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Robert N. Cole
Robert N. Cole
Director of Mass Spectrometry and Proteomics Facility, Director of Mass Spectrometry Core for Johns Hopkins Kimmel Cancer Center
725 N. Wolfe Street
Baltimore MD 21205
Functional interactions of proteins in human health and disease.
Our research is highly collaborative and focuses on developing, optimizing and applying innovative mass spectrometry strategies to reveal the proteins, their modifications, interactomes and adductomes in modulating or monitoring human health and disease.
Albumin Adductome: Air pollution contains many human carcinogens and presents a major health risk. Airborne concentrations of pollutants, however, do not accurately predict internal dose exposure. Covalent adducts to the Cys34 thiol in human serum albumin can serve as internal dosimeters and the half-life of albumin provides a biomonitoring window of up to 3 months. Analyzing the albumin adductome can simultaneously reveal exposure to many pollutants via unique albumin adducts. We are using Cys34 adductomics to characterize longitudinal exposures to airborne pollution with rising incidence of lung and liver cancer. We aim to characterize the temporal changes in the serum albumin adductome as internal dose biomarkers of airborne pollutant exposure; identify pollutant biomarkers that correlated with increased risk of lung or liver cancer; and compare the albumin adductome biomarker profile and dosimetry response to a validated chemopreventive intervention studies for protection from airborne pollutant exposure. Collaboration with John Groopman, Environmental Sciences.
Astrocyte Exosome Cargo in Neurodegenerative Diseases:
Glia-neuron communication through astrocyte-derived extracellular vesicles promotes neurite outgrowth, neuronal survival and helps maintain normal neuronal function. Biogenesis and secretion of astrocyte exosome cargo is altered in response to many extracellular stimuli. We are using quantitative proteomics to reveal stimuli induced changes in proteomic cargo in modulating dendritic and synaptic formation, in early pathogenesis of Alzheimer's disease, and in disruption by morphine or HIV. Collaboration with Norm Haughey, Neurology .
Mapping Huntingtin Post-translational Modifications:
Onset of Huntingtin’s disease may be regulated by post-translational modifications of the huntingtin protein. We are using discovery and targeted proteomics to identify and quantify functional modifications on human huntingtin. Collaboration with Chris Ross, Neurology.
Ganglioside Tool Kit:
Gangliosides have well-established roles in diverse molecular signaling pathways impacting human diseases such as diabetes, cancer, neuro¬degenerative proteinopathies, intellectual disability, and more. Despite notable progress, the wealth of ganglioside functions and ganglioside-protein interactions are poorly understood because of a lack of appropriate and validated tools. We aim to provide accessible and adaptable tools to address this need by developing novel ganglioside probes, their method of delivery and use to characterize the ganglioside-protein interactomes in health and human diseases. Collaboration with Ron Schnaar, Pharmacology.
Proximity Labeling, Protein Coverage and Site Mapping:
Proximity labeling using biotin ligase is a powerful tool in identifying protein interactors. Confirmation of direct interaction is dependent on identifying the biotinylated peptides. Biotinylated proteins or peptides are enriched using streptavidin beads or antibodies to biotin. Typically, the results from biotinylated protein pull downs are high protein coverage with few biotinylated peptides identified, yielding ambiguity of direct binding of proteins identified and the biotinylation site not identified. Pull downs of biotinylated peptides from proteolytic digests of biotinylated proteins results in identifying many biotinylated peptides with little protein coverage. Protein identification based on a single peptide yields ambiguity for protein isoforms or other homologous proteins. We are developing workflows for streptavidin pulldown of biotinylated proteins that yields both reasonable protein coverage with biotinylation site mapping to unambiguously identify protein-binding partners from proximity labeling experiments.
Datta Chaudhuri A, Dasgheyb RM, DeVine LR, Bi H, Cole RN, and Haughey NJ (2020) Stimulus-dependent modifications in astrocyte-derived extracellular vesicle cargo regulate neuronal excitability. Glia 68: 128-144.
Lee, SE, Schulze K, Stewart CP, Cole RN, Wu LS, Eroglu A, Yager JD, Groopman J, Christian P, and West KP, Jr. (2019) Plasma proteome correlates of lipid and lipoprotein: biomarkers of metabolic diversity and inflammation in children of rural Nepal. J Lipid Res 60: 149-160. PMC6314253
Leung DYM, Calatroni A, Zaramela LS, LeBeau PK, Dyjack N, Brar K, David G, Johnson K, Leung S, Ramirez-Gama M, Liang B, Rios C, Montgomery MT, Richers BN, Hall CF, Norquest KA, Jung J, Bronova I, Kreimer S, Conover Talbot C, Jr., Crumrine D, Cole RN, Elias P, Zengler K, Seibold MA, Berdyshev E, and Goleva E (2019) The nonlesional skin surface distinguishes atopic dermatitis with food allergy as a unique endotype. Sci Transl Med 11: eaav2685.
Eroglu A, Schulze KJ, Yager J, Cole RN, Christian P, Nonyane BAS, Lee SE, Wu LSF, Khatry S, Groopman J, and West KP, Jr. (2018) Plasma proteins associated with circulating carotenoids in Nepalese school-aged children. Arch Biochem Biophys 646: 153-160. PMC5937903
Rhoads SN, Monahan ZT, Yee DS, Leung AY, Newcombe CG, O'Meally RN, Cole RN, and Shewmaker FP (2018) The prionlike domain of FUS is multiphosphorylated following DNA damage without altering nuclear localization. Mol Biol Cell 29: 1786-1797. PMC6085830
Dickens AM, Tovar YRLB, Yoo SW, Trout AL, Bae M, Kanmogne M, Megra B, Williams DW, Witwer KW, Gacias M, Tabatadze N, Cole RN, Casaccia P, Berman JW, Anthony DC, and Haughey NJ (2017) Astrocyte-shed extracellular vesicles regulate the peripheral leukocyte response to inflammatory brain lesions. Sci Signal 10: PMC5590230
Ratovitski T, O'Meally RN, Jiang M, Chaerkady R, Chighladze E, Stewart JC, Wang X, Arbez N, Roby E, Alexandris A, Duan W, Vijayvargia R, Seong IS, Lavery DJ, Cole RN, and Ross CA (2017) Post-Translational Modifications (PTMs), Identified on Endogenous Huntingtin, Cluster within Proteolytic Domains between HEAT Repeats. J Proteome Res 16: 2692-2708. PMC5560079
Bullen JW, Tchernyshyov I, Holewinski RJ, DeVine L, Wu F, Venkatraman V, Kass DL, Cole RN, Van Eyk J, and Semenza GL (2016) Protein kinase A-dependent phosphorylation stimulates the transcriptional activity of hypoxia-inducible factor 1. Sci Signal 9: ra56.
Lee SE, Schulze KJ, Cole RN, Wu LS, Yager JD, Groopman J, Christian P, and West KP, Jr. (2016) Biological Systems of Vitamin K: A Plasma Nutriproteomics Study of Subclinical Vitamin K Deficiency in 500 Nepalese Children. OMICS 20: 214-223. PMC4840917
Ratovitski T, Chaerkady R, Kammers K, Stewart JC, Zavala A, Pletnikova O, Troncoso JC, Rudnicki DD, Margolis RL, Cole RN, and Ross CA (2016) Quantitative Proteomic Analysis Reveals Similarities between Huntington's Disease (HD) and Huntington's Disease-Like 2 (HDL2) Human Brains. J Proteome Res 15: 3266-3283.
Lee SE, West KP, Jr., Cole RN, Schulze KJ, Christian P, Wu LS, Yager JD, Groopman J, and Ruczinski I (2015) Plasma Proteome Biomarkers of Inflammation in School Aged Children in Nepal. PLoS One 10: e0144279. PMC4670104.
West KP, Jr., Cole RN, Shrestha S, Schulze KJ, Lee SE, Betz J, Nonyane BA, Wu LS, Yager JD, Groopman JD, and Christian P (2015) A Plasma alpha-Tocopherome Can Be Identified from Proteins Associated with Vitamin E Status in School-Aged Children of Nepal. J Nutr 145: 2646-2656.
Luo W, Lin B, Wang Y, Zhong J, O'Meally R, Cole RN, Pandey A, Levchenko A, and Semenza GL (2014) PHD3-mediated prolyl hydroxylation of nonmuscle actin impairs polymerization and cell motility. Mol Biol Cell 25: 2788-2796. PMC4161513
Cole RN, Ruczinski I, Schulze K, Christian P, Herbrich S, Wu L, Devine LR, O'Meally RN, Shrestha S, Boronina TN, Yager JD, Groopman J, and West KP, Jr. (2013) The plasma proteome identifies expected and novel proteins correlated with micronutrient status in undernourished Nepalese children. J Nutr 143: 1540-1548. NIHMS 637386
Herbrich SM, Cole RN, West KP, Jr., Schulze K, Yager JD, Groopman JD, Christian P, Wu L, O'Meally RN, May DH, McIntosh MW, and Ruczinski I (2013) Statistical Inference from Multiple iTRAQ Experiments without Using Common Reference Standards. J Proteome Res 12: 594-604. PMC4223774
Ratovitski T, Chighladze E, Arbez N, Boronina T, Herbrich S, Cole RN, and Ross CA (2012) Huntingtin protein interactions altered by polyglutamine expansion as determined by quantitative proteomic analysis. Cell Cycle 11: 2006-2021. PMC3359124
Luo W, Hu H, Chang R, Zhong J, Knabel M, O'Meally R, Cole RN, Pandey A, and Semenza GL (2011) Pyruvate kinase M2 is a PHD3-stimulated coactivator for hypoxia-inducible factor 1. Cell 145: 732-744. PMC3130564
Guo Y, Singleton PA, Rowshan A, Gucek M, Cole RN, Graham DR, Van Eyk JE, and Garcia JG (2007) Quantitative proteomic analysis of human endothelial cell membrane rafts: Evidence of MARCKS and MRP regulation in the sphingosine 1-phosphate-induced barrier enhancement. Mol Cell Proteomics 6: 689-696. PMC3782866
Liu YV, Baek JH, Zhang H, Diez R, Cole RN, and Semenza GL (2007) RACK1 competes with HSP90 for binding to HIF-1alpha and is required for O(2)-independent and HSP90 inhibitor-induced degradation of HIF-1alpha. Mol Cell 25: 207-217. PMC2563152
Liu YV, Hubbi ME, Pan F, McDonald KR, Mansharamani M, Cole RN, Liu JO, and Semenza GL (2007) Calcineurin promotes HIF-1alpha expression by dephosphorylating RACK1 and blocking RACK1 dimerization. J Biol Chem 282: 37064-37073. PMC3754800
Dinkova-Kostova AT, Holtzclaw WD, Cole RN, Itoh K, Wakabayashi N, Katoh Y, Yamamoto M, and Talalay P (2002) Direct evidence that sulfhydryl groups of Keap1 are the sensors regulating induction of phase 2 enzymes that protect against carcinogens and oxidants. Proc Natl Acad Sci U S A 99: 11908-11013. PMC129367
Starai VJ, Celic I, Cole RN, Boeke JD, and Escalante-Semerena JC (2002) Sir2-dependent activation of acetyl-CoA synthetase by deacetylation of active lysine. Science 298: 2390-2392. PMID12493915
Wells L, Vosseller K, Cole RN, Cronshaw JM, Matunis MJ, and Hart GW (2002) Mapping sites of O-GlcNAc modification using affinity tags for serine and threonine post-translational modifications. Mol Cell Proteomics 1: 791-804. PMID12438562
Cole RN and Hart GW (2001) Cytosolic O-glycosylation is abundant in nerve terminals. J Neurochem 79: 1080-1089. PMID11739622 Cole RN and Hart GW (1999) Glycosylation sites flank phosphorylation sites on synapsin I: O-linked N-acetylglucosamine residues are localized within domains mediating synapsin I interactions. J Neurochem 73: 418-428. PMID10386995