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Grant Details

Grant Number: 5U01CA235508-03 Interpret this number
Primary Investigator: Young, Jamey
Organization: Vanderbilt University
Project Title: Tools for Leveraging High-Resolution MS Detection of Stable Isotope Enrichments to Upgrade the Information Content of Metabolomics Datasets
Fiscal Year: 2020


PROJECT SUMMARY/ABSTRACT Recent advances in high-resolution mass spectrometry (HRMS) instrumentation have not been fully leveraged to upgrade the information content of metabolomics datasets obtained from stable isotope labeling studies. This is primarily due to lack of validated software tools for extracting and interpreting isotope enrichments from HRMS datasets. The overall objective of the current application is to develop tools that enable the metabolomics community to fully leverage stable isotopes to profile metabolic network dynamics. Two new tools will be implemented within the open-source OpenMS software library, which provides an infrastructure for rapid development and dissemination of mass spectrometry software. The first tool will automate tasks required for extracting isotope enrichment information from HRMS datasets, and the second tool will use this information to group ion peaks into interaction networks based on similar patterns of isotope labeling. The tools will be validated using in-house datasets derived from metabolic flux studies of animal and plant systems, as well as through feedback from the metabolomics community. The rationale for the research is that the software tools will enable metabolomics investigators to address important questions about pathway dynamics and regulation that cannot be answered without the use of stable isotopes. The first aim is to develop a software tool to automate data extraction and quantification of isotopologue distributions from HRMS datasets. The software will provide several key features not included in currently available metabolomics software: i) a graphical, interactive user interface that is appropriate for non-expert users, ii) support for native instrument file formats, iii) support for samples that are labeled with multiple stable isotopes, iv) support for tandem mass spectra, and v) support for multi-group or time-series comparisons. The second aim is to develop a companion software that applies machine learning and correlation-based algorithms to group unknown metabolites into modules and pathways based on similarities in isotope labeling. The third aim is to validate the tools through comparative analysis of stable isotope labeling in test standards and samples from animal and plant tissues, including time-series and dual-tracer experiments. A variety of collaborators and professional working groups will be engaged to test and validate the software, and the tools will be refined based on their feedback. The proposed research is exceptionally innovative because it will provide the advanced software capabilities required for both targeted and untargeted analysis of isotopically labeled metabolites, but in a flexible and user-friendly environment. The research is significant because it will contribute software tools that automate and standardize the data processing steps required to extract and utilize isotope enrichment information from large-scale metabolomics datasets. This work will have an important positive impact on the ability of metabolomics investigators to leverage information from stable isotopes to identify unknown metabolic interactions and quantify flux within metabolic networks. In addition, it will enable entirely new approaches to study metabolic dynamics within biological systems.


SIMPEL: using stable isotopes to elucidate dynamics of context specific metabolism.
Authors: Kambhampati S. , Hubbard A.H. , Koley S. , Gomez J.D. , Marsolais F. , Evans B.S. , Young J.D. , Allen D.K. .
Source: Communications biology, 2024-02-12; 7(1), p. 172.
EPub date: 2024-02-12.
PMID: 38347116
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Arabidopsis ACYL CARRIER PROTEIN4 and RHOMBOID LIKE10 act independently in chloroplast phosphatidate synthesis.
Authors: Xu Y. , Kambhampati S. , Morley S.A. , Cook R. , Froehlich J. , Allen D.K. , Benning C. .
Source: Plant physiology, 2023-11-22; 193(4), p. 2661-2676.
PMID: 37658850
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Program for Integration and Rapid Analysis of Mass Isotopomer Distributions (PIRAMID).
Authors: Gomez J.D. , Wall M.L. , Rahim M. , Kambhampati S. , Evans B.S. , Allen D.K. , Antoniewicz M.R. , Young J.D. .
Source: Bioinformatics (Oxford, England), 2023-11-01; 39(11), .
PMID: 37889279
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Oxidation of hyperpolarized [1-13 C]pyruvate in isolated rat kidneys.
Authors: Sharma G. , Maptue N. , Rahim M. , Trigo Mijes M.L. , Hever T. , Wen X. , Funk A.M. , Malloy C.R. , Young J.D. , Khemtong C. .
Source: NMR in biomedicine, 2023 Mar; 36(3), p. e4857.
EPub date: 2022-11-17.
PMID: 36285844
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Glucose-6-phosphatase catalytic subunit 2 negatively regulates glucose oxidation and insulin secretion in pancreatic β-cells.
Authors: Rahim M. , Nakhe A.Y. , Banerjee D.R. , Overway E.M. , Bosma K.J. , Rosch J.C. , Oeser J.K. , Wang B. , Lippmann E.S. , Jacobson D.A. , et al. .
Source: The Journal of biological chemistry, 2022 Apr; 298(4), p. 101729.
EPub date: 2022-02-15.
PMID: 35176280
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Comparative Metabolic Analysis Reveals a Metabolic Switch in Mature, Hydrated, and Germinated Pollen in Arabidopsis thaliana.
Authors: Wang J. , Kambhampati S. , Allen D.K. , Chen L.Q. .
Source: Frontiers in plant science, 2022; 13, p. 836665.
EPub date: 2022-05-18.
PMID: 35665175
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Suppression of SDP1 Improves Soybean Seed Composition by Increasing Oil and Reducing Undigestible Oligosaccharides.
Authors: Aznar-Moreno J.A. , Mukherjee T. , Morley S.A. , Duressa D. , Kambhampati S. , Chu K.L. , Koley S. , Allen D.K. , Durrett T.P. .
Source: Frontiers in plant science, 2022; 13, p. 863254.
EPub date: 2022-03-23.
PMID: 35401590
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INCA 2.0: A tool for integrated, dynamic modeling of NMR- and MS-based isotopomer measurements and rigorous metabolic flux analysis.
Authors: Rahim M. , Ragavan M. , Deja S. , Merritt M.E. , Burgess S.C. , Young J.D. .
Source: Metabolic engineering, 2022 Jan; 69, p. 275-285.
EPub date: 2021-12-26.
PMID: 34965470
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Metabolic flux analysis of the non-transitory starch tradeoff for lipid production in mature tobacco leaves.
Authors: Chu K.L. , Koley S. , Jenkins L.M. , Bailey S.R. , Kambhampati S. , Foley K. , Arp J.J. , Morley S.A. , Czymmek K.J. , Bates P.D. , et al. .
Source: Metabolic engineering, 2022 Jan; 69, p. 231-248.
EPub date: 2021-12-14.
PMID: 34920088
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In vivo2H/13C flux analysis in metabolism research.
Authors: Bednarski T.K. , Rahim M. , Young J.D. .
Source: Current opinion in biotechnology, 2021 Oct; 71, p. 1-8.
EPub date: 2021-05-25.
PMID: 34048994
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Multitissue 2H/13C flux analysis reveals reciprocal upregulation of renal gluconeogenesis in hepatic PEPCK-C-knockout mice.
Authors: Rahim M. , Hasenour C.M. , Bednarski T.K. , Hughey C.C. , Wasserman D.H. , Young J.D. .
Source: JCI insight, 2021-06-22; 6(12), .
EPub date: 2021-06-22.
PMID: 34156032
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Temporal changes in metabolism late in seed development affect biomass composition.
Authors: Kambhampati S. , Aznar-Moreno J.A. , Bailey S.R. , Arp J.J. , Chu K.L. , Bilyeu K.D. , Durrett T.P. , Allen D.K. .
Source: Plant physiology, 2021-06-11; 186(2), p. 874-890.
PMID: 33693938
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Analyzing Mass Spectrometry Imaging Data of 13C-Labeled Phospholipids in Camelina sativa and Thlaspi arvense (Pennycress) Embryos.
Authors: Romsdahl T.B. , Kambhampati S. , Koley S. , Yadav U.P. , Alonso A.P. , Allen D.K. , Chapman K.D. .
Source: Metabolites, 2021-03-04; 11(3), .
EPub date: 2021-03-04.
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A Practical Guide to Metabolomics Software Development.
Authors: Chang H.Y. , Colby S.M. , Du X. , Gomez J.D. , Helf M.J. , Kechris K. , Kirkpatrick C.R. , Li S. , Patti G.J. , Renslow R.S. , et al. .
Source: Analytical chemistry, 2021-02-02; 93(4), p. 1912-1923.
EPub date: 2021-01-19.
PMID: 33467846
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In Vivo Estimates of Liver Metabolic Flux Assessed by 13C-Propionate and 13C-Lactate Are Impacted by Tracer Recycling and Equilibrium Assumptions.
Authors: Hasenour C.M. , Rahim M. , Young J.D. .
Source: Cell reports, 2020-08-04; 32(5), p. 107986.
PMID: 32755580
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Tracing metabolic flux through time and space with isotope labeling experiments.
Authors: Allen D.K. , Young J.D. .
Source: Current opinion in biotechnology, 2020 Aug; 64, p. 92-100.
EPub date: 2019-12-20.
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Host nutrient milieu drives an essential role for aspartate biosynthesis during invasive Staphylococcus aureus infection.
Authors: Potter A.D. , Butrico C.E. , Ford C.A. , Curry J.M. , Trenary I.A. , Tummarakota S.S. , Hendrix A.S. , Young J.D. , Cassat J.E. .
Source: Proceedings of the National Academy of Sciences of the United States of America, 2020-06-02; 117(22), p. 12394-12401.
EPub date: 2020-05-15.
PMID: 32414924
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