David B Friedman

Summary

Affiliation: Vanderbilt University
Country: USA

Publications

  1. doi request reprint Assessing signal-to-noise in quantitative proteomics: multivariate statistical analysis in DIGE experiments
    David B Friedman
    Proteomics Laboratory, Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN, USA
    Methods Mol Biol 854:31-45. 2012
  2. pmc Novel association of APC with intermediate filaments identified using a new versatile APC antibody
    Yang Wang
    Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
    BMC Cell Biol 10:75. 2009
  3. ncbi request reprint Proteome analysis of human colon cancer by two-dimensional difference gel electrophoresis and mass spectrometry
    David B Friedman
    Mass Spectrometry Research Center, Department of Biochemistry, Vanderbilt University, Nashville, TN 37232 8575, USA
    Proteomics 4:793-811. 2004
  4. doi request reprint The ABRF Proteomics Research Group studies: educational exercises for qualitative and quantitative proteomic analyses
    David B Friedman
    Vanderbilt University School of Medicine, Nashville, TN, USA
    Proteomics 11:1371-81. 2011
  5. ncbi request reprint Multivariable difference gel electrophoresis and mass spectrometry: a case study on transforming growth factor-beta and ERBB2 signaling
    David B Friedman
    Mass Spectrometry Research Center, Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
    Mol Cell Proteomics 6:150-69. 2007
  6. pmc Iron deficiency accelerates Helicobacter pylori-induced carcinogenesis in rodents and humans
    Jennifer M Noto
    Division of Gastroenterology, Department of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA
    J Clin Invest 123:479-92. 2013
  7. pmc Analysis of Helicobacter pylori cagA promoter elements required for salt-induced upregulation of CagA expression
    John T Loh
    Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
    Infect Immun 80:3094-106. 2012
  8. ncbi request reprint Convergence of p53 and transforming growth factor beta (TGFbeta) signaling on activating expression of the tumor suppressor gene maspin in mammary epithelial cells
    Shizhen Emily Wang
    Department of Cancer Biology, Mass Spectrometry Research Center, Breast Cancer Research Program, Vanderbilt Ingram Comprehensive Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
    J Biol Chem 282:5661-9. 2007
  9. pmc Staphylococcus aureus fur regulates the expression of virulence factors that contribute to the pathogenesis of pneumonia
    Victor J Torres
    Department of Microbiology and Immunology, Vanderbilt University Medical Center, 1161 21st Ave South, Nashville, Tennessee 37232 2363, USA
    Infect Immun 78:1618-28. 2010
  10. pmc Analysis of protein expression regulated by the Helicobacter pylori ArsRS two-component signal transduction system
    John T Loh
    Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
    J Bacteriol 192:2034-43. 2010

Research Grants

  1. MALDI-TOF MASS SPECTROMETER
    David Friedman; Fiscal Year: 2003

Detail Information

Publications45

  1. doi request reprint Assessing signal-to-noise in quantitative proteomics: multivariate statistical analysis in DIGE experiments
    David B Friedman
    Proteomics Laboratory, Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, TN, USA
    Methods Mol Biol 854:31-45. 2012
    ....
  2. pmc Novel association of APC with intermediate filaments identified using a new versatile APC antibody
    Yang Wang
    Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
    BMC Cell Biol 10:75. 2009
    ..APC also interacts with the actin cytoskeleton to regulate cell polarity. Until now, interaction of APC with the third cytoskeletal element, intermediate filaments, has remained unexamined...
  3. ncbi request reprint Proteome analysis of human colon cancer by two-dimensional difference gel electrophoresis and mass spectrometry
    David B Friedman
    Mass Spectrometry Research Center, Department of Biochemistry, Vanderbilt University, Nashville, TN 37232 8575, USA
    Proteomics 4:793-811. 2004
    ..Without the benefit of the Cy2-labeled 12 sample mixture internal standard, 42 of these proteins would have been overlooked due to the large degree of variation inherent between normal and tumor samples...
  4. doi request reprint The ABRF Proteomics Research Group studies: educational exercises for qualitative and quantitative proteomic analyses
    David B Friedman
    Vanderbilt University School of Medicine, Nashville, TN, USA
    Proteomics 11:1371-81. 2011
    ..These studies provide a valuable educational resource to research laboratories and core facilities, as well as a mechanism for establishing good laboratory practices...
  5. ncbi request reprint Multivariable difference gel electrophoresis and mass spectrometry: a case study on transforming growth factor-beta and ERBB2 signaling
    David B Friedman
    Mass Spectrometry Research Center, Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
    Mol Cell Proteomics 6:150-69. 2007
    ..Several proteins with a potential role in breast cancer, such as maspin and cathepsin D, were identified as novel molecules associated with TGF-beta signaling...
  6. pmc Iron deficiency accelerates Helicobacter pylori-induced carcinogenesis in rodents and humans
    Jennifer M Noto
    Division of Gastroenterology, Department of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA
    J Clin Invest 123:479-92. 2013
    ..These data demonstrate that iron deficiency enhances H. pylori virulence and represents a measurable biomarker to identify populations of infected persons at high risk for gastric cancer...
  7. pmc Analysis of Helicobacter pylori cagA promoter elements required for salt-induced upregulation of CagA expression
    John T Loh
    Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
    Infect Immun 80:3094-106. 2012
    ..In summary, there is considerable heterogeneity among H. pylori strains in salt-regulated CagA expression, and these differences are attributable to variation in a specific DNA motif upstream of the cagA transcriptional start site...
  8. ncbi request reprint Convergence of p53 and transforming growth factor beta (TGFbeta) signaling on activating expression of the tumor suppressor gene maspin in mammary epithelial cells
    Shizhen Emily Wang
    Department of Cancer Biology, Mass Spectrometry Research Center, Breast Cancer Research Program, Vanderbilt Ingram Comprehensive Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
    J Biol Chem 282:5661-9. 2007
    ..Taken together, these data support cooperation between the p53 and TGFbeta tumor suppressor pathways in the induction of Maspin expression, thus leading to inhibition of cell migration...
  9. pmc Staphylococcus aureus fur regulates the expression of virulence factors that contribute to the pathogenesis of pneumonia
    Victor J Torres
    Department of Microbiology and Immunology, Vanderbilt University Medical Center, 1161 21st Ave South, Nashville, Tennessee 37232 2363, USA
    Infect Immun 78:1618-28. 2010
    ..These findings reveal that Fur is involved in initiating a regulatory program that organizes the expression of virulence factors during the pathogenesis of S. aureus pneumonia...
  10. pmc Analysis of protein expression regulated by the Helicobacter pylori ArsRS two-component signal transduction system
    John T Loh
    Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
    J Bacteriol 192:2034-43. 2010
    ..These results provide further definition of the ArsRS regulon and underscore the importance of the ArsRS system in regulating expression of H. pylori proteins during bacterial growth at both neutral pH and acidic pH...
  11. ncbi request reprint Optimizing the difference gel electrophoresis (DIGE) technology
    David B Friedman
    Proteomics Laboratory, Mass Spectrometry Research Center, Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
    Methods Mol Biol 428:93-124. 2008
    ..Notes are also provided for the use of the alternative saturation labeling chemistry...
  12. pmc Intravenous glial growth factor 2 (GGF2) isoform of neuregulin-1β improves left ventricular function, gene and protein expression in rats after myocardial infarction
    Michael F Hill
    Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
    PLoS ONE 8:e55741. 2013
    ..Potential mechanisms for GGF2 effects on the remote myocardium were explored using microarray and proteomic analysis...
  13. ncbi request reprint Oncogenic KRAS provides a uniquely powerful and variable oncogenic contribution among RAS family members in the colonic epithelium
    Jeffrey W Keller
    Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
    J Cell Physiol 210:740-9. 2007
    ..We therefore conclude that the oncogenic contribution of K-RAS is a function of its multifaceted functionality and is highly context-dependent...
  14. pmc Delineation of a carcinogenic Helicobacter pylori proteome
    Aime T Franco
    Division of Gastroenterology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee 37232 2279, USA
    Mol Cell Proteomics 8:1947-58. 2009
    ..pylori proteins to use in vaccine development and for screening persons infected with strains most likely to induce severe disease...
  15. pmc Electrophilic adduction of ubiquitin activating enzyme E1 by N,N-diethyldithiocarbamate inhibits ubiquitin activation and is accompanied by striatal injury in the rat
    Olga M Viquez
    Department of Pathology Microbiology and Immunology, Vanderbilt University Medical Center, 1161 21st Avenue South, Nashville, TN 37232 2561, USA
    Chem Res Toxicol 25:2310-21. 2012
    ..Additionally, this study supports the predictive value of in vitro screens for identifying sensitive protein targets that can be used to guide subsequent in vivo experiments...
  16. pmc Changes in the striatal proteome of YAC128Q mice exhibit gene-environment interactions between mutant huntingtin and manganese
    Michal Wegrzynowicz
    Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
    J Proteome Res 11:1118-32. 2012
    ..We conclude that the interaction of Mn and mutant HTT may suppress proteomic phenotypes of YAC128Q mice, which could reveal potential targets in novel treatment strategies for HD...
  17. pmc The ubiquitin-proteasome system postsynaptically regulates glutamatergic synaptic function
    Kevin F Haas
    Department of Neurology, Vanderbilt University, Nashville, TN 37235 1634, USA
    Mol Cell Neurosci 35:64-75. 2007
    ..These findings demonstrate postsynaptic proteasome regulation of glutamatergic synaptic function that is mediated through specific regulation of GluRIIB-containing glutamate receptors...
  18. pmc Staphylococcus aureus redirects central metabolism to increase iron availability
    David B Friedman
    Mass Spectrometry Research Center, Department of Biochemistry, Vanderbilt University Medical Center, Nashville, Tennessee, USA
    PLoS Pathog 2:e87. 2006
    ..These findings reveal novel strategies used by S. aureus to acquire scarce nutrients in the hostile host environment and begin to define the iron and heme-dependent regulons of S. aureus...
  19. pmc Proteomic analysis of osteogenic sarcoma: association of tumour necrosis factor with poor prognosis
    Justin M M Cates
    Department of Pathology, Vanderbilt University Medical Center, Nashville, TN, USA
    Int J Exp Pathol 91:335-49. 2010
    ..No significant differences in adverse outcomes were observed based on macrophage migration inhibitory factor expression...
  20. pmc Identification of a myeloid-derived suppressor cell cystatin-like protein that inhibits metastasis
    Angela M Boutte
    Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
    FASEB J 25:2626-37. 2011
    ..The finding suggests that malignant tumors promote invasion/metastasis not only through up-regulation of proteases but also down-regulation of protease inhibitors...
  21. pmc Proteomic investigation of human burn wounds by 2D-difference gel electrophoresis and mass spectrometry
    Alonda C Pollins
    Department of Plastic Surgery, Vanderbilt School of Medicine, Nashville, Tennessee 37232, USA
    J Surg Res 142:143-52. 2007
    ..We applied a global analysis method to identify dynamically changing proteins within the burn environment, which could eventually become biomarkers or targets for treatment...
  22. ncbi request reprint HER2/Neu (ErbB2) signaling to Rac1-Pak1 is temporally and spatially modulated by transforming growth factor beta
    Shizhen Emily Wang
    Department of Cancer Biology, Vanderbilt Ingram Comprehensive Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37232 6307, USA
    Cancer Res 66:9591-600. 2006
    ..Thus, by recruiting the actin skeleton, TGF-beta "cross-links" this signaling complex at cell lamellipodia; this prolongs Rac1 activation and increases metastatic properties and survival of HER2-overexpressing cells...
  23. pmc Protein-protein interactions among Helicobacter pylori cag proteins
    Valerie J Busler
    Department of Microbiology and Immunology, Division of Infectious Diseases, A2200 Medical Center North, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
    J Bacteriol 188:4787-800. 2006
    ..Protein-protein interactions among Cag proteins are likely to have an important role in the assembly of the H. pylori type IV secretion apparatus...
  24. pmc Verification of automated peptide identifications from proteomic tandem mass spectra
    David L Tabb
    Department of Biochemistry, Vanderbilt University Medical Center, Nashville, Tennessee 37232 8340, USA
    Nat Protoc 1:2213-22. 2006
    ..Examples of ion-trap and tandem time-of-flight (TOF/TOF) mass spectra illustrate these principles of fragmentation...
  25. doi request reprint Isoelectric focusing and two-dimensional gel electrophoresis
    David B Friedman
    Mass Spectrometry Research Center, Vanderbilt University, Nashville, Tennessee, USA
    Methods Enzymol 463:515-40. 2009
    ..Electrophoresis18, 2071-2077]. These major improvements will be highlighted in this chapter alongside the principle and theory of 2D gel electrophoresis, as well as detailed methods for general 2D gel electrophoresis best use protocols...
  26. pmc Thr-1989 phosphorylation is a marker of active ataxia telangiectasia-mutated and Rad3-related (ATR) kinase
    Edward A Nam
    Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
    J Biol Chem 286:28707-14. 2011
    ..Our results suggest that, like ATM and DNA-PK, phosphorylation regulates ATR, and phospho-peptide specific antibodies to Thr-1989 provide a proximal marker of ATR activation...
  27. pmc Alterations in the diabetic myocardial proteome coupled with increased myocardial oxidative stress underlies diabetic cardiomyopathy
    Milton Hamblin
    Department of Biomedical Sciences, Division of Cardiovascular Biology, Meharry Medical College, Nashville, TN 37208, USA
    J Mol Cell Cardiol 42:884-95. 2007
    ....
  28. pmc Glycosaminoglycan-binding properties and kinetic characterization of human heparin cofactor II expressed in Escherichia coli
    Suryakala Sarilla
    Department of Pathology, Vanderbilt University School of Medicine, C3321A Medical Center North, Nashville, TN 37232, USA
    Anal Biochem 406:166-75. 2010
    ..This weaker binding may be attributed to interference of the Asn(169)N-glycan with the HCII heparin-binding site...
  29. doi request reprint Predicting dedifferentiation in liposarcoma: a proteomic approach
    Colt M McClain
    Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, 1161 21st Ave South, Nashville, TN 37232, USA
    Virchows Arch 463:85-92. 2013
    ..Expression of SELENBP1 is decreased in the well-differentiated component of DDL compared to ALT. However, variability in the staining patterns in liposarcoma precludes its use as a predictive marker for dedifferentiation...
  30. pmc Structural determinants of Clostridium difficile toxin A glucosyltransferase activity
    Rory N Pruitt
    Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
    J Biol Chem 287:8013-20. 2012
    ..These studies highlight the importance of cellular activation in determining the array of substrates available to the toxins once delivered into the cell...
  31. pmc Thrombospondin-1 acts as a ligand for CD148 tyrosine phosphatase
    Keiko Takahashi
    Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
    Proc Natl Acad Sci U S A 109:1985-90. 2012
    ..These findings provide evidence that CD148 functions as a receptor for TSP1 and mediates its inhibition of cell growth...
  32. ncbi request reprint Protein expression profiling of the drosophila fragile X mutant brain reveals up-regulation of monoamine synthesis
    Yong Q Zhang
    Department of Biological Science, Kennedy Center for Research on Human Development, Vanderbilt University, Nashville, Tennessee 37232 1634, USA
    Mol Cell Proteomics 4:278-90. 2005
    ..Elevated brain levels of dopamine and serotonin provide a plausible mechanistic explanation for aspects of cognitive and behavioral deficits in human patients...
  33. ncbi request reprint Oncogenic serine-threonine kinase receptor-associated protein modulates the function of Ewing sarcoma protein through a novel mechanism
    Govindaraj Anumanthan
    Department of Surgery and Cancer Biology, Vanderbilt Ingram Cancer Center and Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
    Cancer Res 66:10824-32. 2006
    ..Thus, this study provides a novel TGF-beta-independent function of STRAP and describes a mechanism by which STRAP regulates the function of oncogenic EWS protein...
  34. ncbi request reprint Identification of N-linked glycosylation sites in human nephrin using mass spectrometry
    Jamshid Khoshnoodi
    Department of Medicine, Vanderbilt University Medical School, Nashville, Tennessee 37232 2372, USA
    J Mass Spectrom 42:370-9. 2007
    ..Thus, nine of ten potential glycosylation sites in nephrin were experimentally proven to be modified by N-linked glycosylation...
  35. pmc Direct ubiquitination of beta-catenin by Siah-1 and regulation by the exchange factor TBL1
    Yoana N Dimitrova
    Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, USA
    J Biol Chem 285:13507-16. 2010
    ..Siah-1 and TBL1 were found to bind to the same armadillo repeat domain of beta-catenin, suggesting that polyubiquitination of beta-catenin is regulated by competition between Siah-1 and TBL1 during Wnt signaling...
  36. pmc Peripheral nerve protein expression and carbonyl content in N,N-diethlydithiocarbamate myelinopathy
    Olga M Viquez
    Department of Pathology, Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University Medical Center, Nashville, Tennessee 37232 2591, USA
    Chem Res Toxicol 20:370-9. 2007
    ....
  37. ncbi request reprint Proteomic analysis identifies immunophilin FK506 binding protein 4 (FKBP52) as a downstream target of Hoxa10 in the periimplantation mouse uterus
    Takiko Daikoku
    Department of Pediatrics and Cancer Biology, Division of Reproductive and Developmental Biology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
    Mol Endocrinol 19:683-97. 2005
    ..Collectively, these results and the female infertility phenotype of FKBP52 suggest that a Hoxa10-FKBP52 signaling axis is critical to uterine receptivity and implantation...
  38. pmc Domain architecture and biochemical characterization of vertebrate Mcm10
    Patrick D Robertson
    Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37232, USA
    J Biol Chem 283:3338-48. 2008
    ....
  39. ncbi request reprint Quantitative proteomics for two-dimensional gels using difference gel electrophoresis
    David B Friedman
    Department of Biochemistry, Mass Spectrometry Research Center, Nashville, TN, USA
    Methods Mol Biol 367:219-39. 2007
    ....
  40. pmc Proteomics of transformed lymphocytes from a family with familial pulmonary arterial hypertension
    Barbara O Meyrick
    Department of Pathology, Vanderbilt University Medical Center, MCN T 1218, Nashville, TN 37232 2650, USA
    Am J Respir Crit Care Med 177:99-107. 2008
    ..Not all family members with BMPR2 mutations develop pulmonary arterial hypertension (PAH), implying that additional modifier genes or proteins are necessary for full expression of the disease...
  41. pmc Yeast Asc1p and mammalian RACK1 are functionally orthologous core 40S ribosomal proteins that repress gene expression
    Vincent R Gerbasi
    Department of Microbiology and Immunology, Vanderbilt University School of Medicine, 1161 21st Ave South, Nashville, TN 37232 2363, USA
    Mol Cell Biol 24:8276-87. 2004
    ..Our data suggest that one of Asc1p's or RACK1's functions is to repress gene expression...
  42. ncbi request reprint Identification of S-hydroxylysyl-methionine as the covalent cross-link of the noncollagenous (NC1) hexamer of the alpha1alpha1alpha2 collagen IV network: a role for the post-translational modification of lysine 211 to hydroxylysine 211 in hexamer assembly
    Roberto M Vanacore
    Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, KS 66160 7421, USA
    J Biol Chem 280:29300-10. 2005
    ....
  43. ncbi request reprint All about DIGE: quantification technology for differential-display 2D-gel proteomics
    Kathryn S Lilley
    Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
    Expert Rev Proteomics 1:401-9. 2004
    ..This technique promises to be an important tool in clinical proteomics and the study of the mechanism of disease, investigating diagnostic biomarkers and pinpointing novel therapeutic targets...
  44. doi request reprint Guidelines for reporting the use of gel electrophoresis in proteomics
    Frank Gibson
    Nat Biotechnol 26:863-4. 2008
  45. ncbi request reprint The alpha1.alpha2 network of collagen IV. Reinforced stabilization of the noncollagenous domain-1 by noncovalent forces and the absence of Met-Lys cross-links
    Roberto M Vanacore
    Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, Kansas 66160, USA
    J Biol Chem 279:44723-30. 2004
    ..alpha4.alpha5 hexamer, implicating the stabilization event in the etiology and pathogenesis of Goodpasture autoimmune disease...

Research Grants1

  1. MALDI-TOF MASS SPECTROMETER
    David Friedman; Fiscal Year: 2003
    ..The acquisition of the requested PRC-dedicated MALDI-TOF instrument with automated data acquision and bioinformatics will allow the PRC to meet the increasing demand for protein identification services from its user base at Vanderbilt. ..