The Proteomics Core (Core B) provides state-of-the-art instrumentation, methodology, and expertise in proteomics to investigators in this PPG. A unique feature of the Proteomics Core is the availability of cutting? edge quantitative proteomics analysis technologies that allows high sensitivity measurements of proteome changes in models of gastric cancer. The Proteomics Core provides 1) identification of proteins in complex samples, 2) quantitative analyses of differential protein expression from in vitro and in vivo samples, and 3) global analyses of protein modifications. Proteomics Core staff provides consultation on experimentaldesign as well as hands on sample preparation, mass spectrometry analysis, and primary data analysis. Multiple high performance mass spectrometers for LC-MS/MS experiments and MALDI TOF-TOF instruments are available for proteomic analyses. For protein identification from complex samples, analysis involves multidimensional LC-MS/MS followed by automated database searching with Sequest software running on a multiprocessor Linux cluster in the Advanced Computing Center for Research and Education (ACCRE). Protein identifications are evaluated, filtered, and compared using custom lDPicker or commercial Scaffold software. Additional data analysis by TagRecon enables identification of unanticipated modifications or sequence variants from MS/MS data. The Core also provides relative quantitation using stable isotope differential labeling strategies, iTRAQ and SILAC, for samples derived from animal models or from cell culture, respectively. Validation of protein expression changes is accomplished using multiple reaction monitoring LC-MS/MS methods. Project 1 (Peek) will utilize the iTRAQ method to measure proteomic changes in gastric epithelial cells from gerbils infected with carcinogenic H. pylori or mutants fed iron-replete and iron-deplete diets. Project 2 (Wilson) will utilize the same approach to determine changes in gastric epithelial cell proteomes upon EGFR activation. In addition, this Project will utilize the SILAC method to measure changes in the phosphoproteome upon EGFR activation in conditionally immortalized cells. Project 3 (Cover) will employ the iTRAQ method to measure differences in H. pylori output strains from gerbils fed high salt or regular diets. Targeted MRM validation will be employed in all studies to confirm specific proteomic changes

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Research Program Projects (P01)
Project #
2P01CA116087-06
Application #
8632358
Study Section
Special Emphasis Panel (ZCA1-RPRB-C (O1))
Project Start
2014-01-01
Project End
2018-12-31
Budget Start
2014-03-12
Budget End
2014-12-31
Support Year
6
Fiscal Year
2014
Total Cost
$173,978
Indirect Cost
$81,541
Name
Vanderbilt University Medical Center
Department
Type
DUNS #
004413456
City
Nashville
State
TN
Country
United States
Zip Code
37212
Shen, Xi; Liu, Liping; Peek, Richard M et al. (2018) Supplementation of p40, a Lactobacillus rhamnosus GG-derived protein, in early life promotes epidermal growth factor receptor-dependent intestinal development and long-term health outcomes. Mucosal Immunol 11:1316-1328
Mera, Robertino M; Bravo, Luis E; Camargo, M Constanza et al. (2018) Dynamics of Helicobacter pylori infection as a determinant of progression of gastric precancerous lesions: 16-year follow-up of an eradication trial. Gut 67:1239-1246
Singh, Kshipra; Coburn, Lori A; Asim, Mohammad et al. (2018) Ornithine Decarboxylase in Macrophages Exacerbates Colitis and Promotes Colitis-Associated Colon Carcinogenesis by Impairing M1 Immune Responses. Cancer Res 78:4303-4315
Corley, Douglas A; Peek Jr, Richard M (2018) When Should Guidelines Change? A Clarion Call for Evidence Regarding the Benefits and Risks of Screening for Colorectal Cancer at Earlier Ages. Gastroenterology 155:947-949
Gobert, Alain P; Al-Greene, Nicole T; Singh, Kshipra et al. (2018) Distinct Immunomodulatory Effects of Spermine Oxidase in Colitis Induced by Epithelial Injury or Infection. Front Immunol 9:1242
Raghunathan, Krishnan; Foegeding, Nora J; Campbell, Anne M et al. (2018) Determinants of Raft Partitioning of the Helicobacter pylori Pore-Forming Toxin VacA. Infect Immun 86:
Scoville, Elizabeth A; Allaman, Margaret M; Brown, Caroline T et al. (2018) Alterations in Lipid, Amino Acid, and Energy Metabolism Distinguish Crohn's Disease from Ulcerative Colitis and Control Subjects by Serum Metabolomic Profiling. Metabolomics 14:
Sierra, Johanna C; Asim, Mohammad; Verriere, Thomas G et al. (2018) Epidermal growth factor receptor inhibition downregulates Helicobacter pylori-induced epithelial inflammatory responses, DNA damage and gastric carcinogenesis. Gut 67:1247-1260
Blosse, Alice; Lehours, Philippe; Wilson, Keith T et al. (2018) Helicobacter: Inflammation, immunology, and vaccines. Helicobacter 23 Suppl 1:e12517
Coburn, Lori A; Singh, Kshipra; Asim, Mohammad et al. (2018) Loss of solute carrier family 7 member 2 exacerbates inflammation-associated colon tumorigenesis. Oncogene :

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