Systems Biology of Glycosylation

Summary

Principal Investigator: Sriram Neelamegham
Abstract: DESCRIPTION (provided by applicant): Glycosylation is an important post-translational modification of proteins and lipids. This process controls cell recognition and signaling processes that regulate human development, immunity and disease. The current proposal aims to develop Systems Biology based computational and experimental methodologies to enhance our understanding of cellular glycosylation pathways. In particular, our focus is on better understanding the features that regulate the formation of O-linked glycans on human leukocytes. By binding adhesion molecules belonging to the selecting family, these O-glycans play a critical role in regulating leukocyte adhesion to vascular endothelial cells that line blood vessel walls at sites of inflammation and cardiovascular disease. Our overall hypothesis is that "In silico modeling of glycosylation reaction networks can identify rate limiting steps that control the formation of selectin-ligands on human leukocytes. Defined and specific perturbation of these rate-limiting steps can reduce leukocyte-endothelial cell adhesion/migration in vivo during inflammation." The specific aims are: 1) to develop computational models to predict the rate-limiting steps that control cellular glycosylation. 2) To quantify the role of selected glycosyltransferases and the peptide backbone in regulating O-linked glycosylation and leukocyte selecting-binding function. 3) To test the effect of silencing glycosyltransferases on leukocyte retention in the bone marrow, and cell migration to sites of inflammation. The project involves collaboration between investigators with expertise in Systems Biology based modeling, quantitative bioengineering experimentation, proteomics, glycobiology, immunology and animal models. Experimental studies span multiple scales from genes, to proteins/enzymes, to carbohydrate structure and cell adhesion function, both in vitro and in vivo. The computer modeling integrates this information to determine the effect of system perturbation on glycan structure and function. Expected project outcomes include: I) Definition of a new standard called GlycoML for the description of glycosylation reaction networks. ii) Combined use of experiment and theory to reveal potential intra-cellular/metabolic targets of glycosylation that can quantitatively and definitively alter selectin-ligand structures. iii) Definition of the precise a (2, 3)sialyltransferase(s) and a (1, 3) fucosyltransferases(s) that regulate selectin-ligand biosynthesis in human leukocytes. iv) Improved understanding of the role of the peptide backbone in regulating O-glycosylation chain initiation, extension and termination. v) Validation in animal models of inflammation, peritonitis and COPD (chronic obstructive pulmonary disease), key hypothesis generated using computer simulation and ex vivo experimentation.
Funding Period: 2011-09-05 - 2016-06-30
more information: NIH RePORT

Top Publications

  1. pmc Systems glycobiology: biochemical reaction networks regulating glycan structure and function
    Sriram Neelamegham
    Department of Chemical and Biological Engineering, and The NY State Center for Excellence in Bioinformatics and Life Sciences, State University of New York, Buffalo, NY 14260, USA
    Glycobiology 21:1541-53. 2011
  2. pmc Effects of calibration approaches on the accuracy for LC-MS targeted quantification of therapeutic protein
    Eslam Nouri-Nigjeh
    The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Amherst, NY 14260, United States
    Anal Chem 86:3575-84. 2014
  3. pmc A remodeled protein arginine methyltransferase 1 (PRMT1) generates symmetric dimethylarginine
    Shanying Gui
    From the Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322
    J Biol Chem 289:9320-7. 2014
  4. pmc Large-scale, ion-current-based proteomics investigation of bronchoalveolar lavage fluid in chronic obstructive pulmonary disease patients
    Chengjian Tu
    Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, 319 Kapoor Hall, Buffalo, New York 14260, United States
    J Proteome Res 13:627-39. 2014
  5. pmc Ion-current-based proteomic profiling of the retina in a rat model of Smith-Lemli-Opitz syndrome
    Chengjian Tu
    Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14260
    Mol Cell Proteomics 12:3583-98. 2013
  6. pmc The use of surface immobilization of P-selectin glycoprotein ligand-1 on mesenchymal stem cells to facilitate selectin mediated cell tethering and rolling
    Chi Y Lo
    Department of Chemical and Biological Engineering, The State University of New York, 906 Furnas Hall, Buffalo, NY 14260, USA
    Biomaterials 34:8213-22. 2013
  7. pmc Distinct glycosyltransferases synthesize E-selectin ligands in human vs. mouse leukocytes
    Nandini Mondal
    Chemical and Biological Engineering and The NY State Center for Excellence in Bioinformatics and Life Sciences, State University of New York, Buffalo, NY, USA
    Cell Adh Migr 7:288-92. 2013
  8. pmc Competition between core-2 GlcNAc-transferase and ST6GalNAc-transferase regulates the synthesis of the leukocyte selectin ligand on human P-selectin glycoprotein ligand-1
    Chi Y Lo
    Department of Chemical and Biological Engineering, The State University of New York, Buffalo, New York 14260, USA
    J Biol Chem 288:13974-87. 2013
  9. pmc Glycosylation Network Analysis Toolbox: a MATLAB-based environment for systems glycobiology
    Gang Liu
    Department of Chemical and Biological Engineering and The NY State Center for Excellence in Bioinformatics and Life Sciences, State University of New York, Buffalo, NY 14260, USA
    Bioinformatics 29:404-6. 2013
  10. pmc Silencing α1,3-fucosyltransferases in human leukocytes reveals a role for FUT9 enzyme during E-selectin-mediated cell adhesion
    Alexander Buffone
    Department of Chemical and Biological Engineering, State University of New York, Buffalo, New York 14260, USA
    J Biol Chem 288:1620-33. 2013

Research Grants

Detail Information

Publications15

  1. pmc Systems glycobiology: biochemical reaction networks regulating glycan structure and function
    Sriram Neelamegham
    Department of Chemical and Biological Engineering, and The NY State Center for Excellence in Bioinformatics and Life Sciences, State University of New York, Buffalo, NY 14260, USA
    Glycobiology 21:1541-53. 2011
    ....
  2. pmc Effects of calibration approaches on the accuracy for LC-MS targeted quantification of therapeutic protein
    Eslam Nouri-Nigjeh
    The Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Amherst, NY 14260, United States
    Anal Chem 86:3575-84. 2014
    ....
  3. pmc A remodeled protein arginine methyltransferase 1 (PRMT1) generates symmetric dimethylarginine
    Shanying Gui
    From the Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322
    J Biol Chem 289:9320-7. 2014
    ..Our study reveals unique energetic challenges for SDMA-forming methyltransferases and highlights the exquisite control of product formation by active site residues in the PRMTs. ..
  4. pmc Large-scale, ion-current-based proteomics investigation of bronchoalveolar lavage fluid in chronic obstructive pulmonary disease patients
    Chengjian Tu
    Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, 319 Kapoor Hall, Buffalo, New York 14260, United States
    J Proteome Res 13:627-39. 2014
    ..These discoveries could provide new insights for identifying novel biomarkers and pathological mediators in clinical studies. ..
  5. pmc Ion-current-based proteomic profiling of the retina in a rat model of Smith-Lemli-Opitz syndrome
    Chengjian Tu
    Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14260
    Mol Cell Proteomics 12:3583-98. 2013
    ....
  6. pmc The use of surface immobilization of P-selectin glycoprotein ligand-1 on mesenchymal stem cells to facilitate selectin mediated cell tethering and rolling
    Chi Y Lo
    Department of Chemical and Biological Engineering, The State University of New York, 906 Furnas Hall, Buffalo, NY 14260, USA
    Biomaterials 34:8213-22. 2013
    ..Unlike previous work where MSCs could only be captured onto selectin-bearing substrates at low or no-flow conditions, the current work presents a 'glycan engineering' strategy to enable leukocyte-like capture and rolling...
  7. pmc Distinct glycosyltransferases synthesize E-selectin ligands in human vs. mouse leukocytes
    Nandini Mondal
    Chemical and Biological Engineering and The NY State Center for Excellence in Bioinformatics and Life Sciences, State University of New York, Buffalo, NY, USA
    Cell Adh Migr 7:288-92. 2013
    ....
  8. pmc Competition between core-2 GlcNAc-transferase and ST6GalNAc-transferase regulates the synthesis of the leukocyte selectin ligand on human P-selectin glycoprotein ligand-1
    Chi Y Lo
    Department of Chemical and Biological Engineering, The State University of New York, Buffalo, New York 14260, USA
    J Biol Chem 288:13974-87. 2013
    ..Overall, the data describe the glycan microheterogeneity at the PSGL-1 N-terminus. They suggest that a competition between ST6GalNAc2 and C2GnT-1 for the core-1/Galβ1,3GalNAc glycan may regulate leukocyte adhesion under fluid shear...
  9. pmc Glycosylation Network Analysis Toolbox: a MATLAB-based environment for systems glycobiology
    Gang Liu
    Department of Chemical and Biological Engineering and The NY State Center for Excellence in Bioinformatics and Life Sciences, State University of New York, Buffalo, NY 14260, USA
    Bioinformatics 29:404-6. 2013
    ..Curation and manipulation of networks is facilitated using class definitions and glycomics database query tools. High quality visualization of networks and their steady-state and dynamic simulation are also supported...
  10. pmc Silencing α1,3-fucosyltransferases in human leukocytes reveals a role for FUT9 enzyme during E-selectin-mediated cell adhesion
    Alexander Buffone
    Department of Chemical and Biological Engineering, State University of New York, Buffalo, New York 14260, USA
    J Biol Chem 288:1620-33. 2013
    ..This study advances new tools to study human glycoT function. It suggests a species-specific role for FUT9 during the biosynthesis of human E-selectin ligands...
  11. pmc Proteomic analysis reveals diverse classes of arginine methylproteins in mitochondria of trypanosomes
    John C Fisk
    Department of Microbiology and Immunology, School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14124, USA
    Mol Cell Proteomics 12:302-11. 2013
    ..Moreover, these studies establish T. brucei as a model organism for the study of posttranslational modifications...
  12. pmc An ion-current-based, comprehensive and reproducible proteomic strategy for comparative characterization of the cellular responses to novel anti-cancer agents in a prostate cell model
    Chengjian Tu
    Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
    J Proteomics 77:187-201. 2012
    ..Moreover, informative insights into the drug-actions on cell cycle, growth/proliferation, and apoptosis were obtained. This platform technology provides extensive evaluation of drug candidates and facilitates in-depth mechanism studies...
  13. pmc Scaling down the size and increasing the throughput of glycosyltransferase assays: activity changes on stem cell differentiation
    Shilpa A Patil
    Chemical and Biological Engineering, State University of New York, Buffalo, NY 14260, USA
    Anal Biochem 425:135-44. 2012
    ..Overall, simple, rapid, quantitative, and scalable glycoT activity analysis methods are presented. These use a range of natural and synthetic acceptors for the analysis of complex biological specimens that have limited availability...
  14. pmc Understanding glycomechanics using mathematical modeling: a review of current approaches to simulate cellular glycosylation reaction networks
    Apurv Puri
    Department of Chemical and Biological Engineering, and The New York State Center for Excellence in Bioinformatics and Life Sciences, State University of New York, 906 Furnas Hall, Buffalo, NY 14260, USA
    Ann Biomed Eng 40:816-27. 2012
    ..The current review surveys these computational models with focus on the underlying mathematics and assumptions, and with respect to their ability to generate experimentally testable hypotheses...
  15. pmc Systematic assessment of survey scan and MS2-based abundance strategies for label-free quantitative proteomics using high-resolution MS data
    Chengjian Tu
    Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260, United States
    J Proteome Res 13:2069-79. 2014
    ..Therefore, IC achieved an overall superior performance than the MS2-based strategies in terms of reproducibility, missing data, quantitative dynamic range, quantitative accuracy, and biomarker discovery. ..

Research Grants30

  1. Depression, Biobehavioral Mechanisms, &CHD/Mortality Outcomes
    Karina W Davidson; Fiscal Year: 2013
    ..Doing so will identify potentially more successful and personalized intervention strategies, and accelerate our ability to discover the genes implicated in depression's risk for cardiac disease and death. ..
  2. Hyaluronan Matrices in Vascular Pathologies
    Vincent C Hascall; Fiscal Year: 2013
    ..abstract_text> ..
  3. CHEMISTRY AND BIOLOGY OF HEPARAN SULFATE
    UMESH RAMANLAL DESAI; Fiscal Year: 2013
    ..End of Abstract) ..
  4. UNMC EPPLEY CANCER CENTER SUPPORT GRANT
    Kenneth H Cowan; Fiscal Year: 2013
    ....
  5. SELECTIN MEDIATED CELL ADHESION UNDER HYDRODYNAMIC SHEAR
    Sriram Neelamegham; Fiscal Year: 2013
    ..In the long run, we anticipate that novel strategies to antagonize selectin-ligand binding interactions will be identified from this work that may aid future drug design. ..
  6. Pathophysiology of Alveolar Epithelial Lung Injury
    Jacob I Sznajder; Fiscal Year: 2013
    ..The insights gained from the data generated from these studies will provide novel molecular targets for the development of new therapeutic strategies to treat patients with lung injury. ..
  7. Digitalis-Induced Signaling by Cardiac Na+/K+-ATPase
    Amir Askari; Fiscal Year: 2013
    ..abstract_text> ..
  8. New Approaches To Cardiothoracic Tolerance Induction
    Joren C Madsen; Fiscal Year: 2013
    ..We anticipate ongoing progress will continue to contribute to a reduction in the morbidity and mortality associated with solid organ transplantation. ..
  9. Development and Evaluation of Dual Compartment Combination Microbicides
    ROBERT WALTER BUCKHEIT; Fiscal Year: 2013
    ..Through our industrial partnership with ImQuest Pharmaceuticals our methodology and products will have an immediate outlet to further clinical development. ..
  10. Rocky Mountain Regional Center of Excellence or Biodefense and Emerging Infectiou
    John T Belisle; Fiscal Year: 2013
    ..abstract_text> ..
  11. PATHOPHYSIOLOGY OF THE ENDOTHELIUM
    Francis W Luscinskas; Fiscal Year: 2013
    ..g., heart attacks and strokes), as well as other organs and tissues of the body. These mechanistic insights may help identify novel therapeutic targets for the treatment of a broad spectrum of inflammatory diseases. ..
  12. Biosynthesis and Function of Lactosaminyl Glycans in Hematopoiesis
    Robert Sackstein; Fiscal Year: 2013
    ..This research effort should yield new treatments to improve marrow function in such conditions. (End of Abstract) ..
  13. Protein-glycan Interactions in the Vascular System
    Lijun Xia; Fiscal Year: 2013
    ..This information may suggest new approaches to treat heart attacks, strokes, and other cardiovascular disorders. ..
  14. Glycan Modulation of Inflammatory Responses
    Ajit P Varki; Fiscal Year: 2013
    ..abstract_text> ..