2004 — 2005 |
Desaire, Heather R |
P20Activity Code Description: To support planning for new programs, expansion or modification of existing resources, and feasibility studies to explore various approaches to the development of interdisciplinary programs that offer potential solutions to problems of special significance to the mission of the NIH. These exploratory studies may lead to specialized or comprehensive centers. |
Cobre: U Ks: P2: Struc Char Glycoproteins Mass Spec;Infertility, Thyroid Cancer @ University of Kansas Lawrence
glycoproteins; protein structure function; thyroid neoplasm; fertility; clinical research; mass spectrometry;
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0.943 |
2005 — 2009 |
Desaire, Heather R |
R01Activity Code Description: To support a discrete, specified, circumscribed project to be performed by the named investigator(s) in an area representing his or her specific interest and competencies. |
Comparative Glycomics of the Hiv Protein Gp 120 @ University of Kansas Lawrence
DESCRIPTION (provided by applicant): The glycoprotein, gp120, covers the surface of the HIV virus. It plays an essential role in HIV infection, because gp120 binds to receptor sites in the body, as the first step of viral invasion into host cells. Since the virus cannot proliferate without entering host cells, a major thrust of research directed at curing AIDS has focused on stopping the initial cellular invasion. A strategy to destroy the virus prior to cellular invasion has not yet been achieved, because the carbohydrates on gp120 present a barrier to antibody attack. While the glycans present on the HIV virus have been identified as the primary reason that the virus avoids destruction by the immune system, little can be done to overcome the virus's defense mechanism, its glycan shield, because not enough is known about the carbohydrates present at each of the 24 glycosylation sites on the protein. We have identified critical information needed to better understand the virus's defense mechanism: 1) What is the carbohydrate composition at each glycosylation site? 2) What is the topology (the degree of branching) at these sites? 3) Where is there a potential for electrostatic interaction, due to negatively charged carbohydrates, on the surface of the protein? To answer these questions, we will probe glycopeptide structure using advanced mass spectrometric instrumentation, including a MALDI TOF-TOF mass spectrometer and Linear Trap-Fourier Transform Ion Cyclotron Resonance Mass Spectrometer (LTQ-FTMS). We are developing new mass spectrometric methods to probe the location of negatively charged glycoforms within gp120, as well as methods to identify glycopeptide topology. Furthermore, by comparing how each of these factors change from different gp120 isolates, we can determine which portions of the glycoprotein show the least propensity for variation in the carbohydrate content, among the different gp120 isolates. This information will directly impact both structure-function models of gp120, as well as provide direction for future vaccine targets. Collaborators on the project include Dr. George Bousfield, a glycobiologist from Wichita State University, and Drs. Mike Alterman and Todd Williams, Co-Directors of the University of Kansas Proteomics Facility.
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0.943 |
2006 — 2008 |
Desaire, Heather R |
P20Activity Code Description: To support planning for new programs, expansion or modification of existing resources, and feasibility studies to explore various approaches to the development of interdisciplinary programs that offer potential solutions to problems of special significance to the mission of the NIH. These exploratory studies may lead to specialized or comprehensive centers. |
Cobre: U Ks: P2: Struc Char Glycoproteins Mass Spec;Infertility, Thyroid Cance @ University of Kansas Lawrence |
0.943 |
2009 — 2012 |
Desaire, Heather R |
R01Activity Code Description: To support a discrete, specified, circumscribed project to be performed by the named investigator(s) in an area representing his or her specific interest and competencies. |
Development of a Rapid Glycosylation Profiling System Using Mass Spec Data @ University of Kansas Lawrence
DESCRIPTION (provided by applicant): The ultimate goal of this proposal is to develop a fully-automated approach for analysis of glycopeptides and to apply that approach to the analysis of several different HIV-Env glycoproteins. This work would be accomplished by completing three specific aims: AIM 1: Using MS data as the input, develop an algorithm that rapidly identifies glycopeptide compositions for singly glycosylated glycopeptides. AIM 2: Develop an algorithm that characterizes multiply glycosylated glycopeptides. AIM 3: Use the tools in AIMS 1 and 2 to screen for accessible and genetically conserved points on the HIV Env protein. The bulk of the work, Aims 1 and 2, would be completed by synergistically incorporating expertise in mass spectral (MS) data acquisition and analysis with expertise in software design/development. This work can broadly impact human health research because glycopeptide analysis is an enabling bioanalytical technology that can be used to screen for biomarkers of disease or disease state;it can be used to help verify the safety and consistency of glycoprotein-based pharmaceuticals;and it can be used to analyze glycopeptides on HIV Envelope proteins, a major target for HIV vaccine development. After completion of the automated glycosylation profiling system (Aims 1 and 2) this system would be used to identify the glycopeptide composition on a variety of HIV- Env vaccine candidates generated in collaboration with Dr. Barton F. Haynes at Duke University Medical Center. The method for this approach includes preparing tryptic digests of each of the glycoproteins, conducing HPLC-MS and LC-MS/MS analyses on the digested products, and interpreting the results using the developed glycopeptide analysis software. After completion of this work, the glycopeptide profiles of the Env proteins would provide information about epitope accessibility on Env. This is relevant to human health because identifying epitopes on the protein that are consistently exposed across HIV-1 clades is a first step in designing an HIV vaccine that mimics these epitopes and elicits broadly neutralizing antibodies to HIV-1. PUBLIC HEALTH RELEVANCE: We aim to develop tools for the rapid analysis of glycopeptides. Glycopeptides are components of the HIV Env protein, and their analysis could be used to identify Achilles Heels (regions which are consistently exposed and thus vulnerable to antibodies) on the surface of the virus.
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0.943 |
2012 — 2015 |
Desaire, Heather R |
R01Activity Code Description: To support a discrete, specified, circumscribed project to be performed by the named investigator(s) in an area representing his or her specific interest and competencies. |
Characterization of Ptms On Env to Support Hiv Vaccine Development @ University of Kansas Lawrence
DESCRIPTION (provided by applicant): The ultimate goal of this proposal is to develop broadly applicable methods to analyze glycosylation and disulfide bonding of glycoproteins and to apply those methods to the HIV Envelope protein (Env). This work would be accomplished by completing four specific aims: (1) Develop a new glycoproteomic method, where glycosylation site occupancy is quantified and glycoform heterogeneity is simultaneously characterized, all in one experiment. (2) Profile Env glycosylation site occupancy and glycopeptide heterogeneity to answer several important biological questions. (3) Develop an automated analysis protocol for identifying disulfide- linked peptides. (4) Characterize the disulfide bonding of Env to answer several important biological questions. The bulk of the work would be completed by combining expertise in biological sample handling, HPLC, and mass spectral (MS) data acquisition and analysis to develop the necessary tools. The utility of all the tools would be demonstrated by incorporating them to solve problems relevant to HIV vaccine development. Of particular note are studies in Aim 2, where the tools are used to correlate changes in glycan content with changes in vaccine efficacy. This work can broadly impact human health by providing fundamental insights into how post-translational modifications impact HIV vaccine candidates' efficacy. Likewise, methods for glycoprotein and disulfide analysis are enabling bioanalytical technologies that can be used in a variety of venues, from protein structure/function analyses to pharmaceutical development. The application work related to HIV proteins is done in collaboration with Dr. Barton F. Haynes at Duke University Medical Center and Dr. Bing Chen at Harvard University Medical School.
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0.943 |
2014 — 2017 |
Desaire, Heather R |
R01Activity Code Description: To support a discrete, specified, circumscribed project to be performed by the named investigator(s) in an area representing his or her specific interest and competencies. |
Development of a Rapid Glycosylation Profiling System Using Mass Spectrometry Dat @ University of Kansas Lawrence
Abstract: The ultimate goals of this proposal are to develop broadly applicable tools to analyze glycopeptides in complex matrices and to apply those tools for the analysis of human milk and aggressive breast cancer cells. This work would be accomplished by completing three specific aims: (1) Complete our fully automated glycopeptide analysis tool package, which we started during the first period of this grant's funding (2) Develop the usage of massive inclusion lists to increase the number of glycopeptide ions characterized by MS/MS. (3) Tackle two challenges in glycopeptide analyses that are beyond the reach of today's technology: Project 1) Identify glycopeptide-based biomarkers that are only present in aggressive breast cancer. Project 2) Provide a complete profiling of N- and O-linked glycopeptides in human milk. The bulk of the work would be completed by combining expertise in software design, biological sample handling, HPLC, and mass spectrometry to develop the necessary tools. The utility of the tools would be demonstrated by applying them to complete projects relevant women's health: Specifically, we would provide a more detailed insight into the unique properties of human milk than has ever before been provided, and we would characterize the glycosylation on 10-50 known glycopeptide markers of aggressive breast cancer. In addition to the contributions we make to women's health, this work would drive the field of glycoproteomics forward: The methods for glycoprotein analysis are enabling bioanalytical technologies that can be used in a variety of venues, from protein structure/function analyses to pharmaceutical development, to biomarker discovery and development.
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0.943 |
2016 — 2019 |
Desaire, Heather R |
R01Activity Code Description: To support a discrete, specified, circumscribed project to be performed by the named investigator(s) in an area representing his or her specific interest and competencies. |
Generating Native Env Glycosylation in Hiv Vaccine Candidates @ University of Kansas Lawrence
? DESCRIPTION (provided by applicant): Preventing human immunodeficiency virus (HIV-1) transmission by vaccination is a highly desirable, but elusive, goal. Vaccine-induced antibodies that bind the HIV-1 envelope glycoprotein (Env) spike and neutralize the virus are thought to be a desirable component of a protective immune response; as a consequence, recombinantly expressed immunogens containing the exterior portion of Env are generally regarded as an essential element of a prophylactic vaccine. The HIV-1 Env is highly glycosylated, with glycans accounting for about 50% of the glycoprotein mass. These glycans contribute significantly to a number of viral functions, including the ability of HIV-1 to evade antibody responses. The presence and type of glycans on Env-based vaccine candidates influence both immunogenicity and antigenicity of the protein, and several of the gp120 and gp41 glycans serve as epitopes or components of epitopes targeted by potent HIV-1-neutralizing antibodies. If there is any hope of eliciting these types of antibodies during vaccination, the glycans on the Env vaccine must be of the same type as those found on the virus. Therefore, two critical questions facing the field of HIV-1 vaccine development with respect to Env glycosylation are: (1) What is the glycan profile of native HIV-1 Env? and (2) How can that glycan profile be recapitulated in an Env-based vaccine? Answering these two fundamental questions would represent a significant advance in HIV-1 vaccine research: If the glycan profile of a vaccine candidate could match that of native virus, the chances of eliciting effective antibodies that contain glycan-based epitopes would be increased. The two goals of this application are to characterize the glycosylation of Env from the most native source possible, from T-lymphocytes, and to identify ways to express Env with the correct glycosylation in a more tractable cell line that could be used in GMP manufacturing of Env for human clinical trials. This project will be run by a synergistic, collaborative team wit complementary strengths. The group has recently published the glycosylation profile of an HIV-1 membrane Env trimer, taking advantage of highly relevant technical innovations in Env glycoprotein production, sample preparation, and glycosylation analysis; these recent developments provide a strong foundation for the studies proposed herein. The successful completion of the project will provide all vaccine developers with the tools they need to generate native glycosylation profiles on their Env of choice.
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0.943 |
2019 — 2021 |
Desaire, Heather R |
R35Activity Code Description: To provide long term support to an experienced investigator with an outstanding record of research productivity. This support is intended to encourage investigators to embark on long-term projects of unusual potential. |
Mass Spectrometry Measurements For Complex Ptms @ University of Kansas Lawrence
Abstract: Recombinant protein expression technology has revolutionized human health research, enabling scientists to generate large quantities of protein for small-molecule drug discovery campaigns, for the development of protein-based drugs, and for studying protein structure and function. Yet while researchers are adept at producing proteins with known genetic sequences, they possess entirely inadequate knowledge about the protein's post-translational modifications, both during recombinant expression and when the proteins are isolated from endogenous sources. Alterations in a protein's post-translational modifications can change the protein from an active enzyme to a dead one; they can change a protein-based drug from a life-saving molecule to one that is either ineffective or worse, dangerously immunogenic; these seemingly simple ?add- ons? to proteins can be the defining features that determine whether the protein functions as designed or not. Characterizing proteins' PTMs is a necessary prerequisite for identifying disease states, modulating protein binding and function, and producing safe and effective protein-based drugs and vaccines. The long term goals of my research program are to expedite the analysis of post-translational modifications (PTMs) on proteins, to use these analytical tools to answer critical health-related challenges, and to widely distribute the technology. We are pursuing both near-term advancements, such as developing a robust solution to quantifying aberrant disulfide bonds in recombinant proteins, as well as long-range, revolutionary changes in the way proteins are analyzed, by laying the foundational infrastructure needed to bring artificial intelligence solutions to the field of PTM analysis. We will develop and launch these technologies in the context of meaningful biological problems where field advancements cannot be made without information about proteins' PTMs. Solutions in the fields of HIV vaccine design, cancer treatment, and antibody therapy will be targeted first.
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0.943 |
2021 |
Desaire, Heather R |
RF1Activity Code Description: To support a discrete, specific, circumscribed project to be performed by the named investigator(s) in an area representing specific interest and competencies based on the mission of the agency, using standard peer review criteria. This is the multi-year funded equivalent of the R01 but can be used also for multi-year funding of other research project grants such as R03, R21 as appropriate. |
A Study of Race Differences in Alzheimer's Disease Biomarkers @ University of Kansas Lawrence
Abstract We propose to combine mass spectrometry and machine learning to address racial disparities in Alzheimer's disease (AD) research. While African Americans have two to three times the incidence rates of AD than people of European Ancestry, they are underrepresented in past and current AD research studies. The lack of representation leads to a weaker understanding of disease progression and poorer diagnostics for this population. The overarching premise, that advances in diagnosing and treating Alzheimer's disease for all Americans will be stymied unless differences among racial groups are considered, is supported by the literature and demonstrated with preliminary data in the application. The aims of this proposal are, therefore, designed to specifically address the need for a better understanding of Alzheimer's disease in minority groups and to increase the diversity of patients that could be correctly diagnosed with serum-based biomarker panels for AD. Successful completion of the proposed research would accomplish several objectives: We would identify optimal feature selection methods for `omics data; generate the best possible plasma biomarker panel for AD in African Americans; and provide a systematic investigation of the extent to which existing MS- `omics studies' accuracy of predicting AD are modulated by the participants' race.
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0.943 |