Vanderbilt University School of Medicine

Friedman, David B. , Ph.D.
Adjunct Research Associate Professor of Biochemistry

Lab Url: http://www.mc.vanderbilt.edu/root/vumc.php?site=msrc/proteomics_core

Phone Number: 343-7333

Email Address:david.friedman@Vanderbilt.Edu

Friedman, David's picture

Office Address   Mailing Address

9114C Medical Research Building III

9160 MRB III 465 21st Ave. S. 37232-8575


Research Specialty
Proteomics; differential protein expression and protein/peptide mass spectrometry.

Research Description
Proteomics is the study of the dynamic protein expression of a tissue, cell type or organism. As an Associate Director of the Proteomics Laboratory in the Mass Spectrometry Research Center, I direct research and technology that targets differential protein expression upon various experimental treatments/conditions, and subsequent protein identification using mass spectrometry. In addition, the Proteomics Laboratory offers the ability to identify proteins resolved on SDS-PAGE gels or in biochemical fractions, as well as characterize and map sites of post-translational modification using mass spectrometry.

The Proteomics Laboratory offers two main proteomics technology platforms, and also embarks on specialized research problems that often go beyond these commercially-available technologies. The first is sensitive and rapid protein identification technologies using single- and multi-dimensional HPLC peptide separations coupled directly to tandem mass spectrometry. The second technology utilizes established 2D gel technology with newly-available flourscent protein tags. Termed DIGE, this technology allows for multiple samples to be separated together and to be compared to a common standard sample. This allows for quantitative comparisons across a minimal number of 2D gels without interference from gel-to-gel variation. This is coupled with rapid and sensitive protein identification using mass spectrometry.

Publications
Hill, MF, Patel, AV, Murphy, A, Smith, HM, Galindo, CL, Pentassuglia, L, Peng, X, Lenneman, CG, Odiete, O, Friedman, DB, Kronenberg, MW, Zheng, S, Zhao, Z, Song, Y, Harrell, FE, Srinivas, M, Ganguly, A, Iaci, J, Parry, TJ, Caggiano, AO, Sawyer, DB. Intravenous glial growth factor 2 (GGF2) isoform of neuregulin-1?? improves left ventricular function, gene and protein expression in rats after myocardial infarction. PLoS One, 8(2), e55741, 2013.

McClain, CM, Friedman, DB, Hajri, T, Coffin, CM, Cates, JM. Predicting dedifferentiation in liposarcoma: a proteomic approach. Virchows Arch, 463(1), 85-92, 2013.

Noto, JM, Gaddy, JA, Lee, JY, Piazuelo, MB, Friedman, DB, Colvin, DC, Romero-Gallo, J, Suarez, G, Loh, J, Slaughter, JC, Tan, S, Morgan, DR, Wilson, KT, Bravo, LE, Correa, P, Cover, TL, Amieva, MR, Peek, RM. Iron deficiency accelerates Helicobacter pylori-induced carcinogenesis in rodents and humans. J Clin Invest, 123(1), 479-92, 2013.

Friedman, DB. Assessing signal-to-noise in quantitative proteomics: multivariate statistical analysis in DIGE experiments. Methods Mol Biol, 854, 31-45, 2012.

Loh, JT, Friedman, DB, Piazuelo, MB, Bravo, LE, Wilson, KT, Peek, RM, Correa, P, Cover, TL. Analysis of Helicobacter pylori cagA promoter elements required for salt-induced upregulation of CagA expression. Infect Immun, 80(9), 3094-106, 2012.

Pruitt, RN, Chumbler, NM, Rutherford, SA, Farrow, MA, Friedman, DB, Spiller, B, Lacy, DB. Structural determinants of Clostridium difficile toxin A glucosyltransferase activity. J Biol Chem, 287(11), 8013-20, 2012.

Takahashi, K, Mernaugh, RL, Friedman, DB, Weller, R, Tsuboi, N, Yamashita, H, Quaranta, V, Takahashi, T. Thrombospondin-1 acts as a ligand for CD148 tyrosine phosphatase. Proc Natl Acad Sci U S A, 109(6), 1985-90, 2012.

Venkateswaran, A, Friedman, DB, Walsh, AJ, Skala, MC, Sasi, S, Rachakonda, G, Crooks, PA, Freeman, ML, Sekhar, KR. The novel antiangiogenic VJ115 inhibits the NADH oxidase ENOX1 and cytoskeleton-remodeling proteins. Invest New Drugs, , , 2012.

Viquez, OM, Caito, SW, McDonald, WH, Friedman, DB, Valentine, WM. Electrophilic adduction of ubiquitin activating enzyme E1 by N,N-diethyldithiocarbamate inhibits ubiquitin activation and is accompanied by striatal injury in the rat. Chem Res Toxicol, 25(11), 2310-21, 2012.

Wegrzynowicz, M, Holt, HK, Friedman, DB, Bowman, AB. Changes in the striatal proteome of YAC128Q mice exhibit gene-environment interactions between mutant huntingtin and manganese. J Proteome Res, 11(2), 1118-32, 2012.

Boutt??, AM, Friedman, DB, Bogyo, M, Min, Y, Yang, L, Lin, PC. Identification of a myeloid-derived suppressor cell cystatin-like protein that inhibits metastasis. FASEB J, 25(8), 2626-37, 2011.

Friedman, DB, Andacht, TM, Bunger, MK, Chien, AS, Hawke, DH, Krijgsveld, J, Lane, WS, Lilley, KS, MacCoss, MJ, Moritz, RL, Settlage, RE, Sherman, NE, Weintraub, ST, Witkowska, HE, Yates, NA, Turck, CW. The ABRF Proteomics Research Group studies: educational exercises for qualitative and quantitative proteomic analyses. Proteomics, 11(8), 1371-81, 2011.

Nam, EA, Zhao, R, Glick, GG, Bansbach, CE, Friedman, DB, Cortez, D. Thr-1989 phosphorylation is a marker of active ataxia telangiectasia-mutated and Rad3-related (ATR) kinase. J Biol Chem, 286(33), 28707-14, 2011.

Rauth, TP, Slone, J, Crane, G, Correa, H, Friedman, DL, Lovvorn, HN. Laparoscopic nephron-sparing resection of synchronous Wilms tumors in a case of hyperplastic perilobar nephroblastomatosis. J Pediatr Surg, 46(5), 983-8, 2011.

Smith, AL, Friedman, DB, Yu, H, Carnahan, RH, Reynolds, AB. ReCLIP (reversible cross-link immuno-precipitation): an efficient method for interrogation of labile protein complexes. PLoS One, 6(1), e16206, 2011.

Cates, JM, Friedman, DB, Seeley, EH, Dupont, WD, Schwartz, HS, Holt, GE, Caprioli, RM, Young, PP. Proteomic analysis of osteogenic sarcoma: association of tumour necrosis factor with poor prognosis. Int J Exp Pathol, 91(4), 335-49, 2010.

Dimitrova, YN, Li, J, Lee, YT, Rios-Esteves, J, Friedman, DB, Choi, HJ, Weis, WI, Wang, CY, Chazin, WJ. Direct ubiquitination of beta-catenin by Siah-1 and regulation by the exchange factor TBL1. J Biol Chem, 285(18), 13507-16, 2010.

Loh, JT, Gupta, SS, Friedman, DB, Krezel, AM, Cover, TL. Analysis of protein expression regulated by the Helicobacter pylori ArsRS two-component signal transduction system. J Bacteriol, 192(8), 2034-43, 2010. PMCID:2849440

Sarilla, S, Habib, SY, Tollefsen, DM, Friedman, DB, Arnett, DR, Verhamme, IM. Glycosaminoglycan-binding properties and kinetic characterization of human heparin cofactor II expressed in Escherichia coli. Anal Biochem, 406(2), 166-75, 2010.

Torres, VJ, Attia, AS, Mason, WJ, Hood, MI, Corbin, BD, Beasley, FC, Anderson, KL, Stauff, DL, McDonald, WH, Zimmerman, LJ, Friedman, DB, Heinrichs, DE, Dunman, PM, Skaar, EP. Staphylococcus aureus fur regulates the expression of virulence factors that contribute to the pathogenesis of pneumonia. Infect Immun, 78(4), 1618-28, 2010. PMCID:2849423

Franco, AT, Friedman, DB, Nagy, TA, Romero-Gallo, J, Krishna, U, Kendall, A, Israel, DA, Tegtmeyer, N, Washington, MK, Peek, RM. Delineation of a carcinogenic Helicobacter pylori proteome. Mol Cell Proteomics, 8(8), 1947-58, 2009.

Friedman, DB, Hoving, S, Westermeier, R. Isoelectric focusing and two-dimensional gel electrophoresis. Methods Enzymol, 463, 515-40, 2009.

Wang, Y, Azuma, Y, Friedman, DB, Coffey, RJ, Neufeld, KL. Novel association of APC with intermediate filaments identified using a new versatile APC antibody. BMC Cell Biol, 10, 75, 2009. PMCID:2774295

Friedman, DB, Lilley, KS. Optimizing the difference gel electrophoresis (DIGE) technology. Methods Mol Biol, 428, 93-124, 2008.

Gibson, F, Anderson, L, Babnigg, G, Baker, M, Berth, M, Binz, PA, Borthwick, A, Cash, P, Day, BW, Friedman, DB, Garland, D, Gutstein, HB, Hoogland, C, Jones, NA, Khan, A, Klose, J, Lamond, AI, Lemkin, PF, Lilley, KS, Minden, J, Morris, NJ, Paton, NW, Pisano, MR, Prime, JE, Rabilloud, T, Stead, DA, Taylor, CF, Voshol, H, Wipat, A, Jones, AR. Guidelines for reporting the use of gel electrophoresis in proteomics. Nat Biotechnol, 26(8), 863-4, 2008.

Meyrick, BO, Friedman, DB, Billheimer, DD, Cogan, JD, Prince, MA, Phillips, JA, Loyd, JE. Proteomics of transformed lymphocytes from a family with familial pulmonary arterial hypertension. Am J Respir Crit Care Med, 177(1), 99-107, 2008. PMCID:2176118

Friedman, DB. Quantitative proteomics for two-dimensional gels using difference gel electrophoresis. Methods Mol Biol, 367, 219-39, 2007.

Friedman, DB, Wang, SE, Whitwell, CW, Caprioli, RM, Arteaga, CL. Multivariable difference gel electrophoresis and mass spectrometry: a case study on transforming growth factor-beta and ERBB2 signaling. Mol Cell Proteomics, 6(1), 150-69, 2007.

Haas, KF, Miller, SL, Friedman, DB, Broadie, K. The ubiquitin-proteasome system postsynaptically regulates glutamatergic synaptic function. Mol Cell Neurosci, 35(1), 64-75, 2007. PMCID:1936977

Hamblin, M, Friedman, DB, Hill, S, Caprioli, RM, Smith, HM, Hill, MF. Alterations in the diabetic myocardial proteome coupled with increased myocardial oxidative stress underlies diabetic cardiomyopathy. J Mol Cell Cardiol, 42(4), 884-95, 2007. PMCID:2677446

Keller, JW, Franklin, JL, Graves-Deal, R, Friedman, DB, Whitwell, CW, Coffey, RJ. Oncogenic KRAS provides a uniquely powerful and variable oncogenic contribution among RAS family members in the colonic epithelium. J Cell Physiol, 210(3), 740-9, 2007.

Khoshnoodi, J, Hill, S, Tryggvason, K, Hudson, B, Friedman, DB. Identification of N-linked glycosylation sites in human nephrin using mass spectrometry. J Mass Spectrom, 42(3), 370-379, 2007.

Pollins, AC, Friedman, DB, Nanney, LB. Proteomic Investigation of Human Burn Wounds by 2D-Difference Gel Electrophoresis and Mass Spectrometry. J Surg Res, , , 2007. PMCID:2696121

Robertson, PD, Warren, EM, Zhang, H, Friedman, DB, Lary, JW, Cole, JL, Tutter, AV, Walter, JC, Fanning, E, Eichman, BF. Domain architecture and biochemical characterization of vertebrate MCM10. J Biol Chem, , , 2007. PMCID:2753450

Viquez, OM, Valentine, HL, Friedman, DB, Olson, SJ, Valentine, WM. Peripheral Nerve Protein Expression and Carbonyl Content in N,N-Diethlydithiocarbamate Myelinopathy. Chem Res Toxicol, , , 2007. PMCID:2525616

Wang, SE, Narasanna, A, Whitell, CW, Wu, FY, Friedman, DB, Arteaga, CL. Convergence of p53 and Transforming Growth Factor beta (TGFbeta) Signaling on Activating Expression of the Tumor Suppressor Gene maspin in Mammary Epithelial Cells. J Biol Chem, 282(8), 5661-9, 2007.

Anumanthan, G, Halder, SK, Friedman, DB, Datta, PK. Oncogenic serine-threonine kinase receptor-associated protein modulates the function of Ewing sarcoma protein through a novel mechanism. Cancer Res, 66(22), 10824-32, 2006.

Busler, VJ, Torres, VJ, McClain, MS, Tirado, O, Friedman, DB, Cover, TL. Protein-protein interactions among Helicobacter pylori cag proteins. J Bacteriol, 188(13), 4787-800, 2006. PMCID:1482994

Friedman, DB, Stauff, DL, Pishchany, G, Whitwell, CW, Torres, VJ, Skaar, EP. Staphylococcus aureus redirects central metabolism to increase iron availability. PLoS Pathog, 2(8), e87, 2006. PMCID:1557832

Tabb, DL, Friedman, DB, Ham, AJ. Verification of automated peptide identifications from proteomic tandem mass spectra. Nat Protoc, 1(5), 2213-22, 2006.

Wang, SE, Shin, I, Wu, FY, Friedman, DB, Arteaga, CL. HER2/Neu (ErbB2) signaling to Rac1-Pak1 is temporally and spatially modulated by transforming growth factor beta. Cancer Res, 66(19), 9591-600, 2006.

Tian, C, Breyer, RM, Kim, HJ, Karra, MD, Friedman, DB, Karpay, A, Sanders, CR. Solution NMR spectroscopy of the human vasopressin V2 receptor, a G protein-coupled receptor. J Am Chem Soc, 127(22), 8010-1, 2005.

Vanacore, RM, Friedman, DB, Ham, AJ, Sundaramoorthy, M, Hudson, BG. Identification of S-hydroxylysyl211-methionine93 as the covalent crosslink of the noncollagenous (NC1) hexamer of the alpha 1alpha 1alpha 2 collagen IV network: A role for the posttranslational modification of lysine211 to hydroxylysine211 in hexamer assembly. J Biol Chem, , , 2005.

Zhang, Yong Q, Friedman, David B, Wang, Zhe, Woodruff, Elvin, Pan, Luyuan, O''donnell, Janis, Broadie, Kendal. Protein expression profiling of the drosophila fragile X mutant brain reveals upregulation of monoamine synthesis. Mol Cell Proteomics, , , 2005.

Chytil, Anna, Waltner-Law, Mary, West, Robert, Friedman, David, Aakre, Mary, Barker, Dana, Law, Brian. Construction of a cyclin D1-Cdk2 fusion protein to model the biological functions of cyclin D1-Cdk2 complexes. J Biol Chem, 279(46), 47688-98, 2004.

Daikoku, Takiko, Tranguch, Susanne, Friedman, David B, Das, Sanjoy K, Smith, David F, Dey, Sudhansu K. Proteomic analysis identifies immunophilin FKBP52 as a downstream target of Hoxa10 in the periimplantation mouse uterus. Mol Endocrinol, , , 2004.

Friedman, DB, Hill, S, Keller, JW, Merchant, NB, Levy, SE, Coffey, RJ, Caprioli, RM. Proteome analysis of human colon cancer by two-dimensional difference gel electrophoresis and mass spectrometry. Proteomics, 4(3), 793-811, 2004.

Gerbasi, Vincent R, Weaver, Connie M, Hill, Salisha, Friedman, David B, Link, Andrew J. Yeast Asc1p and mammalian RACK1 are functionally orthologous core 40S ribosomal proteins that repress gene expression. Mol Cell Biol, 24(18), 8276-87, 2004. PMCID:515043

Lilley, KS, Friedman, DB. All about DIGE: quantification technology for differential-display 2D-gel proteomics. Expert Rev Proteomics, 1(4), 401-9, 2004.

Vanacore, Roberto M., Shanmugasundararaj, Sivananthaperumal, Friedman, David B., Bondar, Olga, Hudson, Billy G., Sundaramoorthy, Munirathinam. The a1.a2-network of collagen IV: Reinforced stabilization of the noncollagenous domain-1 by noncovalent forces and the absence of Met-Lys crosslinks. J Biol Chem, , , 2004.

Zhang, YQ, Matthies, HJ, Mancuso, J, Andrews, HK, Woodruff, E, Friedman, D, Broadie, K. The Drosophila fragile X-related gene regulates axoneme differentiation during spermatogenesis. Dev Biol, 270(2), 290-307, 2004.

Low, RL, Orton, S, Friedman, DB. A truncated form of DNA topoisomerase IIbeta associates with the mtDNA genome in mammalian mitochondria. Eur J Biochem, 270(20), 4173-86, 2003.

Matsuoka, TA, Zhao, L, Artner, I, Jarrett, HW, Friedman, D, Means, A, Stein, R. Members of the large Maf transcription family regulate insulin gene transcription in islet beta cells. Mol Cell Biol, 23(17), 6049-62, 2003. PMCID:180917

Sekhar, KR, Crooks, PA, Sonar, VN, Friedman, DB, Chan, JY, Meredith, MJ, Starnes, JH, Kelton, KR, Summar, SR, Sasi, S, Freeman, ML. NADPH oxidase activity is essential for Keap1/Nrf2-mediated induction of GCLC in response to 2-indol-3-yl-methylenequinuclidin-3-ols. Cancer Res, 63(17), 5636-45, 2003.

Friedman, DB, Kern, JW, Huneycutt, BJ, Vinh, DB, Crawford, DK, Steiner, E, Scheiltz, D, Yates, J, Resing, KA, Ahn, NG, Winey, M, Davis, TN. Yeast Mps1p phosphorylates the spindle pole component Spc110p in the N-terminal domain. J Biol Chem, 276(21), 17958-67, 2001.

Kironmai, KM, Muniyappa, K, Friedman, DB, Hollingsworth, NM, Byers, B. DNA-binding activities of Hop1 protein, a synaptonemal complex component from Saccharomyces cerevisiae. Mol Cell Biol, 18(3), 1424-35, 1998. PMCID:108856

Friedman, DB, Sundberg, HA, Huang, EY, Davis, TN. The 110-kD spindle pole body component of Saccharomyces cerevisiae is a phosphoprotein that is modified in a cell cycle-dependent manner. J Cell Biol, 132(5), 903-14, 1996. PMCID:2120732

Friedman, DB, Hollingsworth, NM, Byers, B. Insertional mutations in the yeast HOP1 gene: evidence for multimeric assembly in meiosis. Genetics, 136(2), 449-64, 1994. PMCID:1205800

Friedman, DB, Johnson, TE. Three mutants that extend both mean and maximum life span of the nematode, Caenorhabditis elegans, define the age-1 gene. J Gerontol, 43(4), B102-9, 1988.

Friedman, DB, Johnson, TE. A mutation in the age-1 gene in Caenorhabditis elegans lengthens life and reduces hermaphrodite fertility. Genetics, 118(1), 75-86, 1988. PMCID:1203268

Johnson, TE, Friedman, DB, Fitzpatrick, PA, Conley, WL. Mutant genes that extend life span. Basic Life Sci, 42, 91-100, 1987.


Postdoctoral Position Available
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Postdoctoral Position Details
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Updated Date
08/18/2013



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