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Hasenour CM, Banerjee DR, Young JD. Metabolic Fluxes in the Renal Cortex are Dysregulated In Vivo in Response to High-Fat Diet. Diabetes 2024:db230710. [PMID: 38502790 DOI: 10.2337/db23-0710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 03/08/2024] [Indexed: 03/21/2024]
Abstract
Diabetes and obesity are risk factors for kidney disease. While renal glucose production increases in diabetes, recent data suggest that gluconeogenic and oxidative capacity decline in kidney disease. Thus, metabolic dysregulation caused by diet-induced insulin resistance may sensitize the kidney for a loss in function. Here we examined how diet-induced insulin resistance disrupts mitochondrial metabolic fluxes in the renal cortex in vivo. C57Bl/6J mice were rendered insulin resistant through high-fat (HF) feeding; anaplerotic, cataplerotic, and oxidative metabolic fluxes in the cortex were quantified through 13C-isotope tracing during a hyperinsulinemic-euglycemic clamp. As expected, HF-fed mice exhibited increased body weight, gluconeogenesis, and systemic insulin resistance compared to chow-fed mice. Relative to the citric acid cycle, HF-feeding increased metabolic flux through pyruvate carboxylation (anaplerosis) and phosphoenolpyruvate carboxykinase (cataplerosis) while decreasing flux through the pyruvate dehydrogenase complex in the cortex. Furthermore, the relative flux from non-pyruvate sources of acetyl-CoA profoundly increased in the cortex of HF-fed mice, correlating with a marker of oxidative stress. The data demonstrate that HF-feeding spares pyruvate from dehydrogenation at the expense of increasing cataplerosis, which may underpin renal gluconeogenesis during insulin resistance; the results also support the hypothesis that dysregulated oxidative metabolism in the kidney contributes to metabolic disease.
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Affiliation(s)
| | - Deveena R Banerjee
- Department of Molecular Physiology and Biophysics Vanderbilt University, Nashville TN, 37212
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering
- Department of Molecular Physiology and Biophysics Vanderbilt University, Nashville TN, 37212
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2
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Deja S, Fletcher JA, Kim CW, Kucejova B, Fu X, Mizerska M, Villegas M, Pudelko-Malik N, Browder N, Inigo-Vollmer M, Menezes CJ, Mishra P, Berglund ED, Browning JD, Thyfault JP, Young JD, Horton JD, Burgess SC. Hepatic malonyl-CoA synthesis restrains gluconeogenesis by suppressing fat oxidation, pyruvate carboxylation, and amino acid availability. Cell Metab 2024:S1550-4131(24)00050-0. [PMID: 38447582 DOI: 10.1016/j.cmet.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 12/10/2023] [Accepted: 02/09/2024] [Indexed: 03/08/2024]
Abstract
Acetyl-CoA carboxylase (ACC) promotes prandial liver metabolism by producing malonyl-CoA, a substrate for de novo lipogenesis and an inhibitor of CPT-1-mediated fat oxidation. We report that inhibition of ACC also produces unexpected secondary effects on metabolism. Liver-specific double ACC1/2 knockout (LDKO) or pharmacologic inhibition of ACC increased anaplerosis, tricarboxylic acid (TCA) cycle intermediates, and gluconeogenesis by activating hepatic CPT-1 and pyruvate carboxylase flux in the fed state. Fasting should have marginalized the role of ACC, but LDKO mice maintained elevated TCA cycle intermediates and preserved glycemia during fasting. These effects were accompanied by a compensatory induction of proteolysis and increased amino acid supply for gluconeogenesis, which was offset by increased protein synthesis during feeding. Such adaptations may be related to Nrf2 activity, which was induced by ACC inhibition and correlated with fasting amino acids. The findings reveal unexpected roles for malonyl-CoA synthesis in liver and provide insight into the broader effects of pharmacologic ACC inhibition.
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Affiliation(s)
- Stanislaw Deja
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA
| | - Justin A Fletcher
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA; Department of Clinical Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA
| | - Chai-Wan Kim
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA
| | - Blanka Kucejova
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA
| | - Xiaorong Fu
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA; Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA
| | - Monika Mizerska
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA
| | - Morgan Villegas
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA
| | - Natalia Pudelko-Malik
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA; Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Nicholas Browder
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA
| | - Melissa Inigo-Vollmer
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA
| | - Cameron J Menezes
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA
| | - Prashant Mishra
- Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA
| | - Eric D Berglund
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA
| | - Jeffrey D Browning
- Department of Clinical Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA
| | - John P Thyfault
- Departments of Cell Biology and Physiology, Internal Medicine and KU Diabetes Institute, Kansas Medical Center, Kansas City, KS, USA
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37235, USA
| | - Jay D Horton
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA; Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA.
| | - Shawn C Burgess
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA; Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9046, USA.
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3
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Hawes EM, Rahim M, Haratipour Z, Orun AR, O'Rourke ML, Oeser JK, Kim K, Claxton DP, Blind RD, Young JD, O'Brien RM. Biochemical and metabolic characterization of a G6PC2 inhibitor. Biochimie 2024:S0300-9084(24)00050-6. [PMID: 38431189 DOI: 10.1016/j.biochi.2024.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 03/05/2024]
Abstract
Three glucose-6-phosphatase catalytic subunits, that hydrolyze glucose-6-phosphate (G6P) to glucose and inorganic phosphate, have been identified, designated G6PC1-3, but only G6PC1 and G6PC2 have been implicated in the regulation of fasting blood glucose (FBG). Elevated FBG has been associated with multiple adverse clinical outcomes, including increased risk for type 2 diabetes and various cancers. Therefore, G6PC1 and G6PC2 inhibitors that lower FBG may be of prophylactic value for the prevention of multiple conditions. The studies described here characterize a G6PC2 inhibitor, designated VU0945627, previously identified as Compound 3. We show that VU0945627 preferentially inhibits human G6PC2 versus human G6PC1 but activates human G6PC3. VU0945627 is a mixed G6PC2 inhibitor, increasing the Km but reducing the Vmax for G6P hydrolysis. PyRx virtual docking to an AlphaFold2-derived G6PC2 structural model suggests VU0945627 binds two sites in human G6PC2. Mutation of residues in these sites reduces the inhibitory effect of VU0945627. VU0945627 does not inhibit mouse G6PC2 despite its 84% sequence identity with human G6PC2. Mutagenesis studies suggest this lack of inhibition of mouse G6PC2 is due, in part, to a change in residue 318 from histidine in human G6PC2 to proline in mouse G6PC2. Surprisingly, VU0945627 still inhibited glucose cycling in the mouse islet-derived βTC-3 cell line. Studies using intact mouse liver microsomes and PyRx docking suggest that this observation can be explained by an ability of VU0945627 to also inhibit the G6P transporter SLC37A4. These data will inform future computational modeling studies designed to identify G6PC isoform-specific inhibitors.
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Affiliation(s)
- Emily M Hawes
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Mohsin Rahim
- Department of Chemical and Biomolecular Engineering, Vanderbilt School of Engineering, Nashville, TN, 37232, USA
| | - Zeinab Haratipour
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Abigail R Orun
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Margaret L O'Rourke
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - James K Oeser
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Kwangho Kim
- Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Derek P Claxton
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Ray D Blind
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Jamey D Young
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA; Department of Chemical and Biomolecular Engineering, Vanderbilt School of Engineering, Nashville, TN, 37232, USA
| | - Richard M O'Brien
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA.
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Kambhampati S, Hubbard AH, Koley S, Gomez JD, Marsolais F, Evans BS, Young JD, Allen DK. SIMPEL: using stable isotopes to elucidate dynamics of context specific metabolism. Commun Biol 2024; 7:172. [PMID: 38347116 PMCID: PMC10861564 DOI: 10.1038/s42003-024-05844-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 01/23/2024] [Indexed: 02/15/2024] Open
Abstract
The capacity to leverage high resolution mass spectrometry (HRMS) with transient isotope labeling experiments is an untapped opportunity to derive insights on context-specific metabolism, that is difficult to assess quantitatively. Tools are needed to comprehensively mine isotopologue information in an automated, high-throughput way without errors. We describe a tool, Stable Isotope-assisted Metabolomics for Pathway Elucidation (SIMPEL), to simplify analysis and interpretation of isotope-enriched HRMS datasets. The efficacy of SIMPEL is demonstrated through examples of central carbon and lipid metabolism. In the first description, a dual-isotope labeling experiment is paired with SIMPEL and isotopically nonstationary metabolic flux analysis (INST-MFA) to resolve fluxes in central metabolism that would be otherwise challenging to quantify. In the second example, SIMPEL was paired with HRMS-based lipidomics data to describe lipid metabolism based on a single labeling experiment. Available as an R package, SIMPEL extends metabolomics analyses to include isotopologue signatures necessary to quantify metabolic flux.
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Affiliation(s)
- Shrikaar Kambhampati
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA.
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
| | - Allen H Hubbard
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Somnath Koley
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Javier D Gomez
- Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, 37235, USA
| | - Frédéric Marsolais
- London Research and Development Center, London, ON, N5V 4T3, Canada
- Department of Biology, University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Bradley S Evans
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA
| | - Jamey D Young
- Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, 37235, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37235, USA
| | - Doug K Allen
- Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA.
- Agricultural Research Service, US Department of Agriculture, St. Louis, MO, 63132, USA.
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5
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McBride MA, Stothers CL, Fensterheim BA, Caja KR, Owen AM, Hernandez A, Bohannon JK, Patil NK, Ali S, Dalal S, Rahim M, Trenary IA, Young JD, Williams DL, Sherwood ER. Bacteria- and fungus-derived PAMPs induce innate immune memory via similar functional, metabolic, and transcriptional adaptations. J Leukoc Biol 2024; 115:358-373. [PMID: 37793181 PMCID: PMC10872320 DOI: 10.1093/jleuko/qiad120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 08/28/2023] [Accepted: 09/15/2023] [Indexed: 10/06/2023] Open
Abstract
Exposure to pathogen-associated molecular patterns (PAMPs) induces an augmented, broad-spectrum antimicrobial response to subsequent infection, a phenomenon termed innate immune memory. This study examined the effects of treatment with β-glucan, a fungus-derived dectin-1 ligand, or monophosphoryl lipid A (MPLA), a bacteria-derived Toll-like receptor 4 ligand, on innate immune memory with a focus on identifying common cellular and molecular pathways activated by these diverse PAMPs. Treatment with either PAMP prepared the innate immune system to respond more robustly to Pseudomonas aeruginosa infection in vivo by facilitating mobilization of innate leukocytes into blood, recruitment of leukocytes to the site of infection, augmentation of microbial clearance, and attenuation of cytokine production. Examination of macrophages ex vivo showed amplification of metabolism, phagocytosis, and respiratory burst after treatment with either agent, although MPLA more robustly augmented these activities and more effectively facilitated killing of bacteria. Both agents activated gene expression pathways in macrophages that control inflammation, antimicrobial functions, and protein synthesis and suppressed pathways regulating cell division. β-glucan treatment minimally altered macrophage differential gene expression in response to lipopolysaccharide (LPS) challenge, whereas MPLA attenuated the magnitude of the LPS-induced transcriptional response, especially cytokine gene expression. These results show that β-glucan and MPLA similarly augment the innate response to infection in vivo. Yet, MPLA more potently induces alterations in macrophage metabolism, antimicrobial functions, gene transcription and the response to LPS.
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Affiliation(s)
- Margaret A. McBride
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, 1211 Medical Center Drive, Nashville 37232, Tennessee
| | - Cody L. Stothers
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, 1211 Medical Center Drive, Nashville 37232, Tennessee
| | - Benjamin A. Fensterheim
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, 1211 Medical Center Drive, Nashville 37232, Tennessee
| | - Katherine R. Caja
- Department of Anesthesiology, Vanderbilt University Medical Center, 1211 Medical Center Drive, Nashville 37232, Tennessee
| | - Allison M. Owen
- Department of Anesthesiology, Vanderbilt University Medical Center, 1211 Medical Center Drive, Nashville 37232, Tennessee
| | - Antonio Hernandez
- Department of Anesthesiology, Vanderbilt University Medical Center, 1211 Medical Center Drive, Nashville 37232, Tennessee
| | - Julia K. Bohannon
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, 1211 Medical Center Drive, Nashville 37232, Tennessee
- Department of Anesthesiology, Vanderbilt University Medical Center, 1211 Medical Center Drive, Nashville 37232, Tennessee
| | - Naeem K. Patil
- Department of Anesthesiology, Vanderbilt University Medical Center, 1211 Medical Center Drive, Nashville 37232, Tennessee
| | - Sabah Ali
- Department of Anesthesiology, Vanderbilt University Medical Center, 1211 Medical Center Drive, Nashville 37232, Tennessee
| | - Sujata Dalal
- Department of Anesthesiology, Vanderbilt University Medical Center, 1211 Medical Center Drive, Nashville 37232, Tennessee
| | - Mohsin Rahim
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, 2301 Vanderbilt Place, Nashville 37235, Tennessee
| | - Irina A. Trenary
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, 2301 Vanderbilt Place, Nashville 37235, Tennessee
| | - Jamey D. Young
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, 2301 Vanderbilt Place, Nashville 37235, Tennessee
- Department of Molecular Physiology and Biophysics, Vanderbilt University, 2215 Garland Avenue, Nashville 37232, Tennessee
| | - David L. Williams
- Department of Surgery, Quillen College of Medicine, East Tennessee State University, 325 North State of Franklin Road, Johnson City 37604, Tennessee
- Center for Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, 325 North State of Franklin Road, Johnson City 37604, Tennessee
| | - Edward R. Sherwood
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, 1211 Medical Center Drive, Nashville 37232, Tennessee
- Department of Anesthesiology, Vanderbilt University Medical Center, 1211 Medical Center Drive, Nashville 37232, Tennessee
- Department of Surgery, Quillen College of Medicine, East Tennessee State University, 325 North State of Franklin Road, Johnson City 37604, Tennessee
- Center for Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, 325 North State of Franklin Road, Johnson City 37604, Tennessee
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6
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Wang B, Zuniga C, Guarnieri MT, Zengler K, Betenbaugh M, Young JD. Metabolic engineering of Synechococcus elongatus 7942 for enhanced sucrose biosynthesis. Metab Eng 2023; 80:12-24. [PMID: 37678664 DOI: 10.1016/j.ymben.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/28/2023] [Accepted: 09/03/2023] [Indexed: 09/09/2023]
Abstract
The capability of cyanobacteria to produce sucrose from CO2 and light has a remarkable societal and biotechnological impact since sucrose can serve as a carbon and energy source for a variety of heterotrophic organisms and can be converted into value-added products. However, most metabolic engineering efforts have focused on understanding local pathway alterations that drive sucrose biosynthesis and secretion in cyanobacteria rather than analyzing the global flux re-routing that occurs following induction of sucrose production by salt stress. Here, we investigated global metabolic flux alterations in a sucrose-secreting (cscB-overexpressing) strain relative to its wild-type Synechococcus elongatus 7942 parental strain. We used targeted metabolomics, 13C metabolic flux analysis (MFA), and genome-scale modeling (GSM) as complementary approaches to elucidate differences in cellular resource allocation by quantifying metabolic profiles of three cyanobacterial cultures - wild-type S. elongatus 7942 without salt stress (WT), wild-type with salt stress (WT/NaCl), and the cscB-overexpressing strain with salt stress (cscB/NaCl) - all under photoautotrophic conditions. We quantified the substantial rewiring of metabolic fluxes in WT/NaCl and cscB/NaCl cultures relative to WT and identified a metabolic bottleneck limiting carbon fixation and sucrose biosynthesis. This bottleneck was subsequently mitigated through heterologous overexpression of glyceraldehyde-3-phosphate dehydrogenase in an engineered sucrose-secreting strain. Our study also demonstrates that combining 13C-MFA and GSM is a useful strategy to both extend the coverage of MFA beyond central metabolism and to improve the accuracy of flux predictions provided by GSM.
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Affiliation(s)
- Bo Wang
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, 37235, USA
| | - Cristal Zuniga
- Department of Pediatrics, University of California, San Diego, CA, 92093, USA; Department of Biology, San Diego State University, San Diego, CA, 92182, USA
| | - Michael T Guarnieri
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Karsten Zengler
- Department of Pediatrics, University of California, San Diego, CA, 92093, USA; Department of Bioengineering, University of California, San Diego, CA, 92093, USA; Center for Microbiome Innovation, University of California, San Diego, CA, 92093, USA
| | - Michael Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, 37235, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37235, USA.
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7
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Babele PK, Srivastava A, Young JD. Metabolic flux phenotyping of secondary metabolism in cyanobacteria. Trends Microbiol 2023; 31:1118-1130. [PMID: 37331829 DOI: 10.1016/j.tim.2023.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/10/2023] [Accepted: 05/15/2023] [Indexed: 06/20/2023]
Abstract
Cyanobacteria generate energy from photosynthesis and produce various secondary metabolites with diverse commercial and pharmaceutical applications. Unique metabolic and regulatory pathways in cyanobacteria present new challenges for researchers to enhance their product yields, titers, and rates. Therefore, further advancements are critically needed to establish cyanobacteria as a preferred bioproduction platform. Metabolic flux analysis (MFA) quantitatively determines the intracellular flows of carbon within complex biochemical networks, which elucidate the control of metabolic pathways by transcriptional, translational, and allosteric regulatory mechanisms. The emerging field of systems metabolic engineering (SME) involves the use of MFA and other omics technologies to guide the rational development of microbial production strains. This review highlights the potential of MFA and SME to optimize the production of cyanobacterial secondary metabolites and discusses the technical challenges that lie ahead.
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Affiliation(s)
- Piyoosh K Babele
- College of Agriculture, Rani Lakshmi Bai Central Agricultural University Jhansi, 284003, Uttar Pradesh, India.
| | - Amit Srivastava
- University of Jyväskylä, Nanoscience Centre, Department of Biological and Environmental Science, 40014 Jyväskylä, Finland
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, PMB 351604, Nashville, TN 37235-1604, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University, PMB 351604, Nashville, TN 37235-1604, USA.
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8
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Gomez JD, Wall ML, Rahim M, Kambhampati S, Evans BS, Allen DK, Antoniewicz MR, Young JD. Program for Integration and Rapid Analysis of Mass Isotopomer Distributions (PIRAMID). Bioinformatics 2023; 39:btad661. [PMID: 37889279 PMCID: PMC10636274 DOI: 10.1093/bioinformatics/btad661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 04/26/2023] [Accepted: 10/25/2023] [Indexed: 10/28/2023] Open
Abstract
SUMMARY The analysis of stable isotope labeling experiments requires accurate, efficient, and reproducible quantification of mass isotopomer distributions (MIDs), which is not a core feature of general-purpose metabolomics software tools that are optimized to quantify metabolite abundance. Here, we present PIRAMID (Program for Integration and Rapid Analysis of Mass Isotopomer Distributions), a MATLAB-based tool that addresses this need by offering a user-friendly, graphical user interface-driven program to automate the extraction of isotopic information from mass spectrometry (MS) datasets. This tool can simultaneously extract ion chromatograms for various metabolites from multiple data files in common vendor-agnostic file formats, locate chromatographic peaks based on a targeted list of characteristic ions and retention times, and integrate MIDs for each target ion. These MIDs can be corrected for natural isotopic background based on the user-defined molecular formula of each ion. PIRAMID offers support for datasets acquired from low- or high-resolution MS, and single (MS) or tandem (MS/MS) instruments. It also enables the analysis of single or dual labeling experiments using a variety of isotopes (i.e. 2H, 13C, 15N, 18O, 34S). DATA AVAILABILITY AND IMPLEMENTATION MATLAB p-code files are freely available for non-commercial use and can be downloaded from https://mfa.vueinnovations.com/. Commercial licenses are also available. All the data presented in this publication are available under the "Help_menu" folder of the PIRAMID software.
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Affiliation(s)
- Javier D Gomez
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, 37240, United States
| | - Martha L Wall
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, 37240, United States
| | - Mohsin Rahim
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, 37240, United States
| | | | - Bradley S Evans
- Donald Danforth Plant Science Center, Olviette, MO, 63132, United States
| | - Doug K Allen
- Donald Danforth Plant Science Center, Olviette, MO, 63132, United States
- United States Department of Agriculture, Agricultural Research Service, Washington, DC, 20250, United States
| | - Maciek R Antoniewicz
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, United States
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, 37240, United States
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37240, United States
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9
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Sacco SA, McAtee Pereira AG, Trenary I, Smith KD, Betenbaugh MJ, Young JD. Overexpression of peroxisome proliferator-activated receptor γ co-activator-1⍺ (PGC-1⍺) in Chinese hamster ovary cells increases oxidative metabolism and IgG productivity. Metab Eng 2023; 79:108-117. [PMID: 37473833 DOI: 10.1016/j.ymben.2023.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/17/2023] [Accepted: 07/17/2023] [Indexed: 07/22/2023]
Abstract
Chinese hamster ovary (CHO) cells are used extensively to produce protein therapeutics, such as monoclonal antibodies (mAbs), in the biopharmaceutical industry. MAbs are large proteins that are energetically demanding to synthesize and secrete; therefore, high-producing CHO cell lines that are engineered for maximum metabolic efficiency are needed to meet increasing demands for mAb production. Previous studies have identified that high-producing cell lines possess a distinct metabolic phenotype when compared to low-producing cell lines. In particular, it was found that high mAb production is correlated to lactate consumption and elevated TCA cycle flux. We hypothesized that enhancing flux through the mitochondrial TCA cycle and oxidative phosphorylation would lead to increased mAb productivities and final titers. To test this hypothesis, we overexpressed peroxisome proliferator-activated receptor γ co-activator-1⍺ (PGC-1⍺), a gene that promotes mitochondrial metabolism, in an IgG-producing parental CHO cell line. Stable cell pools overexpressing PGC-1⍺ exhibited increased oxygen consumption, indicating increased mitochondrial metabolism, as well as increased mAb specific productivity compared to the parental line. We also performed 13C metabolic flux analysis (MFA) to quantify how PGC-1⍺ overexpression alters intracellular metabolic fluxes, revealing not only increased TCA cycle flux, but global upregulation of cellular metabolic activity. This study demonstrates the potential of rationally engineering the metabolism of industrial cell lines to improve overall mAb productivity and to increase the abundance of high-producing clones in stable cell pools.
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Affiliation(s)
- Sarah A Sacco
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | | | - Irina Trenary
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Kevin D Smith
- Pharmaceutical Development and Manufacturing Sciences, Janssen Research and Development, Spring House, PA, USA
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA.
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10
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Copeland CA, Olenchock BA, Ziehr D, McGarrity S, Leahy K, Young JD, Loscalzo J, Oldham WM. MYC overrides HIF-1α to regulate proliferating primary cell metabolism in hypoxia. eLife 2023; 12:e82597. [PMID: 37428010 DOI: 10.7554/elife.82597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 06/27/2023] [Indexed: 07/11/2023] Open
Abstract
Hypoxia requires metabolic adaptations to sustain energetically demanding cellular activities. While the metabolic consequences of hypoxia have been studied extensively in cancer cell models, comparatively little is known about how primary cell metabolism responds to hypoxia. Thus, we developed metabolic flux models for human lung fibroblast and pulmonary artery smooth muscle cells proliferating in hypoxia. Unexpectedly, we found that hypoxia decreased glycolysis despite activation of hypoxia-inducible factor 1α (HIF-1α) and increased glycolytic enzyme expression. While HIF-1α activation in normoxia by prolyl hydroxylase (PHD) inhibition did increase glycolysis, hypoxia blocked this effect. Multi-omic profiling revealed distinct molecular responses to hypoxia and PHD inhibition, and suggested a critical role for MYC in modulating HIF-1α responses to hypoxia. Consistent with this hypothesis, MYC knockdown in hypoxia increased glycolysis and MYC over-expression in normoxia decreased glycolysis stimulated by PHD inhibition. These data suggest that MYC signaling in hypoxia uncouples an increase in HIF-dependent glycolytic gene transcription from glycolytic flux.
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Affiliation(s)
- Courtney A Copeland
- Department of Medicine, Brigham and Women's Hospital, Boston, United States
- Department of Medicine, Harvard Medical School, Boston, United States
| | - Benjamin A Olenchock
- Department of Medicine, Brigham and Women's Hospital, Boston, United States
- Department of Medicine, Harvard Medical School, Boston, United States
| | - David Ziehr
- Department of Medicine, Brigham and Women's Hospital, Boston, United States
- Department of Medicine, Harvard Medical School, Boston, United States
- Department of Medicine, Massachusetts General Hospital, Boston, United States
| | - Sarah McGarrity
- Department of Medicine, Brigham and Women's Hospital, Boston, United States
- Department of Medicine, Harvard Medical School, Boston, United States
- Center for Systems Biology, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Kevin Leahy
- Department of Medicine, Brigham and Women's Hospital, Boston, United States
- Department of Medicine, Harvard Medical School, Boston, United States
| | - Jamey D Young
- Departments of Chemical & Biomolecular Engineering and Molecular Physiology & Biophysics, Vanderbilt University, Nashville, United States
| | - Joseph Loscalzo
- Department of Medicine, Brigham and Women's Hospital, Boston, United States
- Department of Medicine, Harvard Medical School, Boston, United States
| | - William M Oldham
- Department of Medicine, Brigham and Women's Hospital, Boston, United States
- Department of Medicine, Harvard Medical School, Boston, United States
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11
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Sharma G, Maptue N, Rahim M, Trigo Mijes ML, Hever T, Wen X, Funk AM, Malloy CR, Young JD, Khemtong C. Oxidation of hyperpolarized [1- 13 C]pyruvate in isolated rat kidneys. NMR Biomed 2023; 36:e4857. [PMID: 36285844 PMCID: PMC9980878 DOI: 10.1002/nbm.4857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/05/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
Kidneys play a central role in numerous disorders but current imaging methods have limited utility to probe renal metabolism. Hyperpolarized (HP) 13 C magnetic resonance imaging is uniquely suited to provide metabolite-specific information about key biochemical pathways and it offers the further advantage that renal imaging is practical in humans. This study evaluated the feasibility of hyperpolarization examinations in a widely used model for analysis of renal physiology, the isolated kidney, which enables isolation of renal metabolism from the effects of other organs and validation of HP results by independent measurements. Isolated rat kidneys were supplied with either HP [1-13 C]pyruvate only or HP [1-13 C]pyruvate plus octanoate. Metabolic activity in both groups was confirmed by stable renal oxygen consumption. HP [1-13 C]pyruvate was readily metabolized to [13 C]bicarbonate, [1-13 C]lactate, and [1-13 C]alanine, detectable seconds after HP [1-13 C]pyruvate was injected. Octanoate suppressed but did not eliminate the production of HP [13 C]bicarbonate from [1-13 C]pyruvate. Steady-state flux analyses using non-HP 13 C substrates validated the utilization of HP [1-13 C]pyruvate, as observed by HP 13 C NMR. In the presence of octanoate, lactate is generated from a tricarboxylic acid cycle intermediate, oxaloacetate. The isolated rat kidney may serve as an excellent model for investigating and establishing new HP 13 C metabolic probes for future kidney imaging applications.
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Affiliation(s)
- Gaurav Sharma
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nesmine Maptue
- Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, University of Florida, Gainesville, FL, USA
| | - Mohsin Rahim
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Miriam L. Trigo Mijes
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Thomas Hever
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiaodong Wen
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Alexander M. Funk
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Craig R. Malloy
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
- VA North Texas Health Care System, Dallas, TX, USA
| | - Jamey D. Young
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Chalermchai Khemtong
- Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, University of Florida, Gainesville, FL, USA
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, USA
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12
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Harford M, Villarroel M, Jorge J, Redfern O, Finnegan E, Davidson S, Young JD, Tarassenko L, Watkinson P. Contactless skin perfusion monitoring with video cameras: tracking pharmacological vasoconstriction and vasodilation using photoplethysmographic changes. Physiol Meas 2022; 43. [PMID: 36270506 DOI: 10.1088/1361-6579/ac9c82] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/21/2022] [Indexed: 02/07/2023]
Abstract
Objectives.Clinical assessment of skin perfusion informs prognosis in critically ill patients. Video camera monitoring could provide an objective, continuous method to monitor skin perfusion. In this prospective, interventional study of healthy volunteers, we tested whether video camera-derived photoplethysmography imaging and colour measurements could detect drug-induced skin perfusion changes.Approach.We monitored the lower limbs of 30 volunteers using video cameras while administering phenylephrine (a vasoconstrictor) and glyceryl trinitrate (a vasodilator). We report relative pixel intensity changes from baseline, as absolute values are sensitive to environmental factors. The primary outcome was the pre- to peak- infusion green channel amplitude change in the pulsatile PPGi waveform component. Secondary outcomes were pre-to-peak changes in the photoplethysmographic imaging waveform baseline, skin colour hue and skin colour saturation.Main results.The 30 participants had a median age of 29 years (IQR 25-34), sixteen (53%) were male. A 34.7% (p= 0.0001) mean decrease in the amplitude of the pulsatile photoplethysmographic imaging waveform occurred following phenylephrine infusion. A 30.7% (p= 0.000004) mean increase occurred following glyceryl trinitrate infusion. The photoplethysmographic imaging baseline decreased with phenylephrine by 2.1% (p= 0.000 02) and increased with glyceryl trinitrate by 0.5% (p= 0.026). Skin colour hue changed in opposite direction with phenylephrine (-0.0013,p= 0.0002) and glyceryl trinitrate (+0.0006,p= 0.019). Skin colour saturation decreased with phenylephrine by 0.0022 (p= 0.0002), with no significant change observed with glyceryl trinitrate (+0.0005,p= 0.21).Significance.Drug-induced vasoconstriction and vasodilation are associated with detectable changes in photoplethysmographic imaging waveform parameters and skin hue. Our findings suggest video cameras have great potential for continuous, contactless skin perfusion monitoring.
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Affiliation(s)
- M Harford
- Critical Care Research Group, Kadoorie Centre for Critical Care Research and Education, Nuffield Department of Clinical Neurosciences, University of Oxford, United Kingdom.,Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, United Kingdom.,Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - M Villarroel
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, United Kingdom
| | - J Jorge
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, United Kingdom
| | - O Redfern
- Critical Care Research Group, Kadoorie Centre for Critical Care Research and Education, Nuffield Department of Clinical Neurosciences, University of Oxford, United Kingdom
| | - E Finnegan
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, United Kingdom
| | - S Davidson
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, United Kingdom
| | - J D Young
- Critical Care Research Group, Kadoorie Centre for Critical Care Research and Education, Nuffield Department of Clinical Neurosciences, University of Oxford, United Kingdom
| | - L Tarassenko
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, United Kingdom
| | - P Watkinson
- Critical Care Research Group, Kadoorie Centre for Critical Care Research and Education, Nuffield Department of Clinical Neurosciences, University of Oxford, United Kingdom.,Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
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13
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Esquejo RM, Albuquerque B, Sher A, Blatnik M, Wald K, Peloquin M, Delmore J, Kindt E, Li W, Young JD, Cameron K, Miller RA. AMPK activation is sufficient to increase skeletal muscle glucose uptake and glycogen synthesis but is not required for contraction-mediated increases in glucose metabolism. Heliyon 2022; 8:e11091. [PMID: 36303906 PMCID: PMC9593205 DOI: 10.1016/j.heliyon.2022.e11091] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/13/2021] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
The AMP-activated protein kinase (AMPK) is a cellular sensor of energetics and when activated in skeletal muscle during contraction can impart changes in skeletal muscle metabolism. Therapeutics that selectively activate AMPK have been developed to lower glucose levels through increased glucose disposal rates as an approach to abrogate the hyperglycemic state of diabetes; however, the metabolic fate of glucose following AMPK activation remains unclear. We have used a combination of in vivo evaluation of glucose homeostasis and ex vivo skeletal muscle incubation to systematically evaluate metabolism following pharmacological activation of AMPK with PF-739, comparing this with AMPK activation through sustained intermittent electrical stimulation of contraction. These methods to activate AMPK result in increased glucose uptake but divergent metabolism of glucose: pharmacological activation results in increased glycogen accumulation while contraction-induced glucose uptake results in increased lactate formation and glucose oxidation. These results provide additional evidence to support a role for AMPK in control of skeletal muscle metabolism and additional insight into the potential for AMPK stimulation with small molecule direct activators.
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Affiliation(s)
- Ryan M. Esquejo
- Internal Medicine Research Unit, Pfizer Inc., Cambridge, MA 02139, United States
| | - Bina Albuquerque
- Internal Medicine Research Unit, Pfizer Inc., Cambridge, MA 02139, United States
| | - Anna Sher
- Internal Medicine Research Unit, Pfizer Inc., Cambridge, MA 02139, United States
| | - Matthew Blatnik
- Early Clinical Development, Pfizer Inc., Groton, CT 06340, United States
| | - Kyle Wald
- Early Clinical Development, Pfizer Inc., Groton, CT 06340, United States
| | - Matthew Peloquin
- Internal Medicine Research Unit, Pfizer Inc., Cambridge, MA 02139, United States
| | - Jake Delmore
- Internal Medicine Research Unit, Pfizer Inc., Cambridge, MA 02139, United States
| | - Erick Kindt
- Worldwide Research, Development, and Medical Affairs, Pfizer Inc., La Jolla, CA 92037, United States
| | - Wenlin Li
- Worldwide Research, Development, and Medical Affairs, Pfizer Inc., La Jolla, CA 92037, United States
| | - Jamey D. Young
- Department of Chemical & Biomolecular Engineering, Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN 37235-1604, United States
| | - Kim Cameron
- Worldwide Research, Development, and Medical Affairs, Pfizer Inc., Cambridge, MA 02139, United States
| | - Russell A. Miller
- Internal Medicine Research Unit, Pfizer Inc., Cambridge, MA 02139, United States,Corresponding author.
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14
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Wang B, Young JD. 13C-Isotope-Assisted Assessment of Metabolic Quenching During Sample Collection from Suspension Cell Cultures. Anal Chem 2022; 94:7787-7794. [PMID: 35613318 DOI: 10.1021/acs.analchem.1c05338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metabolomics and fluxomics are core approaches to directly profile and interrogate cellular metabolism in response to various genetic or environmental perturbations. In order to accurately measure the abundance and isotope enrichment of intracellular metabolites, cell culture samples must be rapidly harvested and cold quenched to preserve the in vivo metabolic state of the cells at the time of sample collection. When dealing with suspension cultures, this process is complicated by the need to separate the liquid culture media from cellular biomass prior to metabolite extraction. Here, we examine the efficacy of several commonly used metabolic quenching methods, using the model cyanobacterium Synechocystis sp. PCC 6803 as an example. Multiple 13C-labeled compounds, including 13C-bicarbonate, 13C-glucose, and 13C-glutamine, were used as tracers during the sample collection and the cold-quenching process to assess the extent of metabolic turnover after cells were harvested from culture flasks. We show that the combination of rapid filtration followed by 100% cold (-80 °C) methanol quenching exhibits the highest quenching efficiency, while mixing cell samples with a partially frozen 30% methanol slurry (-24 °C) followed by centrifugation is slightly less effective at quenching metabolism but enables less laborious sample processing. By contrast, rapidly mixing the cells with a saline ice slurry (∼0 °C) is less effective, as indicated by high isotope-labeling rates after sample harvest, while mixing the cells with 60% cold methanol (-65 °C) prior to centrifugation causes significant metabolite loss. This study demonstrates a rigorous, quantitative, and broadly applicable method for assessing the metabolic quenching efficacy of protocols used for sample collection in metabolomics and fluxomics studies.
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Affiliation(s)
- Bo Wang
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States.,Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37235, United States
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15
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Sacco SA, Tuckowski AM, Trenary I, Kraft L, Betenbaugh MJ, Young JD, Smith KD. Attenuation of glutamine synthetase selection marker improves product titer and reduces glutamine overflow in Chinese hamster ovary cells. Biotechnol Bioeng 2022; 119:1712-1727. [PMID: 35312045 DOI: 10.1002/bit.28084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 02/25/2022] [Accepted: 03/07/2022] [Indexed: 11/10/2022]
Abstract
The glutamine synthetase (GS) expression system is commonly used to ensure stable transgene integration and amplification in CHO host lines. Transfected cell populations are typically grown in the presence of the GS inhibitor, methionine sulfoximine (MSX), to further select for increased transgene copy number. However, high levels of GS activity produce excess glutamine. We hypothesized that attenuating the GS promoter while keeping the strong IgG promoter on the GS-IgG expression vector would result in a more efficient cellular metabolic phenotype. Herein, we characterized CHO cell lines expressing GS from either an attenuated promoter or an SV40 promoter and selected with/without MSX. CHO cells with the attenuated GS promoter had higher IgG specific productivity and lower glutamine production compared to cells with SV40-driven GS expression. Selection with MSX increased both specific productivity and glutamine production, regardless of GS promoter strength. 13 C metabolic flux analysis (MFA) was performed to further assess metabolic differences between these cell lines. Interestingly, central carbon metabolism was unaltered by the attenuated GS promoter while the fate of glutamate and glutamine varied depending on promoter strength and selection conditions. This study highlights the ability to optimize the GS expression system to improve IgG production and reduce wasteful glutamine overflow, without significantly altering central metabolism. Additionally, a detailed supplementary analysis of two "lactate runaway" reactors provides insight into the poorly understood phenomenon of excess lactate production by some CHO cell cultures. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Sarah A Sacco
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Angela M Tuckowski
- Biotherapeutics Development, Janssen Research and Development, Spring House, PA, USA.,Department of Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, USA
| | - Irina Trenary
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Lauren Kraft
- Biotherapeutics Development, Janssen Research and Development, Spring House, PA, USA
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA.,Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Kevin D Smith
- Biotherapeutics Development, Janssen Research and Development, Spring House, PA, USA.,Asimov, 1325 Boylston St, Boston, MA, 02215
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16
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Zheng AO, Sher A, Fridman D, Musante CJ, Young JD. Pool size measurements improve precision of flux estimates but increase sensitivity to unmodeled reactions outside the core network in isotopically nonstationary metabolic flux analysis (INST-MFA). Biotechnol J 2022; 17:e2000427. [PMID: 35085426 DOI: 10.1002/biot.202000427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 11/08/2022]
Abstract
Metabolic flux analysis (MFA) involves model-based estimation of metabolic reaction rates (i.e., fluxes) and, in some cases, metabolite content (i.e., pool sizes) from experimental measurements. Applying MFA to biological data helps determine the fate of substrates and the activity of specific pathways within metabolic networks. However, reliably estimating fluxes by using simplified "core" models to predict the dynamics of larger metabolic networks remains a challenge. One point of uncertainty relates to the advantages and potential pitfalls of including pool size measurements as experimental inputs for isotopically nonstationary MFA (INST-MFA). Here, we directly assessed the role of pool sizes using various core models and simulated datasets. To investigate the effects of pool size measurements on INST-MFA, we assessed the accuracy and precision of flux estimates obtained using different subsets of data (e.g., with or without pool size measurements) and simple network models that either matched or differed from the true network. The inclusion of pool size measurements provided incremental improvements to the precision of the flux estimates. However, adding pool size measurements increased the sensitivity of the flux solution to unmodeled reactions outside the core network. These results were confirmed using a large E. coli model that is representative of realistic metabolic networks examined in MFA studies. Our findings indicate that accurate flux estimates can be obtained in the absence of pool size measurements, even when using core models that lack full network coverage. Addition of pool size measurements to INST-MFA datasets may reveal the activity of non-core reactions that influence the labeling dynamics and therefore necessitate network expansion in order to reconcile all available data to the model. Our findings also emphasize the key role that goodness-of-fit testing plays in assessing the quality of model fits obtained with INST-MFA. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Amy O Zheng
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Anna Sher
- Pfizer Worldwide Research, Development and Medical, Cambridge, MA, USA
| | | | - Cynthia J Musante
- Pfizer Worldwide Research, Development and Medical, Cambridge, MA, USA
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA.,Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
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17
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Helmuth CL, Woerner DR, Ballou MA, Manahan JL, Coppin CM, Long NS, Hoffman AA, Young JD, Smock TM, Hales KE. Effects of physical activity and feed and water restriction at reimplanting time on feed intake patterns, growth performance, and carcass characteristics of finishing beef steers. Transl Anim Sci 2022; 6:txac008. [PMID: 35233510 PMCID: PMC8882254 DOI: 10.1093/tas/txac008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Indexed: 11/21/2022] Open
Abstract
In the feedlot, there can be a decrease in dry matter intake (DMI) associated with reimplanting cattle that negatively affects growth performance. This study was conducted to determine the mechanisms causing a decrease in DMI after reimplanting and identify a strategy to mitigate the decrease. Crossbred steers (n = 200; 10 pens/treatment; initial bodyweight [BW] = 386 ± 4.9 kg) were used in a randomized complete block design experiment. Cattle were implanted with Revalor-IS on day 0. Treatments included a Revalor-200 implant on day 90 before feeding with the following management practices imposed: 1) steers were returned to their home pen immediately after reimplant (PCON); 2) steers were placed in pens and restricted from feed and water for 4 h (RES); 3) steers were walked an additional 805 m after reimplant and then returned home (LOC); 4) steers were restricted from feed and water for 4 h and walked an additional 805 m (RES + LOC); 5) steers were given an oral bolus of Megasphaera elsdenii (Lactipro; MS Biotec, Wamego, KS) and were restricted from feed and water for 4 h, and then walked an additional 805 m (LACT). One hundred steers were given an ear tag to record minutes of activity (ESense Flex Tags, Allflex Livestock Intelligence, Madison, WI). As a percentage of BW, DMI was 5% greater (P = 0.01) from reimplant to end for PCON vs. RES, LOC, and RES + LOC treatments. Likewise, as a percentage of BW, DMI was 6.6% greater (P = 0.03) from reimplant to end and 4.0% greater (P = 0.05) overall for the PCON treatment vs. the LOC treatment. Overall, DMI as a percentage of BW was 3.3% greater (P = 0.02) for PCON vs. RES, LOC, and RES + LOC treatments. There was an increase in G:F from reimplant to end (P = 0.05) for RES + LOC vs. the LACT treatment. From these data, we conclude that restricting cattle from feed and water for 4 h after reimplanting did not alter subsequent DMI. Increasing locomotion had the greatest negative effect on DMI and growth performance. Management strategies to decrease locomotion associated with reimplanting would be beneficial to DMI and overall growth performance of finishing beef steers.
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Affiliation(s)
- C L Helmuth
- Department of Animal & Food Sciences, Texas Tech University, Lubbock, USA
| | - D R Woerner
- Department of Animal & Food Sciences, Texas Tech University, Lubbock, USA
| | - M A Ballou
- Department of Animal & Food Sciences, Texas Tech University, Lubbock, USA
| | - J L Manahan
- Department of Animal & Food Sciences, Texas Tech University, Lubbock, USA
| | - C M Coppin
- Department of Animal & Food Sciences, Texas Tech University, Lubbock, USA
| | - N S Long
- Department of Animal & Food Sciences, Texas Tech University, Lubbock, USA
| | - A A Hoffman
- Department of Animal & Food Sciences, Texas Tech University, Lubbock, USA
| | - J D Young
- Department of Animal & Food Sciences, Texas Tech University, Lubbock, USA
| | - T M Smock
- Department of Animal & Food Sciences, Texas Tech University, Lubbock, USA
| | - K E Hales
- Department of Animal & Food Sciences, Texas Tech University, Lubbock, USA
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18
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Rahim M, Ragavan M, Deja S, Merritt ME, Burgess SC, Young JD. INCA 2.0: A tool for integrated, dynamic modeling of NMR- and MS-based isotopomer measurements and rigorous metabolic flux analysis. Metab Eng 2022; 69:275-285. [PMID: 34965470 PMCID: PMC8789327 DOI: 10.1016/j.ymben.2021.12.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 12/17/2021] [Accepted: 12/22/2021] [Indexed: 01/03/2023]
Abstract
Metabolic flux analysis (MFA) combines experimental measurements and computational modeling to determine biochemical reaction rates in live biological systems. Advancements in analytical instrumentation, such as nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS), have facilitated chemical separation and quantification of isotopically enriched metabolites. However, no software packages have been previously described that can integrate isotopomer measurements from both MS and NMR analytical platforms and have the flexibility to estimate metabolic fluxes from either isotopic steady-state or dynamic labeling experiments. By applying physiologically relevant cardiac and hepatic metabolic models to assess NMR isotopomer measurements, we herein test and validate new modeling capabilities of our enhanced flux analysis software tool, INCA 2.0. We demonstrate that INCA 2.0 can simulate and regress steady-state 13C NMR datasets from perfused hearts with an accuracy comparable to other established flux assessment tools. Furthermore, by simulating the infusion of three different 13C acetate tracers, we show that MFA based on dynamic 13C NMR measurements can more precisely resolve cardiac fluxes compared to isotopically steady-state flux analysis. Finally, we show that estimation of hepatic fluxes using combined 13C NMR and MS datasets improves the precision of estimated fluxes by up to 50%. Overall, our results illustrate how the recently added NMR data modeling capabilities of INCA 2.0 can enable entirely new experimental designs that lead to improved flux resolution and can be applied to a wide range of biological systems and measurement time courses.
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Affiliation(s)
- Mohsin Rahim
- Department of Chemical and Biomolecular, Vanderbilt University, School of Engineering, Nashville, TN 37212
| | - Mukundan Ragavan
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida
| | - Stanislaw Deja
- Center for Human Nutrition, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Matthew E. Merritt
- Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, Florida
| | - Shawn C. Burgess
- Center for Human Nutrition, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jamey D. Young
- Department of Chemical and Biomolecular, Vanderbilt University, School of Engineering, Nashville, TN 37212,Department of Molecular Physiology and Biophysics, Vanderbilt University, School of Engineering, Nashville, TN 37212,To whom correspondence should be addressed: Department of Chemical and Biomolecular, Olin Hall 107, 2400 Highland Ave, Vanderbilt University, Nashville, TN 37212,
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20
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Robinson AJ, House GL, Morales DP, Kelliher JM, Gallegos-Graves LV, LeBrun ES, Davenport KW, Palmieri F, Lohberger A, Bregnard D, Estoppey A, Buffi M, Paul C, Junier T, Hervé V, Cailleau G, Lupini S, Nguyen HN, Zheng AO, Gimenes LJ, Bindschedller S, Rodrigues DF, Werner JH, Young JD, Junier P, Chain PSG. Widespread bacterial diversity within the bacteriome of fungi. Commun Biol 2021; 4:1168. [PMID: 34621007 PMCID: PMC8497576 DOI: 10.1038/s42003-021-02693-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 09/20/2021] [Indexed: 02/08/2023] Open
Abstract
Knowledge of associations between fungal hosts and their bacterial associates has steadily grown in recent years as the number and diversity of examinations have increased, but current knowledge is predominantly limited to a small number of fungal taxa and bacterial partners. Here, we screened for potential bacterial associates in over 700 phylogenetically diverse fungal isolates, representing 366 genera, or a tenfold increase compared with previously examined fungal genera, including isolates from several previously unexplored phyla. Both a 16 S rDNA-based exploration of fungal isolates from four distinct culture collections spanning North America, South America and Europe, and a bioinformatic screen for bacterial-specific sequences within fungal genome sequencing projects, revealed that a surprisingly diverse array of bacterial associates are frequently found in otherwise axenic fungal cultures. We demonstrate that bacterial associations with diverse fungal hosts appear to be the rule, rather than the exception, and deserve increased consideration in microbiome studies and in examinations of microbial interactions.
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Affiliation(s)
- Aaron J Robinson
- Biosecurity and Public Health Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Geoffrey L House
- Biosecurity and Public Health Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Demosthenes P Morales
- Biosecurity and Public Health Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
- Center of Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Julia M Kelliher
- Biosecurity and Public Health Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - La Verne Gallegos-Graves
- Biosecurity and Public Health Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Erick S LeBrun
- Biosecurity and Public Health Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Karen W Davenport
- Biosecurity and Public Health Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Fabio Palmieri
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Andrea Lohberger
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Danaé Bregnard
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Aislinn Estoppey
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Matteo Buffi
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Christophe Paul
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Thomas Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Vincent Hervé
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Guillaume Cailleau
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Simone Lupini
- Department of Civil and Environmental Engineering, University of Houston, Houston, TX, 77004, USA
| | - Hang N Nguyen
- Department of Civil and Environmental Engineering, University of Houston, Houston, TX, 77004, USA
| | - Amy O Zheng
- Department of Chemical and Biomolecular Engineering and Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37235-1604, USA
| | - Luciana Jandelli Gimenes
- Center for Environmental Research and Training, University of São Paulo, Cubatão, São Paulo, 11.540 -990, Brazil
| | - Saskia Bindschedller
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Debora F Rodrigues
- Department of Civil and Environmental Engineering, University of Houston, Houston, TX, 77004, USA
| | - James H Werner
- Center of Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering and Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37235-1604, USA
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH-2000, Neuchâtel, Switzerland
| | - Patrick S G Chain
- Biosecurity and Public Health Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.
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21
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Rahim M, Hasenour CM, Bednarski TK, Hughey CC, Wasserman DH, Young JD. Multitissue 2H/13C flux analysis reveals reciprocal upregulation of renal gluconeogenesis in hepatic PEPCK-C-knockout mice. JCI Insight 2021; 6:e149278. [PMID: 34156032 PMCID: PMC8262479 DOI: 10.1172/jci.insight.149278] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The liver is the major source of glucose production during fasting under normal physiological conditions. However, the kidney may also contribute to maintaining glucose homeostasis in certain circumstances. To test the ability of the kidney to compensate for impaired hepatic glucose production in vivo, we developed a stable isotope approach to simultaneously quantify gluconeogenic and oxidative metabolic fluxes in the liver and kidney. Hepatic gluconeogenesis from phosphoenolpyruvate was disrupted via liver-specific knockout of cytosolic phosphoenolpyruvate carboxykinase (PEPCK-C; KO). 2H/13C isotopes were infused in fasted KO and WT littermate mice, and fluxes were estimated from isotopic measurements of tissue and plasma metabolites using a multicompartment metabolic model. Hepatic gluconeogenesis and glucose production were reduced in KO mice, yet whole-body glucose production and arterial glucose were unaffected. Glucose homeostasis was maintained by a compensatory rise in renal glucose production and gluconeogenesis. Renal oxidative metabolic fluxes of KO mice increased to sustain the energetic and metabolic demands of elevated gluconeogenesis. These results show the reciprocity of the liver and kidney in maintaining glucose homeostasis by coordinated regulation of gluconeogenic flux through PEPCK-C. Combining stable isotopes with mathematical modeling provides a versatile platform to assess multitissue metabolism in various genetic, pathophysiological, physiological, and pharmacological settings.
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Affiliation(s)
- Mohsin Rahim
- Department of Chemical and Biomolecular Engineering and
| | | | | | - Curtis C Hughey
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - David H Wasserman
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering and.,Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
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22
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Bednarski TK, Rahim M, Young JD. In vivo 2H/ 13C flux analysis in metabolism research. Curr Opin Biotechnol 2021; 71:1-8. [PMID: 34048994 DOI: 10.1016/j.copbio.2021.04.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/29/2021] [Accepted: 04/26/2021] [Indexed: 12/12/2022]
Abstract
Identifying the factors and mechanisms that regulate metabolism under normal and diseased states requires methods to quantify metabolic fluxes of live tissues within their physiological milieu. A number of recent developments have expanded the reach and depth of isotope-based in vivo flux analysis, which have in turn challenged existing dogmas in metabolism research. First, minimally invasive techniques of intravenous isotope infusion and sampling have advanced in vivo metabolic tracer studies in animal models and human subjects. Second, recent breakthroughs in analytical instrumentation have expanded the scope of isotope labeling measurements and reduced sample volume requirements. Third, innovative modeling approaches and publicly available software tools have facilitated rigorous analysis of sophisticated experimental designs involving multiple tracers and expansive metabolomics datasets. These developments have enabled comprehensive in vivo quantification of metabolic fluxes in specific tissues and have set the stage for integrated multi-tissue flux assays.
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Affiliation(s)
- Tomasz K Bednarski
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Mohsin Rahim
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA.
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23
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Hasenour CM, Rahim M, Young JD. In Vivo Estimates of Liver Metabolic Flux Assessed by 13C-Propionate and 13C-Lactate Are Impacted by Tracer Recycling and Equilibrium Assumptions. Cell Rep 2021; 32:107986. [PMID: 32755580 PMCID: PMC7451222 DOI: 10.1016/j.celrep.2020.107986] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 06/01/2020] [Accepted: 07/13/2020] [Indexed: 01/08/2023] Open
Abstract
Isotope-based assessment of metabolic flux is achieved through a judicious balance of measurements and assumptions. Recent publications debate the validity of key assumptions used to model stable isotope labeling of liver metabolism in vivo. Here, we examine the controversy surrounding estimates of liver citric acid cycle and gluconeogenesis fluxes using a flexible modeling platform that enables rigorous testing of standard assumptions. Fasted C57BL/6J mice are infused with [13C3]lactate or [13C3]propionate isotopes, and hepatic fluxes are regressed using models with gradually increasing complexity and relaxed assumptions. We confirm that liver pyruvate cycling fluxes are incongruent between different 13C tracers in models with conventional assumptions. When models are expanded to include more labeling measurements and fewer constraining assumptions, however, liver pyruvate cycling is significant, and inconsistencies in hepatic flux estimates using [13C3]lactate and [13C3]propionate isotopes emanate, in part, from peripheral tracer recycling and incomplete isotope equilibration within the citric acid cycle.
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Affiliation(s)
- Clinton M Hasenour
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235, USA
| | - Mohsin Rahim
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235, USA
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37235, USA.
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24
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Junier P, Cailleau G, Palmieri I, Vallotton C, Trautschold OC, Junier T, Paul C, Bregnard D, Palmieri F, Estoppey A, Buffi M, Lohberger A, Robinson A, Kelliher JM, Davenport K, House GL, Morales D, Gallegos-Graves LV, Dichosa AEK, Lupini S, Nguyen HN, Young JD, Rodrigues DF, Parra-Vasquez ANG, Bindschedler S, Chain PSG. Democratization of fungal highway columns as a tool to investigate bacteria associated with soil fungi. FEMS Microbiol Ecol 2021; 97:6095729. [PMID: 33440006 PMCID: PMC7878174 DOI: 10.1093/femsec/fiab003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 01/11/2021] [Indexed: 11/13/2022] Open
Abstract
Bacteria–fungi interactions (BFIs) are essential in ecosystem functioning. These interactions are modulated not only by local nutritional conditions but also by the physicochemical constraints and 3D structure of the environmental niche. In soils, the unsaturated and complex nature of the substrate restricts the dispersal and activity of bacteria. Under unsaturated conditions, some bacteria engage with filamentous fungi in an interaction (fungal highways) in which they use fungal hyphae to disperse. Based on a previous experimental device to enrich pairs of organisms engaging in this interaction in soils, we present here the design and validation of a modified version of this sampling system constructed using additive printing. The 3D printed devices were tested using a novel application in which a target fungus, the common coprophilous fungus Coprinopsis cinerea, was used as bait to recruit and identify bacterial partners using its mycelium for dispersal. Bacteria of the genera Pseudomonas, Sphingobacterium and Stenotrophomonas were highly enriched in association with C. cinerea. Developing and producing these new easy-to-use tools to investigate how bacteria overcome dispersal limitations in cooperation with fungi is important to unravel the mechanisms by which BFIs affect processes at an ecosystem scale in soils and other unsaturated environments.
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Affiliation(s)
- Pilar Junier
- Corresponding author: Rue Emile-Argand 9, CH-2000, Neuchatel, Switzerland. Tel: +41327182244; Fax: +41327183001; E-mail: ; MS-M888, TA43-0001, SM30 Bikini Atoll Road, Los Alamos 87545 USA
| | - Guillaume Cailleau
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Ilona Palmieri
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Celine Vallotton
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Olivia C Trautschold
- Materials Science and Technology, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Thomas Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
- Vital-IT Group, Swiss Institute of Bioinformatics, CH, 1015, Lausanne, Switzerland
| | - Christophe Paul
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Danae Bregnard
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Fabio Palmieri
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Aislinn Estoppey
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Matteo Buffi
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Andrea Lohberger
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Aaron Robinson
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Julia M Kelliher
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Karen Davenport
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Geoffrey L House
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Demosthenes Morales
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | | | - Armand E K Dichosa
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Simone Lupini
- Civil and Environmental Engineering, University of Houston, Houston, TX 77004, USA
| | - Hang N Nguyen
- Civil and Environmental Engineering, University of Houston, Houston, TX 77004, USA
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, and Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37212, USA
| | - Debora F Rodrigues
- Civil and Environmental Engineering, University of Houston, Houston, TX 77004, USA
| | | | - Saskia Bindschedler
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, CH, 2000, Neuchâtel, Switzerland
| | - Patrick S G Chain
- Corresponding author: Rue Emile-Argand 9, CH-2000, Neuchatel, Switzerland. Tel: +41327182244; Fax: +41327183001; E-mail: ; MS-M888, TA43-0001, SM30 Bikini Atoll Road, Los Alamos 87545 USA
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25
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Chang HY, Colby SM, Du X, Gomez JD, Helf MJ, Kechris K, Kirkpatrick CR, Li S, Patti GJ, Renslow RS, Subramaniam S, Verma M, Xia J, Young JD. A Practical Guide to Metabolomics Software Development. Anal Chem 2021; 93:1912-1923. [PMID: 33467846 PMCID: PMC7859930 DOI: 10.1021/acs.analchem.0c03581] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
A growing number
of software tools have been developed for metabolomics
data processing and analysis. Many new tools are contributed by metabolomics
practitioners who have limited prior experience with software development,
and the tools are subsequently implemented by users with expertise
that ranges from basic point-and-click data analysis to advanced coding.
This Perspective is intended to introduce metabolomics software users
and developers to important considerations that determine the overall
impact of a publicly available tool within the scientific community.
The recommendations reflect the collective experience of an NIH-sponsored
Metabolomics Consortium working group that was formed with the goal
of researching guidelines and best practices for metabolomics tool
development. The recommendations are aimed at metabolomics researchers
with little formal background in programming and are organized into
three stages: (i) preparation, (ii) tool development, and (iii) distribution
and maintenance.
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Affiliation(s)
- Hui-Yin Chang
- Department of Pathology, University of Michigan, 1301 Catherine Street, Ann Arbor, Michigan 48109, United States.,Department of Biomedical Sciences and Engineering, National Central University, No. 300, Zhongda Road, Zhongli District, Taoyuan City 320, Taiwan
| | - Sean M Colby
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN: K8-98, Richland, Washington 99352, United States
| | - Xiuxia Du
- Department of Bioinformatics & Genomics, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, North Carolina 28223, United States
| | - Javier D Gomez
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, PMB 351604, 2301 Vanderbilt Place, Nashville, Tennessee 37235, United States
| | - Maximilian J Helf
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, 533 Tower Road, Ithaca, New York 14853, United States
| | - Katerina Kechris
- Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, 13001 East 17th Place B119, Aurora, Colorado 80045, United States
| | - Christine R Kirkpatrick
- San Diego Supercomputer Center, University of California San Diego, MC 0505, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Shuzhao Li
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, Connecticut 06032, United States
| | - Gary J Patti
- Department of Chemistry, Department of Medicine, and Siteman Cancer Center, Washington University in St. Louis, CB 1134, One Brookings Drive, St. Louis, Missouri 63130, United States
| | - Ryan S Renslow
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN: K8-98, Richland, Washington 99352, United States.,Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, P.O. Box 646515, Pullman, Washington 99164, United States
| | - Shankar Subramaniam
- San Diego Supercomputer Center, University of California San Diego, MC 0505, 9500 Gilman Drive, La Jolla, California 92093, United States.,Department of Bioengineering, Department of Computer Science and Engineering, Department of Cellular and Molecular Medicine, and Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive #0412, La Jolla, California 92093, United States
| | - Mukesh Verma
- Epidemiology and Genomics Research Program, National Cancer Institute, National Institutes of Health, Suite 4E102, 9609 Medical Center Drive, MSC 9763, Rockville, Maryland 20850, United States
| | - Jianguo Xia
- Faculty of Agricultural and Environmental Sciences, McGill University, 21111 Lakeshore Road, Ste. Anne de Bellevue, Quebec H9X 3 V9, Canada
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, PMB 351604, 2301 Vanderbilt Place, Nashville, Tennessee 37235, United States.,Department of Molecular Physiology and Biophysics, Vanderbilt University, PMB 351604, 2301 Vanderbilt Place, Nashville, Tennessee 37235, United States
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26
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Pannala VR, Estes SK, Rahim M, Trenary I, O’Brien TP, Shiota C, Printz RL, Reifman J, Shiota M, Young JD, Wallqvist A. Toxicant-Induced Metabolic Alterations in Lipid and Amino Acid Pathways Are Predictive of Acute Liver Toxicity in Rats. Int J Mol Sci 2020; 21:ijms21218250. [PMID: 33158035 PMCID: PMC7663358 DOI: 10.3390/ijms21218250] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/30/2020] [Accepted: 11/02/2020] [Indexed: 02/07/2023] Open
Abstract
Liver disease and disorders associated with aberrant hepatocyte metabolism can be initiated via drug and environmental toxicant exposures. In this study, we tested the hypothesis that gene and metabolic profiling can reveal commonalities in liver response to different toxicants and provide the capability to identify early signatures of acute liver toxicity. We used Sprague Dawley rats and three classical hepatotoxicants: acetaminophen (2 g/kg), bromobenzene (0.4 g/kg), and carbon tetrachloride (0.3 g/kg), to identify early perturbations in liver metabolism after a single acute exposure dose. We measured changes in liver genes and plasma metabolites at two time points (5 and 10 h) and used genome-scale metabolic models to identify commonalities in liver responses across the three toxicants. We found strong correlations for gene and metabolic profiles between the toxicants, indicative of similarities in the liver response to toxicity. We identified several injury-specific pathways in lipid and amino acid metabolism that changed similarly across the three toxicants. Our findings suggest that several plasma metabolites in lipid and amino acid metabolism are strongly associated with the progression of liver toxicity, and as such, could be targeted and clinically assessed for their potential as early predictors of acute liver toxicity.
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Affiliation(s)
- Venkat R. Pannala
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, MD 21702, USA;
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA
- Correspondence: (V.R.P.); (J.D.Y.); (A.W.); Tel.: +1-301-619-1976 (V.R.P.); +1-615-343-4253 (J.D.Y.); +1-301-619-1989 (A.W.); Fax: +301-619-1983 (A.W. & V.R.P.); +615-343-7951 (J.D.Y.)
| | - Shanea K. Estes
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (S.K.E.); (T.P.O.); (C.S.); (R.L.P.); (M.S.)
| | - Mohsin Rahim
- Department of Chemical and Biomolecular Engineering, Vanderbilt University School of Engineering, Nashville, TN 37232, USA; (M.R.); (I.T.)
| | - Irina Trenary
- Department of Chemical and Biomolecular Engineering, Vanderbilt University School of Engineering, Nashville, TN 37232, USA; (M.R.); (I.T.)
| | - Tracy P. O’Brien
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (S.K.E.); (T.P.O.); (C.S.); (R.L.P.); (M.S.)
| | - Chiyo Shiota
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (S.K.E.); (T.P.O.); (C.S.); (R.L.P.); (M.S.)
| | - Richard L. Printz
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (S.K.E.); (T.P.O.); (C.S.); (R.L.P.); (M.S.)
| | - Jaques Reifman
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, MD 21702, USA;
| | - Masakazu Shiota
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (S.K.E.); (T.P.O.); (C.S.); (R.L.P.); (M.S.)
| | - Jamey D. Young
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (S.K.E.); (T.P.O.); (C.S.); (R.L.P.); (M.S.)
- Department of Chemical and Biomolecular Engineering, Vanderbilt University School of Engineering, Nashville, TN 37232, USA; (M.R.); (I.T.)
- Correspondence: (V.R.P.); (J.D.Y.); (A.W.); Tel.: +1-301-619-1976 (V.R.P.); +1-615-343-4253 (J.D.Y.); +1-301-619-1989 (A.W.); Fax: +301-619-1983 (A.W. & V.R.P.); +615-343-7951 (J.D.Y.)
| | - Anders Wallqvist
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, MD 21702, USA;
- Correspondence: (V.R.P.); (J.D.Y.); (A.W.); Tel.: +1-301-619-1976 (V.R.P.); +1-615-343-4253 (J.D.Y.); +1-301-619-1989 (A.W.); Fax: +301-619-1983 (A.W. & V.R.P.); +615-343-7951 (J.D.Y.)
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27
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Cheah YE, Xu Y, Sacco SA, Babele PK, Zheng AO, Johnson CH, Young JD. Systematic identification and elimination of flux bottlenecks in the aldehyde production pathway of Synechococcus elongatus PCC 7942. Metab Eng 2020; 60:56-65. [PMID: 32222320 PMCID: PMC7217728 DOI: 10.1016/j.ymben.2020.03.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/27/2020] [Accepted: 03/17/2020] [Indexed: 02/06/2023]
Abstract
Isotopically nonstationary metabolic flux analysis (INST-MFA) provides a versatile platform to quantitatively assess in vivo metabolic activities of autotrophic systems. By applying INST-MFA to recombinant aldehyde-producing cyanobacteria, we identified metabolic alterations that correlated with increased strain performance in order to guide rational metabolic engineering. We identified four reactions adjacent to the pyruvate node that varied significantly with increasing aldehyde production: pyruvate kinase (PK) and acetolactate synthase (ALS) fluxes were directly correlated with product formation, while pyruvate dehydrogenase (PDH) and phosphoenolpyruvate carboxylase (PPC) fluxes were inversely correlated. Overexpression of enzymes for PK or ALS did not result in further improvements to the previous best-performing strain, while downregulation of PDH expression (through antisense RNA expression) or PPC flux (through expression of the reverse reaction, phosphoenolpyruvate carboxykinase) provided significant improvements. These results illustrate the potential of INST-MFA to enable a systematic approach for iterative identification and removal of pathway bottlenecks in autotrophic host cells.
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Affiliation(s)
- Yi Ern Cheah
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Yao Xu
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Sarah A Sacco
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Piyoosh K Babele
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Amy O Zheng
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Carl Hirschie Johnson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA.
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Bosma KJ, Rahim M, Oeser JK, McGuinness OP, Young JD, O'Brien RM. G6PC2 confers protection against hypoglycemia upon ketogenic diet feeding and prolonged fasting. Mol Metab 2020; 41:101043. [PMID: 32569842 PMCID: PMC7369601 DOI: 10.1016/j.molmet.2020.101043] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/26/2020] [Accepted: 06/16/2020] [Indexed: 12/14/2022] Open
Abstract
Objective G6PC2 is predominantly expressed in pancreatic islet beta cells. G6PC2 hydrolyzes glucose-6-phosphate to glucose and inorganic phosphate, thereby creating a futile substrate cycle that opposes the action of glucokinase. This substrate cycle determines the sensitivity of glucose-stimulated insulin secretion to glucose and hence regulates fasting blood glucose (FBG) but not fasting plasma insulin (FPI) levels. Our objective was to explore the physiological benefit this cycle confers. Methods We investigated the response of wild type (WT) and G6pc2 knockout (KO) mice to changes in nutrition. Results Pancreatic G6pc2 expression was little changed by ketogenic diet feeding but was inhibited by 24 hr fasting and strongly induced by high fat feeding. When challenged with either a ketogenic diet or 24 hr fasting, blood glucose fell to 70 mg/dl or less in G6pc2 KO but not WT mice, suggesting that G6PC2 may have evolved, in part, to prevent hypoglycemia. Prolonged ketogenic diet feeding reduced the effect of G6pc2 deletion on FBG. The hyperglycemia associated with high fat feeding was partially blunted in G6pc2 KO mice, suggesting that under these conditions the presence of G6PC2 is detrimental. As expected, FPI changed but did not differ between WT and KO mice in response to fasting, ketogenic and high fat feeding. Conclusions Since elevated FBG levels are associated with increased risk for cardiovascular-associated mortality (CAM), these studies suggest that, while G6PC2 inhibitors would be useful for lowering FBG and the risk of CAM, partial inhibition will be important to avoid the risk of hypoglycemia. G6pc2 deletion lowers fasting blood glucose (FBG) in chow and high fat fed mice. Elevated FBG increases the risk of cardiovascular-associated mortality (CAM). G6pc2 deletion results in hypoglycemia in mice on a ketogenic diet. G6pc2 deletion results in hypoglycemia in mice following prolonged fasting. G6PC2 inhibitors may prevent CAM but increase risk of hypoglycemia.
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Affiliation(s)
- Karin J Bosma
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Mohsin Rahim
- Department of Chemical and Biomolecular Engineering, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - James K Oeser
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Owen P McGuinness
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jamey D Young
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Chemical and Biomolecular Engineering, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Richard M O'Brien
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
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29
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Bosma KJ, Rahim M, Singh K, Goleva SB, Wall ML, Xia J, Syring KE, Oeser JK, Poffenberger G, McGuinness OP, Means AL, Powers AC, Li WH, Davis LK, Young JD, O’Brien RM. Pancreatic islet beta cell-specific deletion of G6pc2 reduces fasting blood glucose. J Mol Endocrinol 2020; 64:235-248. [PMID: 32213654 PMCID: PMC7331801 DOI: 10.1530/jme-20-0031] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 03/13/2020] [Indexed: 12/25/2022]
Abstract
The G6PC1, G6PC2 and G6PC3 genes encode distinct glucose-6-phosphatase catalytic subunit (G6PC) isoforms. In mice, germline deletion of G6pc2 lowers fasting blood glucose (FBG) without affecting fasting plasma insulin (FPI) while, in isolated islets, glucose-6-phosphatase activity and glucose cycling are abolished and glucose-stimulated insulin secretion (GSIS) is enhanced at submaximal but not high glucose. These observations are all consistent with a model in which G6PC2 regulates the sensitivity of GSIS to glucose by opposing the action of glucokinase. G6PC2 is highly expressed in human and mouse islet beta cells however, various studies have shown trace G6PC2 expression in multiple tissues raising the possibility that G6PC2 also affects FBG through non-islet cell actions. Using real-time PCR we show here that expression of G6pc1 and/or G6pc3 are much greater than G6pc2 in peripheral tissues, whereas G6pc2 expression is much higher than G6pc3 in both pancreas and islets with G6pc1 expression not detected. In adult mice, beta cell-specific deletion of G6pc2 was sufficient to reduce FBG without changing FPI. In addition, electronic health record-derived phenotype analyses showed no association between G6PC2 expression and phenotypes clearly unrelated to islet function in humans. Finally, we show that germline G6pc2 deletion enhances glycolysis in mouse islets and that glucose cycling can also be detected in human islets. These observations are all consistent with a mechanism by which G6PC2 action in islets is sufficient to regulate the sensitivity of GSIS to glucose and hence influence FBG without affecting FPI.
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Affiliation(s)
- Karin J. Bosma
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Mohsin Rahim
- Department of Chemical and Biomolecular Engineering, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Kritika Singh
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Slavina B. Goleva
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Martha L. Wall
- Department of Chemical and Biomolecular Engineering, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Jing Xia
- Departments of Cell Biology and of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039
| | - Kristen E. Syring
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - James K. Oeser
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Greg Poffenberger
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Owen P. McGuinness
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Anna L. Means
- Department of Surgery, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Alvin C. Powers
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232
- VA Tennessee Valley Healthcare System, Nashville, TN 37232
| | - Wen-hong Li
- Departments of Cell Biology and of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-9039
| | - Lea K. Davis
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Jamey D. Young
- Department of Chemical and Biomolecular Engineering, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Richard M. O’Brien
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232
- To whom correspondence should be addressed: Department of Molecular Physiology and Biophysics, 8415 MRB IV, 2213 Garland Ave, Vanderbilt University Medical School, Nashville, TN 37232-0615,
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Kook S, Meng S, Rasmussen ML, Trenary I, Young JD, Gama V, Guttentag SH. Impaired Mitochondrial Respiration in Hermansky‐Pudlak Syndrome 1‐Defective Alveolar Type 2 Cells is Associated with Enhanced Mitochondrial Fission. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.04611] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Bednarski TK, Rahim M, Trenary I, Young JD. The effect of SERCA2 activation on liver metabolism during acute lipotoxicity
in vivo. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.06408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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32
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Hasenour CM, Kennedy AJ, Bednarski T, Trenary IA, Eudy BJ, da Silva RP, Boyd KL, Young JD. Vitamin E does not prevent Western diet-induced NASH progression and increases metabolic flux dysregulation in mice. J Lipid Res 2020; 61:707-721. [PMID: 32086244 DOI: 10.1194/jlr.ra119000183] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 02/18/2020] [Indexed: 12/13/2022] Open
Abstract
Fatty liver involves ectopic lipid accumulation and dysregulated hepatic oxidative metabolism, which can progress to a state of elevated inflammation and fibrosis referred to as nonalcoholic steatohepatitis (NASH). The factors that control progression from simple steatosis to NASH are not fully known. Here, we tested the hypothesis that dietary vitamin E (VitE) supplementation would prevent NASH progression and associated metabolic alterations induced by a Western diet (WD). Hyperphagic melanocortin-4 receptor-deficient (MC4R-/-) mice were fed chow, chow+VitE, WD, or WD+VitE starting at 8 or 20 weeks of age. All groups exhibited extensive hepatic steatosis by the end of the study (28 weeks of age). WD feeding exacerbated liver disease severity without inducing proportional changes in liver triglycerides. Eight weeks of WD accelerated liver pyruvate cycling, and 20 weeks of WD extensively upregulated liver glucose and oxidative metabolism assessed by 2H/13C flux analysis. VitE supplementation failed to reduce the histological features of NASH. Rather, WD+VitE increased the abundance and saturation of liver ceramides and accelerated metabolic flux dysregulation compared with 8 weeks of WD alone. In summary, VitE did not limit NASH pathogenesis in genetically obese mice, but instead increased some indicators of metabolic dysfunction.
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Affiliation(s)
- Clinton M Hasenour
- Departments of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN
| | - Arion J Kennedy
- Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN
| | - Tomasz Bednarski
- Departments of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN
| | - Irina A Trenary
- Departments of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN
| | - Brandon J Eudy
- Department of Food Science and Human Nutrition, University of Florida, Gainesville, FL
| | - Robin P da Silva
- Department of Food Science and Human Nutrition, University of Florida, Gainesville, FL
| | - Kelli L Boyd
- Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN
| | - Jamey D Young
- Departments of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN; Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN; Mouse Metabolic Phenotyping Center, Vanderbilt University, Nashville, TN. mailto:
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Biagi MJ, Schriever CA, Chiampas TD, Michienzi SM, Patel MC, Young JD, Badowski ME. Development of gynecomastia following initiation of bictegravir/emtricitabine/tenofovir alafenamide. Int J STD AIDS 2020; 31:380-382. [PMID: 32041480 DOI: 10.1177/0956462419895665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Bictegravir/emtricitabine/tenofovir alafenamide (BIC/FTC/TAF) is a recently approved single-tablet antiretroviral regimen and is recommended as a first-line agent. No cases of gynecomastia were reported in clinical trials. We report development of ultrasound-confirmed gynecomastia in a previously antiretroviral-naïve patient approximately two months after starting BIC/FTC/TAF, which resolved ten weeks after discontinuing bictegravir/emtricitabine/tenofovir alafenamide (BIC/FTC/TAF) based therapy.
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Affiliation(s)
- M J Biagi
- College of Pharmacy, University of Illinois at Chicago, Rockford, IL, USA
| | - C A Schriever
- College of Pharmacy, University of Illinois at Chicago, Rockford, IL, USA
| | - T D Chiampas
- Infectious Diseases Pharmacotherapy Section, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - S M Michienzi
- Infectious Diseases Pharmacotherapy Section, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - M C Patel
- Section of Infectious Diseases, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - J D Young
- Division of Infectious Diseases, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - M E Badowski
- Infectious Diseases Pharmacotherapy Section, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
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34
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Pannala VR, Vinnakota KC, Estes SK, Trenary I, OˈBrien TP, Printz RL, Papin JA, Reifman J, Oyama T, Shiota M, Young JD, Wallqvist A. Genome-Scale Model-Based Identification of Metabolite Indicators for Early Detection of Kidney Toxicity. Toxicol Sci 2020; 173:293-312. [PMID: 31722432 PMCID: PMC8000070 DOI: 10.1093/toxsci/kfz228] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Identifying early indicators of toxicant-induced organ damage is critical to provide effective treatment. To discover such indicators and the underlying mechanisms of toxicity, we used gentamicin as an exemplar kidney toxicant and performed systematic perturbation studies in Sprague Dawley rats. We obtained high-throughput data 7 and 13 h after administration of a single dose of gentamicin (0.5 g/kg) and identified global changes in genes in the liver and kidneys, metabolites in the plasma and urine, and absolute fluxes in central carbon metabolism. We used these measured changes in genes in the liver and kidney as constraints to a rat multitissue genome-scale metabolic network model to investigate the mechanism of gentamicin-induced kidney toxicity and identify metabolites associated with changes in tissue gene expression. Our experimental analysis revealed that gentamicin-induced metabolic perturbations could be detected as early as 7 h postexposure. Our integrated systems-level analyses suggest that changes in kidney gene expression drive most of the significant metabolite alterations in the urine. The analyses thus allowed us to identify several significantly enriched injury-specific pathways in the kidney underlying gentamicin-induced toxicity, as well as metabolites in these pathways that could serve as potential early indicators of kidney damage.
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Affiliation(s)
- Venkat R Pannala
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, Maryland 21702
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland 20817
| | - Kalyan C Vinnakota
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, Maryland 21702
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland 20817
| | - Shanea K Estes
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Irina Trenary
- Department of Chemical and Biomolecular Engineering, Vanderbilt University School of Engineering, Nashville, Tennessee
| | - Tracy P OˈBrien
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Richard L Printz
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jason A Papin
- Department of Biomedical Engineering, University of Virginia, Charlottesville, Virginia
| | - Jaques Reifman
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, Maryland 21702
| | - Tatsuya Oyama
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, Maryland 21702
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland 20817
| | - Masakazu Shiota
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jamey D Young
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee
- Department of Chemical and Biomolecular Engineering, Vanderbilt University School of Engineering, Nashville, Tennessee
| | - Anders Wallqvist
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Fort Detrick, Maryland 21702
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Deja S, Fu X, Fletcher JA, Kucejova B, Browning JD, Young JD, Burgess SC. Simultaneous tracers and a unified model of positional and mass isotopomers for quantification of metabolic flux in liver. Metab Eng 2019; 59:1-14. [PMID: 31891762 DOI: 10.1016/j.ymben.2019.12.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 12/12/2019] [Accepted: 12/21/2019] [Indexed: 12/23/2022]
Abstract
Computational models based on the metabolism of stable isotope tracers can yield valuable insight into the metabolic basis of disease. The complexity of these models is limited by the number of tracers and the ability to characterize tracer labeling in downstream metabolites. NMR spectroscopy is ideal for multiple tracer experiments since it precisely detects the position of tracer nuclei in molecules, but it lacks sensitivity for detecting low-concentration metabolites. GC-MS detects stable isotope mass enrichment in low-concentration metabolites, but lacks nuclei and positional specificity. We performed liver perfusions and in vivo infusions of 2H and 13C tracers, yielding complex glucose isotopomers that were assigned by NMR and fit to a newly developed metabolic model. Fluxes regressed from 2H and 13C NMR positional isotopomer enrichments served to validate GC-MS-based flux estimates obtained from the same experimental samples. NMR-derived fluxes were largely recapitulated by modeling the mass isotopomer distributions of six glucose fragment ions measured by GC-MS. Modest differences related to limited fragmentation coverage of glucose C1-C3 were identified, but fluxes such as gluconeogenesis, glycogenolysis, cataplerosis and TCA cycle flux were tightly correlated between the methods. Most importantly, modeling of GC-MS data could assign fluxes in primary mouse hepatocytes, an experiment that is impractical by 2H or 13C NMR.
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Affiliation(s)
- Stanislaw Deja
- Center for Human Nutrition, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Xiaorong Fu
- Center for Human Nutrition, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Justin A Fletcher
- Center for Human Nutrition, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Blanka Kucejova
- Center for Human Nutrition, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jeffrey D Browning
- Department of Clinical Nutrition, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, 37235, USA.
| | - Shawn C Burgess
- Center for Human Nutrition, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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Allen DK, Young JD. Tracing metabolic flux through time and space with isotope labeling experiments. Curr Opin Biotechnol 2019; 64:92-100. [PMID: 31864070 PMCID: PMC7302994 DOI: 10.1016/j.copbio.2019.11.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 11/02/2019] [Accepted: 11/04/2019] [Indexed: 12/11/2022]
Abstract
Metabolism is dynamic and must function in context-specific ways to adjust to changes in the surrounding cellular and ecological environment. When isotopic tracers are used, metabolite flow (i.e. metabolic flux) can be quantified through biochemical networks to assess metabolic pathway operation. The cellular activities considered across multiple tissues and organs result in the observed phenotype and can be analyzed to discover emergent, whole-system properties of biology and elucidate misconceptions about network operation. However, temporal and spatial challenges remain significant hurdles and require novel approaches and creative solutions. We survey current investigations in higher plant and animal systems focused on dynamic isotope labeling experiments, spatially resolved measurement strategies, and observations from re-analysis of our own studies that suggest prospects for future work. Related discoveries will be necessary to push the frontier of our understanding of metabolism to suggest novel solutions to cure disease and feed a growing future world population.
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Affiliation(s)
- Doug K Allen
- United States Department of Agriculture-Agricultural Research Service, Plant Genetics Research Unit, 975 North Warson Road, St. Louis, MO 63132, United States; Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, United States.
| | - Jamey D Young
- Department of Chemical & Biomolecular Engineering, Vanderbilt University, PMB 351604, 2301 Vanderbilt Place, Nashville, TN 37235, United States; Department of Molecular Physiology & Biophysics, Vanderbilt University, PMB 351604, 2301 Vanderbilt Place, Nashville, TN 37235, United States.
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Babele PK, Young JD. Applications of stable isotope-based metabolomics and fluxomics toward synthetic biology of cyanobacteria. Wiley Interdiscip Rev Syst Biol Med 2019; 12:e1472. [PMID: 31816180 DOI: 10.1002/wsbm.1472] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 10/24/2019] [Accepted: 11/16/2019] [Indexed: 12/17/2022]
Abstract
Unique features of cyanobacteria (e.g., photosynthesis and nitrogen fixation) make them potential candidates for production of biofuels and other value-added biochemicals. As prokaryotes, they can be readily engineered using synthetic and systems biology tools. Metabolic engineering of cyanobacteria for the synthesis of desired compounds requires in-depth knowledge of central carbon and nitrogen metabolism, pathway fluxes, and their regulation. Metabolomics and fluxomics offer the comprehensive analysis of metabolism by directly characterizing the biochemical activities of cells. This information is acquired by measuring the abundance of key metabolites and their rates of interconversion, which can be achieved by labeling cells with stable isotopes, quantifying metabolite pool sizes and isotope incorporation by gas chromatography/liquid chromatography-mass spectrometry GC/LC-MS or nuclear magnetic resonance (NMR), and mathematical modeling to estimate in vivo metabolic fluxes. Herein, we review progress that has been made to adapt metabolomics and fluxomics tools to examine model cyanobacterial species. We summarize the application of metabolic flux analysis (MFA) strategies to identify metabolic bottlenecks that can be targeted to boost cell growth, improve stress tolerance, or enhance biochemical production in cyanobacteria. Despite the advances in metabolomics, fluxomics, and other synthetic and systems biology tools during the past years, further efforts are required to increase our understanding of cyanobacterial metabolism in order to create efficient photosynthetic hosts for the production of value-added compounds. This article is categorized under: Laboratory Methods and Technologies > Metabolomics Biological Mechanisms > Metabolism Analytical and Computational Methods > Analytical Methods.
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Affiliation(s)
- Piyoosh Kumar Babele
- Chemical & Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee
| | - Jamey D Young
- Chemical & Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee.,Molecular Physiology & Biophysics, Vanderbilt University, Nashville, Tennessee
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Harford M, Catherall J, Gerry S, Young JD, Watkinson P. Availability and performance of image-based, non-contact methods of monitoring heart rate, blood pressure, respiratory rate, and oxygen saturation: a systematic review. Physiol Meas 2019; 40:06TR01. [PMID: 31051494 DOI: 10.1088/1361-6579/ab1f1d] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Over the last 15 years, developments in camera technology have coincided with increased availability and affordability. This has led to an increasing interest in using these technologies in healthcare settings. Image-based monitoring methods potentially allow multiple vital signs to be measured concurrently using a non-contact sensor. We have undertaken a systematic review of the current availability and performance of these monitoring methods. APPROACH A multiple database search was conducted using MEDLINE, Embase, CINAHL, Cochrane Library, OpenGrey, IEEE Xplore Library and ACM Digital Library to July 2018. We included studies comparing image-based heart rate, respiratory rate, oxygen saturation and blood pressure monitoring methods against one or more validated reference device(s). Each included study was assessed using the modified GRRAS criteria for reporting bias. MAIN RESULTS Of 30 279 identified studies, 161 were included in the final analysis. Twenty studies (20/161, 12%) were carried out on patients in clinical settings, while the remainder were conducted in academic settings using healthy volunteer populations. The 18-40 age group was best represented across the identified studies. One hundred and twenty studies (120/161, 75%) estimated heart rate, followed by 62 studies (62/161, 39%) estimating respiratory rate. Fewer studies focused on oxygen saturation (11/161, 7%) or blood pressure (6/161, 4%) estimation. Fifty-one heart rate studies (51/120, 43%) and 24 respiratory rate studies (24/62, 39%) used Bland-Altman analysis to report their results. Of the heart rate studies, 28 studies (28/51, 55%) showed agreement within industry standards of [Formula: see text]5 beats per minute. Only two studies achieved this within clinical settings. Of the respiratory rate studies, 13 studies (13/24, 54%) showed agreement within industry standards of [Formula: see text]3 breaths per minute, but only one study achieved this in a clinical setting. Statistical analysis was heterogeneous across studies with frequent inappropriate use of correlation. The majority of studies (99/161, 61%) monitored subjects for under 5 min. Three studies (3/161, 2%) monitored subjects for over 60 min, all of which were conducted in hospital settings. SIGNIFICANCE Heart rate and respiratory rate monitoring using video images is currently possible and performs within clinically acceptable limits under experimental conditions. Camera-derived estimates were less accurate in the proportion of studies conducted in clinical settings. We would encourage thorough reporting of the population studied, details of clinically relevant aspects of methodology, and the use of appropriate statistical methods in future studies. Systematic review registration: PROSPERO CRD42016029167 Protocol: https://systematicreviewsjournal.biomedcentral.com/articles/10.1186/s13643-017-0615-3.
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Affiliation(s)
- M Harford
- Kadoorie Centre for Critical Care Research and Education, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
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Abstract
Excessive noise in hospitals adversely affects patients' sleep and recovery, causes stress and fatigue in staff and hampers communication. The World Health Organization suggests sound levels should be limited to 35 decibels. This is probably unachievable in intensive care units, but some reduction from current levels should be possible. A preliminary step would be to identify principal sources of noise. As part of a larger project investigating techniques to reduce environmental noise, we installed a microphone array system in one with four beds in an adult general intensive care unit. This continuously measured locations and sound pressure levels of noise sources. This report summarises results recorded over one year. Data were collected between 7 April 2017 and 16 April 2018 inclusive. Data for a whole day were available for 248 days. The sound location system revealed that the majority of loud sounds originated from extremely limited areas, very close to patients' ears. This proximity maximises the adverse effects of high environmental noise levels for patients. Some of this was likely to be appropriate communication between the patient, their caring staff and visitors. However, a significant proportion of loud sounds may originate from equipment alarms which are sited at the bedside. A redesign of the intensive care unit environment to move alarm sounds away from the bed-side might significantly reduce the environmental noise burden to patients.
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Affiliation(s)
- J L Darbyshire
- Nuffield Department of Clinical Neurosciences, University of Oxford, UK
| | | | - J Cheer
- Institute of Sound and Vibration Research, Southampton University, Southampton, UK
| | - F M Fazi
- Institute of Sound and Vibration Research, Southampton University, Southampton, UK
| | - J D Young
- Nuffield Department of Clinical Neurosciences, University of Oxford, UK
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40
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Pannala VR, Vinnakota KC, Rawls KD, Estes SK, O'Brien TP, Printz RL, Papin JA, Reifman J, Shiota M, Young JD, Wallqvist A. Mechanistic identification of biofluid metabolite changes as markers of acetaminophen-induced liver toxicity in rats. Toxicol Appl Pharmacol 2019; 372:19-32. [PMID: 30974156 DOI: 10.1016/j.taap.2019.04.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/22/2019] [Accepted: 04/05/2019] [Indexed: 12/12/2022]
Abstract
Acetaminophen (APAP) is the most commonly used analgesic and antipyretic drug in the world. Yet, it poses a major risk of liver injury when taken in excess of the therapeutic dose. Current clinical markers do not detect the early onset of liver injury associated with excess APAP-information that is vital to reverse injury progression through available therapeutic interventions. Hence, several studies have used transcriptomics, proteomics, and metabolomics technologies, both independently and in combination, in an attempt to discover potential early markers of liver injury. However, the casual relationship between these observations and their relation to the APAP mechanism of liver toxicity are not clearly understood. Here, we used Sprague-Dawley rats orally gavaged with a single dose of 2 g/kg of APAP to collect tissue samples from the liver and kidney for transcriptomic analysis and plasma and urine samples for metabolomic analysis. We developed and used a multi-tissue, metabolism-based modeling approach to integrate these data, characterize the effect of excess APAP levels on liver metabolism, and identify a panel of plasma and urine metabolites that are associated with APAP-induced liver toxicity. Our analyses, which indicated that pathways involved in nucleotide-, lipid-, and amino acid-related metabolism in the liver were most strongly affected within 10 h following APAP treatment, identified a list of potential metabolites in these pathways that could serve as plausible markers of APAP-induced liver injury. Our approach identifies toxicant-induced changes in endogenous metabolism, is applicable to other toxicants based on transcriptomic data, and provides a mechanistic framework for interpreting metabolite alterations.
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Affiliation(s)
- Venkat R Pannala
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA; Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD 21702, USA.
| | - Kalyan C Vinnakota
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD 20817, USA; Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD 21702, USA
| | - Kristopher D Rawls
- Department of Biomedical Engineering, University of Virginia, Box 800759, Health System, Charlottesville, Virginia 22908, USA
| | - Shanea K Estes
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Tracy P O'Brien
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Richard L Printz
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jason A Papin
- Department of Biomedical Engineering, University of Virginia, Box 800759, Health System, Charlottesville, Virginia 22908, USA
| | - Jaques Reifman
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD 21702, USA
| | - Masakazu Shiota
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jamey D Young
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Chemical and Biomolecular Engineering, Vanderbilt University School of Engineering, Nashville, TN 37232, USA.
| | - Anders Wallqvist
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD 21702, USA.
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41
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Vinnakota KC, Pannala VR, Wall ML, Rahim M, Estes SK, Trenary I, O'Brien TP, Printz RL, Reifman J, Shiota M, Young JD, Wallqvist A. Network Modeling of Liver Metabolism to Predict Plasma Metabolite Changes During Short-Term Fasting in the Laboratory Rat. Front Physiol 2019; 10:161. [PMID: 30881311 PMCID: PMC6405515 DOI: 10.3389/fphys.2019.00161] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 02/11/2019] [Indexed: 12/20/2022] Open
Abstract
The liver—a central metabolic organ that integrates whole-body metabolism to maintain glucose and fatty-acid regulation, and detoxify ammonia—is susceptible to injuries induced by drugs and toxic substances. Although plasma metabolite profiles are increasingly investigated for their potential to detect liver injury earlier than current clinical markers, their utility may be compromised because such profiles are affected by the nutritional state and the physiological state of the animal, and by contributions from extrahepatic sources. To tease apart the contributions of liver and non-liver sources to alterations in plasma metabolite profiles, here we sought to computationally isolate the plasma metabolite changes originating in the liver during short-term fasting. We used a constraint-based metabolic modeling approach to integrate central carbon fluxes measured in our study, and physiological flux boundary conditions gathered from the literature, into a genome-scale model of rat liver metabolism. We then measured plasma metabolite profiles in rats fasted for 5–7 or 10–13 h to test our model predictions. Our computational model accounted for two-thirds of the observed directions of change (an increase or decrease) in plasma metabolites, indicating their origin in the liver. Specifically, our work suggests that changes in plasma lipid metabolites, which are reliably predicted by our liver metabolism model, are key features of short-term fasting. Our approach provides a mechanistic model for identifying plasma metabolite changes originating in the liver.
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Affiliation(s)
- Kalyan C Vinnakota
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States.,Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, United States Army Medical Research and Materiel Command, Fort Detrick, MD, United States
| | - Venkat R Pannala
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD, United States.,Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, United States Army Medical Research and Materiel Command, Fort Detrick, MD, United States
| | - Martha L Wall
- Department of Chemical and Biomolecular Engineering, Vanderbilt University School of Engineering, Nashville, TN, United States
| | - Mohsin Rahim
- Department of Chemical and Biomolecular Engineering, Vanderbilt University School of Engineering, Nashville, TN, United States
| | - Shanea K Estes
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Irina Trenary
- Department of Chemical and Biomolecular Engineering, Vanderbilt University School of Engineering, Nashville, TN, United States
| | - Tracy P O'Brien
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Richard L Printz
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Jaques Reifman
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, United States Army Medical Research and Materiel Command, Fort Detrick, MD, United States
| | - Masakazu Shiota
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, Vanderbilt University School of Engineering, Nashville, TN, United States.,Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Anders Wallqvist
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, United States Army Medical Research and Materiel Command, Fort Detrick, MD, United States
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42
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Egnatchik RA, Leamy AK, Sacco SA, Cheah YE, Shiota M, Young JD. Glutamate-oxaloacetate transaminase activity promotes palmitate lipotoxicity in rat hepatocytes by enhancing anaplerosis and citric acid cycle flux. J Biol Chem 2018; 294:3081-3090. [PMID: 30563841 DOI: 10.1074/jbc.ra118.004869] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 12/04/2018] [Indexed: 12/17/2022] Open
Abstract
Hepatocyte lipotoxicity is characterized by aberrant mitochondrial metabolism, which predisposes cells to oxidative stress and apoptosis. Previously, we reported that translocation of calcium from the endoplasmic reticulum to mitochondria of palmitate-treated hepatocytes activates anaplerotic flux from glutamine to α-ketoglutarate (αKG), which subsequently enters the citric acid cycle (CAC) for oxidation. We hypothesized that increased glutamine anaplerosis fuels elevations in CAC flux and oxidative stress following palmitate treatment. To test this hypothesis, primary rat hepatocytes or immortalized H4IIEC3 rat hepatoma cells were treated with lipotoxic levels of palmitate while modulating anaplerotic pathways leading to αKG. We found that culture media supplemented with glutamine, glutamate, or dimethyl-αKG increased palmitate lipotoxicity compared with media that lacked these anaplerotic substrates. Knockdown of glutamate-oxaloacetate transaminase activity significantly reduced the lipotoxic effects of palmitate, whereas knockdown of glutamate dehydrogenase (Glud1) had no effect on palmitate lipotoxicity. 13C flux analysis of H4IIEC3 cells co-treated with palmitate and the pan-transaminase inhibitor aminooxyacetic acid confirmed that reductions in lipotoxic markers were associated with decreases in anaplerosis, CAC flux, and oxygen consumption. Taken together, these results demonstrate that lipotoxic palmitate treatments enhance anaplerosis in cultured rat hepatocytes, causing a shift to aberrant transaminase metabolism that fuels CAC dysregulation and oxidative stress.
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Affiliation(s)
| | | | | | | | - Masakazu Shiota
- Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37235
| | - Jamey D Young
- From Chemical and Biomolecular Engineering and .,Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37235
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43
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Rotman L, Luo X, Thompson A, Mackesy-Amiti ME, Young LR, Young JD. Risk of neurosyphilis in HIV-infected persons with syphilis lacking signs or symptoms of central nervous system infection. HIV Med 2018; 20:27-32. [PMID: 30402918 DOI: 10.1111/hiv.12677] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2018] [Indexed: 11/29/2022]
Abstract
OBJECTIVES People living with HIV (PLWH) are at increased risk of asymptomatic neurosyphilis; thus, it has been common practice to perform a lumbar puncture (LP) in all PLWH presenting with syphilis regardless of stage, signs or symptoms. However, this practice varies widely among clinicians. Our objective was to elucidate the number of LPs required to diagnose a single case of asymptomatic neurosyphilis. METHODS We performed an electronic health record (EHR) review of PLWH who were diagnosed with syphilis of any stage over a 10-year period. EHRs were reviewed to determine the number of subjects who had an LP performed, what proportion had neurological signs or symptoms, and whether a diagnosis of neurosyphilis was made at presentation or follow-up. RESULTS In 261 separate episodes of syphilis in 230 subjects, we found the major risk factors for asymptomatic neurosyphilis to be low CD4 T-cell count (P = 0.0007), high rapid plasma reagin (RPR) titre (P = 0.019) and lack of HIV virological suppression (P = 0.003). The majority of our subjects (78%) with neurosyphilis presented with central nervous system (CNS) symptoms. We estimate, if standard practice is to perform LP in all patients, that the number needed to test (NNTT) = 38. CONCLUSIONS This large number of potentially unnecessary LPs, along with heterogeneity of presentation, and the never-nil risk of asymptomatic neurosyphilis should be incorporated into clinical decision-making. The majority of PLWH presenting with a serological diagnosis of syphilis, but no neurological signs or symptoms, do not necessarily require an LP for an evaluation of asymptomatic neurosyphilis.
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Affiliation(s)
- L Rotman
- Department of Internal Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - X Luo
- Department of Internal Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - A Thompson
- Division of Infectious Diseases, Immunology & International Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - M E Mackesy-Amiti
- School of Public Health, University of Illinois at Chicago, Chicago, IL, USA
| | - L R Young
- Jesse Brown Veterans Affairs Medical Center, Chicago, IL, USA
| | - J D Young
- Department of Internal Medicine, University of Illinois at Chicago, Chicago, IL, USA.,Division of Infectious Diseases, Immunology & International Medicine, University of Illinois at Chicago, Chicago, IL, USA.,Jesse Brown Veterans Affairs Medical Center, Chicago, IL, USA
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44
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Gerth AMJ, Hatch RA, Young JD, Watkinson PJ. Changes in health-related quality of life after discharge from an intensive care unit: a systematic review. Anaesthesia 2018; 74:100-108. [PMID: 30291744 PMCID: PMC6586053 DOI: 10.1111/anae.14444] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2018] [Indexed: 12/26/2022]
Abstract
Quality of life after critical illness is becoming increasingly important as survival improves. Various measures have been used to study the quality of life of patients discharged from intensive care. We systematically reviewed validated measures of quality of life and their results. We searched PubMed, CENTRAL, CINAHL, Web of Science and Open Grey for studies of quality of life, measured after discharge from intensive care. We categorised studied populations as: general; restricted to level‐3 care or critical care beyond 5 days; and septic patients. We included quality of life measured at any time after hospital discharge. We identified 48 studies. Thirty‐one studies used the Medical Outcomes Study 36‐Item Short Form Health Survey (SF‐36) and 19 used the EuroQol‐5D (EQ‐5D); eight used both and nine used alternative validated measures. Follow‐up rates ranged from 26–100%. Quality of life after critical care was worse than for age‐ and sex‐matched populations. Quality of life improved for one year after hospital discharge. The aspects of life that improved most were physical function, physical role, vitality and social function. However, these domains were also the least likely to recover to population norms as they were more profoundly affected by critical illness.
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Affiliation(s)
- A M J Gerth
- Critical Care Research Group, Nuffield Department of Clinical Neurosciences, University of Oxford, UK
| | - R A Hatch
- Critical Care Research Group, Nuffield Department of Clinical Neurosciences, University of Oxford, UK
| | - J D Young
- Critical Care Research Group, Nuffield Department of Clinical Neurosciences, University of Oxford, UK
| | - P J Watkinson
- Critical Care Research Group, Nuffield Department of Clinical Neurosciences, University of Oxford, UK
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45
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Pannala VR, Wall ML, Estes SK, Trenary I, O'Brien TP, Printz RL, Vinnakota KC, Reifman J, Shiota M, Young JD, Wallqvist A. Metabolic network-based predictions of toxicant-induced metabolite changes in the laboratory rat. Sci Rep 2018; 8:11678. [PMID: 30076366 PMCID: PMC6076258 DOI: 10.1038/s41598-018-30149-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 07/23/2018] [Indexed: 12/11/2022] Open
Abstract
In order to provide timely treatment for organ damage initiated by therapeutic drugs or exposure to environmental toxicants, we first need to identify markers that provide an early diagnosis of potential adverse effects before permanent damage occurs. Specifically, the liver, as a primary organ prone to toxicants-induced injuries, lacks diagnostic markers that are specific and sensitive to the early onset of injury. Here, to identify plasma metabolites as markers of early toxicant-induced injury, we used a constraint-based modeling approach with a genome-scale network reconstruction of rat liver metabolism to incorporate perturbations of gene expression induced by acetaminophen, a known hepatotoxicant. A comparison of the model results against the global metabolic profiling data revealed that our approach satisfactorily predicted altered plasma metabolite levels as early as 5 h after exposure to 2 g/kg of acetaminophen, and that 10 h after treatment the predictions significantly improved when we integrated measured central carbon fluxes. Our approach is solely driven by gene expression and physiological boundary conditions, and does not rely on any toxicant-specific model component. As such, it provides a mechanistic model that serves as a first step in identifying a list of putative plasma metabolites that could change due to toxicant-induced perturbations.
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Affiliation(s)
- Venkat R Pannala
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD, 21702, USA.
| | - Martha L Wall
- Department of Chemical and Biomolecular Engineering, Vanderbilt University School of Engineering, Nashville, TN, 37232, USA
| | - Shanea K Estes
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Irina Trenary
- Department of Chemical and Biomolecular Engineering, Vanderbilt University School of Engineering, Nashville, TN, 37232, USA
| | - Tracy P O'Brien
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Richard L Printz
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Kalyan C Vinnakota
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD, 21702, USA
| | - Jaques Reifman
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD, 21702, USA
| | - Masakazu Shiota
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Jamey D Young
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA. .,Department of Chemical and Biomolecular Engineering, Vanderbilt University School of Engineering, Nashville, TN, 37232, USA.
| | - Anders Wallqvist
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, MD, 21702, USA.
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46
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Rodrigues NDN, Staniforth M, Young JD, Peperstraete Y, Cole-Filipiak NC, Gord JR, Walsh PS, Hewett DM, Zwier TS, Stavros VG. Towards elucidating the photochemistry of the sunscreen filter ethyl ferulate using time-resolved gas-phase spectroscopy. Faraday Discuss 2018; 194:709-729. [PMID: 27711798 DOI: 10.1039/c6fd00079g] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ultrafast time-resolved ion yield (TR-IY) and velocity map imaging spectroscopies are employed to reveal the relaxation dynamics after photoexcitation in ethyl 4-hydroxy-3-methoxycinnamate (ethyl ferulate, EF), an active ingredient in commercially available sunscreens. In keeping with a bottom-up strategy, the building blocks of EF, 2-methoxy-4-vinylphenol (MVP) and 4-hydroxy-3-methoxycinnamyl alcohol (coniferyl alcohol, ConA), were also studied to assist in our understanding of the dynamics of EF as we build up in molecular complexity. In contrast to the excited state dynamics of MVP and ConA, which are described by a single time constant (>900 ps), the dynamics of EF are described by three time constants (15 ± 4 ps, 148 ± 47 ps, and >900 ps). A mechanism is proposed involving internal conversion (IC) between the initially excited S1(11ππ*) and S2(11nπ*) states followed by intramolecular vibrational redistribution (IVR) on both states, in competition with intersystem crossing onto neighbouring triplet states (15 ± 4 ps). IVR and IC within the triplet manifold then ensues (148 ± 47 ps) to populate a low-lying triplet state (>900 ps). Importantly, the fluorescence spectrum of EF at the S1 origin, along with the associated lifetime (6.9 ± 0.1 ns), suggests that population is trapped, during initial IVR, on the S1(11ππ*) state. This serves to demonstrate the complex, competing dynamics in this sunscreen filter molecule.
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Affiliation(s)
- N D N Rodrigues
- University of Warwick, Department of Chemistry, CV4 7AL, Coventry, UK.
| | - M Staniforth
- University of Warwick, Department of Chemistry, CV4 7AL, Coventry, UK.
| | - J D Young
- University of Warwick, Department of Chemistry, CV4 7AL, Coventry, UK.
| | - Y Peperstraete
- University of Warwick, Department of Chemistry, CV4 7AL, Coventry, UK. and ENS de Cachan, 61 Avenue du Président Wilson, 94230, Cachan, France
| | - N C Cole-Filipiak
- University of Warwick, Department of Chemistry, CV4 7AL, Coventry, UK.
| | - J R Gord
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA
| | - P S Walsh
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA
| | - D M Hewett
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA
| | - T S Zwier
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA
| | - V G Stavros
- University of Warwick, Department of Chemistry, CV4 7AL, Coventry, UK.
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47
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Fensterheim BA, Young JD, Luan L, Kleinbard RR, Stothers CL, Patil NK, McAtee-Pereira AG, Guo Y, Trenary I, Hernandez A, Fults JB, Williams DL, Sherwood ER, Bohannon JK. The TLR4 Agonist Monophosphoryl Lipid A Drives Broad Resistance to Infection via Dynamic Reprogramming of Macrophage Metabolism. J Immunol 2018; 200:3777-3789. [PMID: 29686054 PMCID: PMC5964009 DOI: 10.4049/jimmunol.1800085] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 03/28/2018] [Indexed: 12/21/2022]
Abstract
Monophosphoryl lipid A (MPLA) is a clinically used TLR4 agonist that has been found to drive nonspecific resistance to infection for up to 2 wk. However, the molecular mechanisms conferring protection are not well understood. In this study, we found that MPLA prompts resistance to infection, in part, by inducing a sustained and dynamic metabolic program in macrophages that supports improved pathogen clearance. Mice treated with MPLA had enhanced resistance to infection with Staphylococcus aureus and Candida albicans that was associated with augmented microbial clearance and organ protection. Tissue macrophages, which exhibited augmented phagocytosis and respiratory burst after MPLA treatment, were required for the beneficial effects of MPLA. Further analysis of the macrophage phenotype revealed that early TLR4-driven aerobic glycolysis was later coupled with mitochondrial biogenesis, enhanced malate shuttling, and increased mitochondrial ATP production. This metabolic program was initiated by overlapping and redundant contributions of MyD88- and TRIF-dependent signaling pathways as well as downstream mTOR activation. Blockade of mTOR signaling inhibited the development of the metabolic and functional macrophage phenotype and ablated MPLA-induced resistance to infection in vivo. Our findings reveal that MPLA drives macrophage metabolic reprogramming that evolves over a period of days to support a macrophage phenotype highly effective at mediating microbe clearance and that this results in nonspecific resistance to infection.
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Affiliation(s)
- Benjamin A Fensterheim
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN 37212
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37212
| | - Liming Luan
- Department of Anesthesiology, Vanderbilt University Medical Center, Nashville, TN 37232; and
| | - Ruby R Kleinbard
- Department of Anesthesiology, Vanderbilt University Medical Center, Nashville, TN 37232; and
| | - Cody L Stothers
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN 37212
| | - Naeem K Patil
- Department of Anesthesiology, Vanderbilt University Medical Center, Nashville, TN 37232; and
| | | | - Yin Guo
- Department of Anesthesiology, Vanderbilt University Medical Center, Nashville, TN 37232; and
| | - Irina Trenary
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37235
| | - Antonio Hernandez
- Department of Anesthesiology, Vanderbilt University Medical Center, Nashville, TN 37232; and
| | - Jessica B Fults
- Department of Anesthesiology, Vanderbilt University Medical Center, Nashville, TN 37232; and
| | - David L Williams
- Department of Surgery, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614
| | - Edward R Sherwood
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN 37212
- Department of Anesthesiology, Vanderbilt University Medical Center, Nashville, TN 37232; and
| | - Julia K Bohannon
- Department of Anesthesiology, Vanderbilt University Medical Center, Nashville, TN 37232; and
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48
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Ji X, Qian J, Rahman SMJ, Siska PJ, Zou Y, Harris BK, Hoeksema MD, Trenary IA, Heidi C, Eisenberg R, Rathmell JC, Young JD, Massion PP. xCT (SLC7A11)-mediated metabolic reprogramming promotes non-small cell lung cancer progression. Oncogene 2018; 37:5007-5019. [PMID: 29789716 PMCID: PMC6127081 DOI: 10.1038/s41388-018-0307-z] [Citation(s) in RCA: 189] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 03/23/2018] [Accepted: 04/13/2018] [Indexed: 01/10/2023]
Abstract
Many tumors increase uptake and dependence on glucose, cystine or glutamine. These basic observations on cancer cell metabolism have opened multiple new diagnostic and therapeutic avenues in cancer research. Recent studies demonstrated that smoking could induce the expression of xCT (SLC7A11) in oral cancer cells, suggesting that overexpression of xCT may support lung tumor progression. We hypothesized that overexpression of xCT occurs in lung cancer cells to satisfy the metabolic requirements for growth and survival. Our results demonstrated that 1) xCT was highly expressed at the cytoplasmic membrane in non-small cell lung cancer (NSCLC), 2) the expression of xCT was correlated with advanced stage and predicted a worse 5-year survival, 3) targeting xCT transport activity in xCT overexpressing NSCLC cells with sulfasalazine decreased cell proliferation and invasion in vitro and in vivo and 4) increased dependence on glutamine was observed in xCT overexpressed normal airway epithelial cells. These results suggested that xCT regulate metabolic requirements during lung cancer progression and be a potential therapeutic target in NSCLC.
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Affiliation(s)
- Xiangming Ji
- Cancer Early Detection and Prevention Initiative, Vanderbilt Ingram Cancer Center, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA.,Department of Nutrition, Byrdine F. Lewis School of Nursing and Health Professions, Georgia State University, Atlanta, 30302, USA
| | - Jun Qian
- Cancer Early Detection and Prevention Initiative, Vanderbilt Ingram Cancer Center, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - S M Jamshedur Rahman
- Cancer Early Detection and Prevention Initiative, Vanderbilt Ingram Cancer Center, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Peter J Siska
- Department of Internal Medicine III, University Hospital Regensburg, 93053, Regensburg, Germany
| | - Yong Zou
- Cancer Early Detection and Prevention Initiative, Vanderbilt Ingram Cancer Center, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Bradford K Harris
- Cancer Early Detection and Prevention Initiative, Vanderbilt Ingram Cancer Center, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Megan D Hoeksema
- Cancer Early Detection and Prevention Initiative, Vanderbilt Ingram Cancer Center, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Irina A Trenary
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, USA
| | - Chen Heidi
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Rosana Eisenberg
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, USA
| | - Jeffrey C Rathmell
- Department of Internal Medicine III, University Hospital Regensburg, 93053, Regensburg, Germany
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, USA
| | - Pierre P Massion
- Cancer Early Detection and Prevention Initiative, Vanderbilt Ingram Cancer Center, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA. .,Veterans Affairs, Tennessee Valley Healthcare System, Nashville, TN, 37212, USA.
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49
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Abstract
Typically, 13C flux analysis relies on assumptions of both metabolic and isotopic steady state. If metabolism is steady but isotope labeling is not allowed to fully equilibrate, isotopically nonstationary metabolic flux analysis (INST-MFA) can be used to estimate fluxes. This requires solution of differential equations that describe the time-dependent labeling of network metabolites, while iteratively adjusting the flux and pool size parameters to match the transient labeling measurements. INST-MFA holds a number of unique advantages over approaches that rely solely upon steady-state isotope enrichments. First, INST-MFA can be applied to estimate fluxes in autotrophic systems, which consume only single-carbon substrates. Second, INST-MFA is ideally suited to systems that label slowly due to the presence of large intermediate pools or pathway bottlenecks. Finally, INST-MFA provides increased measurement sensitivity to estimate reversible exchange fluxes and metabolite pool sizes, which represents a potential framework for integrating metabolomic analysis with 13C flux analysis. This review highlights the unique capabilities of INST-MFA, describes newly available software tools that automate INST-MFA calculations, presents several practical examples of recent INST-MFA applications, and discusses the technical challenges that lie ahead.
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Affiliation(s)
- Yi Ern Cheah
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, PMB 351604, Nashville, TN 37235-1604, USA
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, PMB 351604, Nashville, TN 37235-1604, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University, PMB 351604, Nashville, TN 37235-1604, USA.
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50
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McAtee Pereira AG, Walther JL, Hollenbach M, Young JD. 13 C Flux Analysis Reveals that Rebalancing Medium Amino Acid Composition can Reduce Ammonia Production while Preserving Central Carbon Metabolism of CHO Cell Cultures. Biotechnol J 2018; 13:e1700518. [PMID: 29405605 DOI: 10.1002/biot.201700518] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 01/10/2018] [Indexed: 11/10/2022]
Abstract
13 C metabolic flux analysis (MFA) provides a rigorous approach to quantify intracellular metabolism of industrial cell lines. In this study, 13 C MFA was used to characterize the metabolic response of Chinese hamster ovary (CHO) cells to a novel medium variant designed to reduce ammonia production. Ammonia inhibits growth and viability of CHO cell cultures, alters glycosylation of recombinant proteins, and enhances product degradation. Ammonia production was reduced by manipulating the amino acid composition of the culture medium; specifically, glutamine, glutamate, asparagine, aspartate, and serine levels were adjusted. Parallel 13 C flux analysis experiments determined that, while ammonia production decreased by roughly 40%, CHO cell metabolic phenotype, growth, viability, and monoclonal antibody (mAb) titer were not significantly altered by the changes in media composition. This study illustrates how 13 C flux analysis can be applied to assess the metabolic effects of media manipulations on mammalian cell cultures. The analysis revealed that adjusting the amino acid composition of CHO cell culture media can effectively reduce ammonia production while preserving fluxes throughout central carbon metabolism.
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Affiliation(s)
- Allison G McAtee Pereira
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee, USA
| | - Jason L Walther
- Bioprocess Development, Sanofi, 02142, Boston, Massachusetts, USA
| | - Myles Hollenbach
- Bioprocess Development, Sanofi, 02142, Boston, Massachusetts, USA
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee, USA.,Department of Molecular Physiology and Biophysics, Vanderbilt University, 37235, Nashville, Tennessee, USA
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