct nonmalignant cell lines, oncogenic KRAS promotes transformation by inhibiting TET1 expression via the ERK-signaling pathway. This reduces chromatin occupancy of TET1 at TSG promoters, lowers levels of 5hmC, and increases levels of 5mC and 5mC-dependent transcriptional silencing. Restoration of TET1 expression by ERK pathway inhibition or ectopic TET1 reintroduction in KRAS-transformed cells reactivates TSGs and inhibits colony formation. KRAS knockdown increases TET1 expression and diminishes colony-forming ability, whereas KRAS/TET1 double knockdown bypasses the KRAS dependence of KRAS-addicted cancer cells. Thus, suppression of TET1-dependent DNA demethylation is critical for KRAS-mediated transformation. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.
    Cell reports. 11/2014;
  • Source
    Bo-Kuan Wu, Szu-Chieh Mei, Charles Brenner
    [Show abstract] [Hide abstract]
    ABSTRACT: Site-specific hypermethylation of tumor suppressor genes accompanied by genome-wide hypomethylation are epigenetic hallmarks of malignancy. However, the molecular mechanisms that drive these linked changes in DNA methylation remain obscure. DNA methyltransferase 1 (DNMT1), the principle enzyme responsible for maintaining methylation patterns is commonly dysregulated in tumors. Replication foci targeting sequence (RFTS) is an N-terminal domain of DNMT1 that inhibits DNA-binding and catalytic activity, suggesting that RFTS deletion would result in a gain of DNMT1 function. However, a substantial body of data suggested that RFTS is required for DNMT1 activity. Here, we demonstrate that deletion of RFTS alters DNMT1-dependent DNA methylation during malignant transformation. Compared to full-length DNMT1, ectopic expression of hyperactive DNMT1-DRFTS caused greater malignant transformation and enhanced promoter methylation with condensed chromatin structure that silenced DAPK and DUOX1 expression. Simultaneously, deletion of RFTS impaired DNMT1 chromatin association with pericentromeric Satellite 2 (SAT2) repeat sequences and produced DNA demethylation at SAT2 repeats and globally. To our knowledge, RFTS-deleted DNMT1 is the first single factor that can reprogram focal hypermethylation and global hypomethylation in parallel during malignant transformation. Our evidence suggests that the RFTS domain of DNMT1 is a target responsible for epigenetic changes in cancer.
    Cell cycle (Georgetown, Tex.) 10/2014; 13(20):3222-3231. · 5.24 Impact Factor
  • Charles Brenner
    [Show abstract] [Hide abstract]
    ABSTRACT: An enzyme that links two metabolic hubs has been found to be upregulated in the fat cells of overweight mice. Inhibition of the gene encoding this enzyme protects mice from diet-induced obesity. See Letter p.258
    Nature 04/2014; 508(7495):194-5. · 38.60 Impact Factor
  • Source
    Szu-Chieh Mei, Charles Brenner
    [Show abstract] [Hide abstract]
    ABSTRACT: Saccharomyces cerevisiae is calorie-restricted by lowering glucose from 2% to 0.5%. Under low glucose conditions, replicative lifespan is extended in a manner that depends on the NAD+-dependent protein lysine deacetylase Sir2 and NAD+ salvage enzymes. Because NAD+ is required for glucose utilization and Sir2 function, it was postulated that glucose levels alter the levels of NAD+ metabolites that tune Sir2 function. Though NAD+ precursor vitamins, which increase the levels of all NAD+ metabolites, can extend yeast replicative lifespan, glucose restriction does not significantly change the levels or ratios of intracellular NAD+ metabolites. To test whether glucose restriction affects protein copy numbers, we developed a technology that combines the measurement of Urh1 specific activity and quantification of relative expression between Urh1 and any other protein. The technology was applied to obtain the protein copy numbers of enzymes involved in NAD+ metabolism in rich and synthetic yeast media. Our data indicated that Sir2 and Pnc1, two enzymes that sequentially convert NAD+ to nicotinamide and then to nicotinic acid, are up-regulated by glucose restriction in rich media, and that Pnc1 alone is up-regulated in synthetic media while levels of all other enzymes are unchanged. These data suggest that production or export of nicotinic acid might be a connection between NAD+ and calorie restriction-mediated lifespan extension in yeast.
    PLoS ONE 01/2014; 9(9):e106496. · 3.53 Impact Factor
  • Source
    Szu-Chieh Mei, Charles Brenner
    [Show abstract] [Hide abstract]
    ABSTRACT: Using high-throughput chemical and genetic screening, Matheny and colleagues (in this issue of Chemistry & Biology) identified STF-118804, an inhibitor of nicotinamide phosphoribosyltransferase, as a cell type-specific inhibitor of mixed-lineage leukemia with MLL chromosomal rearrangements. The approach was powerful, as is the potential for NAD as a specific cancer target.
    Chemistry & biology 11/2013; 20(11):1307-1308. · 6.52 Impact Factor
  • Sirisha Ghanta, Ruth E Grossmann, Charles Brenner
    [Show abstract] [Hide abstract]
    ABSTRACT: Abstract Hormone systems evolved over 500 million years of animal natural history to motivate feeding behavior and convert excess calories to fat. These systems produced vertebrates, including humans, who are famine-resistant but sensitive to obesity in environments of persistent overnutrition. We looked for cell-intrinsic metabolic features, which might have been subject to an evolutionary drive favoring lipogenesis. Mitochondrial protein acetylation appears to be such a system. Because mitochondrial acetyl-coA is the central mediator of fuel oxidation and is saturable, this metabolite is postulated to be the fundamental indicator of energy excess, which imprints a memory of nutritional imbalances by covalent modification. Fungal and invertebrate mitochondria have highly acetylated mitochondrial proteomes without an apparent mitochondrially targeted protein lysine acetyltransferase. Thus, mitochondrial acetylation is hypothesized to have evolved as a nonenzymatic phenomenon. Because the pKa of a nonperturbed Lys is 10.4 and linkage of a carbonyl carbon to an ε amino group cannot be formed with a protonated Lys, we hypothesize that acetylation occurs on residues with depressed pKa values, accounting for the propensity of acetylation to hit active sites and suggesting that regulatory Lys residues may have been under selective pressure to avoid or attract acetylation throughout animal evolution. In addition, a shortage of mitochondrial oxaloacetate under ketotic conditions can explain why macronutrient insufficiency also produces mitochondrial hyperacetylation. Reduced mitochondrial activity during times of overnutrition and undernutrition would improve fitness by virtue of resource conservation. Micronutrient insufficiency is predicted to exacerbate mitochondrial hyperacetylation. Nicotinamide riboside and Sirt3 activity are predicted to relieve mitochondrial inhibition.
    Critical Reviews in Biochemistry and Molecular Biology 09/2013; · 5.58 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: The RAS protooncogene has a central role in regulation of cell proliferation, and point mutations leading to oncogenic activation of Ras occur in a large number of human cancers. Silencing of tumor-suppressor genes by DNA methyltransferase 1 (Dnmt1) is essential for oncogenic cellular transformation by Ras, and Dnmt1 is overexpressed in numerous human cancers. Here we provide new evidence that the pleiotropic regulator of G protein signaling (RGS) family member RGS6 suppresses Ras-induced cellular transformation by facilitating Tip60-mediated degradation of Dmnt1 and promoting apoptosis. Employing mouse embryonic fibroblasts from wild-type and RGS6(-/-) mice, we found that oncogenic Ras induced upregulation of RGS6, which in turn blocked Ras-induced cellular transformation. RGS6 functions to suppress cellular transformation in response to oncogenic Ras by downregulating Dnmt1 protein expression leading to inhibition of Dnmt1-mediated anti-apoptotic activity. Further experiments showed that RGS6 functions as a scaffolding protein for both Dnmt1 and Tip60 and is required for Tip60-mediated acetylation of Dnmt1 and subsequent Dnmt1 ubiquitylation and degradation. The RGS domain of RGS6, known only for its GTPase-activating protein activity toward Gα subunits, was sufficient to mediate Tip60 association with RGS6. This work demonstrates a novel signaling action for RGS6 in negative regulation of oncogene-induced transformation and provides new insights into our understanding of the mechanisms underlying Ras-induced oncogenic transformation and regulation of Dnmt1 expression. Importantly, these findings identify RGS6 as an essential cellular defender against oncogenic stress and a potential therapeutic target for developing new cancer treatments.Oncogene advance online publication, 2 September 2013; doi:10.1038/onc.2013.324.
    Oncogene 09/2013; · 8.56 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Methylation of cytosines in CpG dinucleotides is the predominant epigenetic mark on vertebrate DNA. DNA methylation is associated with transcriptional repression. The pattern of DNA methylation changes during development and with disease. Human DNA methyltransferase 1 (Dnmt1), a 1616 amino acid multi-domain enzyme, is essential for maintenance of DNA methylation in proliferating cells and is considered an important cancer drug target. Using a fluorigenic, endonuclease-coupled DNA methylation assay with an activated form of Dnmt1 engineered to lack the replication foci targeting sequence domain, we discovered that laccaic acid A (LCA), a highly substituted anthraquinone natural product, is a direct inhibitor with a 310 nM Ki. LCA is competitive with the DNA substrate in in vitro methylation assays and alters the expression of methylated genes in MCF-7 breast cancer cells synergistically with 5-aza-2'-deoxycytidine. LCA represents a novel class of Dnmt-targeted molecular probes, with biochemical properties that allow it to distinguish between non DNA-bound and DNA-bound Dnmt1.
    Journal of Biological Chemistry 07/2013; · 4.65 Impact Factor
  • Source
    Charles Brenner
    [Show abstract] [Hide abstract]
    ABSTRACT: The 2015 redesign of the Medical College Admissions Test (MCAT) is a disruptive event that has stimulated a great deal of discussion in undergraduate educational circles. These discussions include figuring out who will teach biochemistry, whether nonmajor chemistry courses should be changed, whether the psychosocial material to be tested constitutes academic behavioral science or the sensibilities that come from exposure to different cultures, and determining whether resources need to shift. The 2015 MCAT has also begun to alter admissions requirements and curricula in medical, pharmacy, and dental schools. Though many medical schools are taking the position that biochemistry will already have been covered as an undergraduate requirement and seem to be deemphasizing molecular science in the first-year curriculum, at least one college of dentistry has embraced the better prepared first-year student in order to offer advanced biochemistry and genomics that will build on undergraduate biochemistry.
    Journal of chemical education 07/2013; 90(7):807-812. · 0.82 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: DNA methyltransferase 1 (DNMT1) is the enzyme most responsible for epigenetic modification of human DNA and the intended target of approved cancer drugs such as 5-aza-cytidine and 5-aza-2'-deoxycytidine. 5-aza nucleosides have complex mechanisms of action that require incorporation into DNA, and covalent trapping and proteolysis of DNMT isozymes. Direct DNMT inhibitors are needed to refine understanding of the role of specific DNMT isozymes in cancer etiology and, potentially, to improve cancer prevention and treatment. Here, we developed a high throughput pipeline for identification of direct DNMT1 inhibitors. The components of this screen include an activated form of DNMT1, a restriction enzyme-coupled fluorigenic assay performed in 384 well plates with a z-factor of 0.66, a counter screen against the restriction enzyme, a screen to eliminate DNA intercalators, and a differential scanning fluorimetry assay to validate direct binders. Using the Microsource Spectrum collection of 2320 compounds, this screen identified nine compounds with dose responses ranging from 300 nM to 11 µM, representing at least two different pharmacophores with DNMT1 inhibitory activity. Seven of nine inhibitors identified exhibited two to four-fold selectivity for DNMT1 versus DNMT3A.
    PLoS ONE 01/2013; 8(11):e78752. · 3.53 Impact Factor
  • Source
    Samuel Aj Trammell, Charles Brenner
    [Show abstract] [Hide abstract]
    ABSTRACT: Nicotinamide adenine dinucleotide (NAD(+)) is a coenzyme for hydride transfer reactions and a substrate for sirtuins and other NAD(+)-consuming enzymes. The abundance of NAD (+), NAD(+) biosynthetic intermediates, and related nucleotides reflects the metabolic state of cells and tissues. High performance liquid chromatography (HPLC) followed by ultraviolet-visible (UV-Vis) spectroscopic analysis of NAD(+) metabolites does not offer the specificity and sensitivity necessary for robust quantification of complex samples. Thus, we developed a targeted, quantitative assay of the NAD(+) metabolome with the use of HPLC coupled to mass spectrometry. Here we discuss NAD(+) metabolism as well as the technical challenges required for reliable quantification of the NAD(+) metabolites. The new method incorporates new separations and improves upon a previously published method that suffered from the problem of ionization suppression for particular compounds.
    Computational and structural biotechnology journal. 01/2013; 4:e201301012.
  • Charles Brenner
    [Show abstract] [Hide abstract]
    ABSTRACT: Approximately two million students matriculate into American colleges and universities per year. Almost 20% of these students begin taking a series of courses specified by advisers of health preprofessionals. The single most important influence on health profession advisers and on course selection for this huge population of learners is the Medical College Admissions Test (MCAT), which was last revised in 1991, 10 years before publication of the first draft human genome sequence. In preparation for the 2015 MCAT, there is a broad discussion among stakeholders of how best to revise undergraduate and medical education in the molecular sciences to prepare researchers and doctors to acquire, analyze and use individual genomic and metabolomic data in the coming decades. Getting these changes right is among the most important educational problems of our era. © 2013 by The International Union of Biochemistry and Molecular Biology, 2013.
    Biochemistry and Molecular Biology Education 12/2012; · 0.70 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: 2-Deoxy-C-nucleosides are a subcategory of C-nucleosides that has not been explored extensively, largely because the synthesis is less facile. Flexible synthetic procedures giving access to 2-deoxy-C-nucleosides are therefore of interest. To exemplify the versatility and highlight the limitations of a synthetic route recently developed to that effect, the first synthesis of 2-deoxy benzamide riboside is reported. Biological properties of this novel C-nucleoside are also discussed.
    Bioorganic & medicinal chemistry letters 06/2012; 22(16):5204-7. · 2.65 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Dnmt1 (DNA methyltransferase 1) is the principal enzyme responsible for maintenance of cytosine methylation at CpG dinucleotides in the mammalian genome. The N-terminal replication focus targeting sequence (RFTS) domain of Dnmt1 has been implicated in subcellular localization, protein association, and catalytic function. However, progress in understanding its function has been limited by the lack of assays for and a structure of this domain. Here, we show that the naked DNA- and polynucleosome-binding activities of Dnmt1 are inhibited by the RFTS domain, which functions by virtue of binding the catalytic domain to the exclusion of DNA. Kinetic analysis with a fluorogenic DNA substrate established the RFTS domain as a 600-fold inhibitor of Dnmt1 enzymatic activity. The crystal structure of the RFTS domain reveals a novel fold and supports a mechanism in which an RFTS-targeted Dnmt1-binding protein, such as Uhrf1, may activate Dnmt1 for DNA binding.
    Journal of Biological Chemistry 03/2011; 286(17):15344-51. · 4.65 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: NAD(+) is both a co-enzyme for hydride transfer enzymes and a substrate of sirtuins and other NAD(+) consuming enzymes. NAD(+) biosynthesis is required for two different regimens that extend lifespan in yeast. NAD(+) is synthesized from tryptophan and the three vitamin precursors of NAD(+): nicotinic acid, nicotinamide and nicotinamide riboside. Supplementation of yeast cells with NAD(+) precursors increases intracellular NAD(+) levels and extends replicative lifespan. Here we show that both nicotinamide riboside and nicotinic acid are not only vitamins but are also exported metabolites. We found that the deletion of the nicotinamide riboside transporter, Nrt1, leads to increased export of nicotinamide riboside. This discovery was exploited to engineer a strain to produce high levels of extracellular nicotinamide riboside, which was recovered in purified form. We further demonstrate that extracellular nicotinamide is readily converted to extracellular nicotinic acid in a manner that requires intracellular nicotinamidase activity. Like nicotinamide riboside, export of nicotinic acid is elevated by the deletion of the nicotinic acid transporter, Tna1. The data indicate that NAD(+) metabolism has a critical extracellular element in the yeast system and suggest that cells regulate intracellular NAD(+) metabolism by balancing import and export of NAD(+) precursor vitamins.
    PLoS ONE 01/2011; 6(5):e19710. · 3.53 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: NAD+ is a coenzyme for hydride transfer enzymes and a substrate for sirtuins and other NAD+-dependent ADPribose transfer enzymes. In wild-type Saccharomyces cerevisiae, calorie restriction accomplished by glucose limitation extends replicative lifespan in a manner that depends on Sir2 and the NAD+ salvage enzymes, nicotinic acid phosphoribosyl transferase and nicotinamidase. Though alterations in the NAD+ to nicotinamide ratio and the NAD+ to NADH ratio are anticipated by models to account for the effects of calorie restriction, the nature of a putative change in NAD+ metabolism requires analytical definition and quantification of the key metabolites. Hydrophilic interaction chromatography followed by tandem electrospray mass spectrometry were used to identify the 12 compounds that constitute the core NAD+ metabolome and 6 related nucleosides and nucleotides. Whereas yeast extract and nicotinic acid increase net NAD+ synthesis in a manner that can account for extended lifespan, glucose restriction does not alter NAD+ or nicotinamide levels in ways that would increase Sir2 activity. The results constrain the possible mechanisms by which calorie restriction may regulate Sir2 and suggest that provision of vitamins and calorie restriction extend lifespan by different mechanisms.
    BMC Chemical Biology 02/2010; 10:2. · 1.60 Impact Factor
  • Source
    Katrina L. Bogan, Charles Brenner
    [Show abstract] [Hide abstract]
    ABSTRACT: 5′-Nucleotidase (EC 3.1.3.5) designates a set of enzymes, which catalyze the hydrolysis of ribonucleoside and deoxyribonucleoside monophosphates into the corresponding nucleosides plus orthophosphate. 5′-Nucleotidases are classified according to subcellular localization, nucleobase specificity and their ability to hydrolyze deoxynucleoside monophosphate substrates. Membrane-bound 5′-nucleotidases are ectoenzymes principally involved in salvage of extracellular nucleosides, and often display a preference toward adenosine monophosphate, thereby modulating signal transduction cascades involving purinergic receptors. Cytosolic 5′-nucleotidases are members of the haloacid dehalogenase superfamily of enzymes, which are two-domain proteins containing a modified Rossman fold as the core and a variable cap structure. Extracellular and intracellular 5′-nucleotidase activities participate in purine and pyrimidine salvage to support balanced synthesis of nucleotides, which is critical for maintaining high fidelity DNA replication. While the production of ribonucleosides from ribonucleotides by 5′-nucleotidases remains the most well studied function, it appears that the physiological functions of these activities are more broad. Indeed, Sdt1, previously termed a pyrimidine-specific 5′-nucleotidase, and Isn1, previously termed an inosine monophosphate (IMP)-specific 5′-nucleotidase, have recently been implicated in catabolic processes in nicotinamide adenine dinucleotide (NAD+) metabolism, and are regulated by the NAD+ precursor vitamin nicotinic acid, glucose and phosphate availability in the medium. In addition, Usha, Pho5, Sdt1 and Phm8 are phosphate starvation-induced 5′-nucleotidases with diverse substrate specificities that liberate phosphate under phosphate starvation conditions. Here we review 5′-nucleotidase enzyme structure, catalytic mechanism and substrate specificity and focus on new biological roles for these enzymes in nucleotide, NAD+ and phosphate metabolism.
    New Journal of Chemistry 01/2010; 34(5). · 3.16 Impact Factor
  • Katrina L. Bogan, Charles Brenner
    ChemInform 01/2010; 41(34).
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Recently, we discovered that nicotinamide riboside and nicotinic acid riboside are biosynthetic precursors of NAD(+), which are utilized through two pathways consisting of distinct enzymes. In addition, we have shown that exogenously supplied nicotinamide riboside is imported into yeast cells by a dedicated transporter, and it extends replicative lifespan on high glucose medium. Here, we show that nicotinamide riboside and nicotinic acid riboside are authentic intracellular metabolites in yeast. Secreted nicotinamide riboside was detected with a biological assay, and intracellular levels of nicotinamide riboside, nicotinic acid riboside, and other NAD(+) metabolites were determined by a liquid chromatography-mass spectrometry method. A biochemical genomic screen indicated that three yeast enzymes possess nicotinamide mononucleotide 5'-nucleotidase activity in vitro. Metabolic profiling of knock-out mutants established that Isn1 and Sdt1 are responsible for production of nicotinamide riboside and nicotinic acid riboside in cells. Isn1, initially classified as an IMP-specific 5'-nucleotidase, and Sdt1, initially classified as a pyrimidine 5'-nucleotidase, are additionally responsible for dephosphorylation of pyridine mononucleotides. Sdt1 overexpression is growth-inhibitory to cells in a manner that depends on its active site and correlates with reduced cellular NAD(+). Expression of Isn1 protein is positively regulated by the availability of nicotinic acid and glucose. These results reveal unanticipated and highly regulated steps in NAD(+) metabolism.
    Journal of Biological Chemistry 10/2009; 284(50):34861-9. · 4.65 Impact Factor

Publication Stats

2k Citations
484.61 Total Impact Points

Institutions

  • 2009–2014
    • University of Iowa
      • • Department of Biochemistry
      • • Carver College of Medicine
      Iowa City, Iowa, United States
  • 2007–2011
    • University of Toronto
      • Structural Genomics Consortium
      Toronto, Ontario, Canada
  • 2010
    • University of Michigan
      • Department of Chemistry
      Ann Arbor, MI, United States
  • 2005–2010
    • Geisel School of Medicine at Dartmouth
      • Department of Genetics
      Hanover, New Hampshire, United States
  • 2003–2009
    • Dartmouth College
      • • Department of Biological Sciences
      • • Department of Genetics
      Hanover, New Hampshire, United States
  • 1997–2006
    • Thomas Jefferson University
      • • Department of Biochemistry and Molecular Biology
      • • Kimmel Cancer Center
      Philadelphia, PA, United States
    • Brandeis University
      • Department of Biochemistry
      Waltham, MA, United States
  • 2001–2004
    • The Philadelphia Center
      Philadelphia, Pennsylvania, United States
  • 1998
    • CSU Mentor
      Long Beach, California, United States
    • The University of Sheffield
      • Department of Chemistry
      Sheffield, ENG, United Kingdom