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Martinez W, Zhang Q, Linden MA, Schacher N, Darvish S, Mirek ET, Levy JL, Jonsson WO, Anthony TG, Hamilton KL. Rates of protein synthesis are maintained in brain but reduced in skeletal muscle during dietary sulfur amino acid restriction. FRONTIERS IN AGING 2022; 3:975129. [PMID: 36091469 PMCID: PMC9450999 DOI: 10.3389/fragi.2022.975129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022]
Abstract
Dietary interventions such as sulfur amino acid restriction (SAAR) target multiple drivers of aging, and show promise for preventing or delaying the onset of chronic diseases. SAAR promotes metabolic health and longevity in laboratory animals. The effects of SAAR on proteostasis remain relatively unexplored. We previously reported that SAAR promotes mitochondrial proteostatic maintenance, despite suppression of global protein synthesis, in two peripheral tissues, the liver and skeletal muscle. However, the brain, a tissue vulnerable to age-related neurodegenerative diseases due to the loss of proteostasis, has not been thoroughly studied. Therefore, we sought to reveal proteostatic responses in the brains of mice fed SAAR for 35 days. Here, we demonstrate that male C57Bl/6J mice fed two levels of SAAR maintained rates of protein synthesis in all sub-cellular fractions of the pre-frontal cortex. In comparison, rates of skeletal muscle protein synthesis in SAAR fed mice were slower than control-fed mice. To gain mechanistic insight, we examined several key nutrient/energy sensitive signaling proteins: AMP-activated protein kinase (AMPK), eukaryotic initiation factor 2 (eIF2), and ribosomal protein S6 (rpS6). SAAR had minimal to modest effects on the total abundance and phosphorylation of these proteins in both tissues. Our results indicate that the pre-frontal cortex in brain is resistant to perturbations in protein synthesis in mice fed SAAR, unlike skeletal muscle, which had a reduction in global protein synthesis. The results from this study demonstrate that proteostatic control in brain is of higher priority than skeletal muscle during dietary SAAR.
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Affiliation(s)
- Wenceslao Martinez
- Department of Health and Exercise Science, Colorado State University, Fort Collins, CO, United States
| | - Qian Zhang
- Department of Health and Exercise Science, Colorado State University, Fort Collins, CO, United States
| | - Melissa A. Linden
- Department of Health and Exercise Science, Colorado State University, Fort Collins, CO, United States
| | - Nate Schacher
- Department of Health and Exercise Science, Colorado State University, Fort Collins, CO, United States
| | - Sanna Darvish
- Department of Health and Exercise Science, Colorado State University, Fort Collins, CO, United States
| | - Emily T. Mirek
- Department of Nutritional Sciences and the New Jersey Institute for Food, Nutrition and Health, Rutgers University, New Brunswick, NB, United States
| | - Jordan L. Levy
- Department of Nutritional Sciences and the New Jersey Institute for Food, Nutrition and Health, Rutgers University, New Brunswick, NB, United States
| | - William O. Jonsson
- Department of Nutritional Sciences and the New Jersey Institute for Food, Nutrition and Health, Rutgers University, New Brunswick, NB, United States
| | - Tracy G. Anthony
- Department of Nutritional Sciences and the New Jersey Institute for Food, Nutrition and Health, Rutgers University, New Brunswick, NB, United States
| | - Karyn L. Hamilton
- Department of Health and Exercise Science, Colorado State University, Fort Collins, CO, United States,Columbine Health Systems Center for Healthy Aging, Colorado State University, Fort Collins, CO, United States,*Correspondence: Karyn L. Hamilton,
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High-Resolution Mass Spectrometry for In Vivo Proteome Dynamics using Heavy Water Metabolic Labeling. Int J Mol Sci 2020; 21:ijms21217821. [PMID: 33105654 PMCID: PMC7672638 DOI: 10.3390/ijms21217821] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/15/2020] [Accepted: 10/18/2020] [Indexed: 02/07/2023] Open
Abstract
Cellular proteins are continuously degraded and synthesized. The turnover of proteins is essential to many cellular functions. Combined with metabolic labeling using stable isotopes, LC-MS estimates proteome dynamics in high-throughput and on a large scale. Modern mass spectrometers allow a range of instrumental settings to optimize experimental output for specific research goals. One such setting which affects the results for dynamic proteome studies is the mass resolution. The resolution is vital for distinguishing target species from co-eluting contaminants with close mass-to-charge ratios. However, for estimations of proteome dynamics from metabolic labeling with stable isotopes, the spectral accuracy is highly important. Studies examining the effects of increased mass resolutions (in modern mass spectrometers) on the proteome turnover output and accuracy have been lacking. Here, we use a publicly available heavy water labeling and mass spectral data sets of murine serum proteome (acquired on Orbitrap Fusion and Agilent 6530 QToF) to analyze the effect of mass resolution of the Orbitrap mass analyzer on the proteome dynamics estimation. Increased mass resolution affected the spectral accuracy and the number acquired tandem mass spectra.
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Sadygov RG, Avva J, Rahman M, Lee K, Ilchenko S, Kasumov T, Borzou A. d2ome, Software for in Vivo Protein Turnover Analysis Using Heavy Water Labeling and LC-MS, Reveals Alterations of Hepatic Proteome Dynamics in a Mouse Model of NAFLD. J Proteome Res 2018; 17:3740-3748. [PMID: 30265007 DOI: 10.1021/acs.jproteome.8b00417] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metabolic labeling with heavy water followed by LC-MS is a high throughput approach to study proteostasis in vivo. Advances in mass spectrometry and sample processing have allowed consistent detection of thousands of proteins at multiple time points. However, freely available automated bioinformatics tools to analyze and extract protein decay rate constants are lacking. Here, we describe d2ome-a robust, automated software solution for in vivo protein turnover analysis. d2ome is highly scalable, uses innovative approaches to nonlinear fitting, implements Grubbs' outlier detection and removal, uses weighted-averaging of replicates, applies a data dependent elution time windowing, and uses mass accuracy in peak detection. Here, we discuss the application of d2ome in a comparative study of protein turnover in the livers of normal vs Western diet-fed LDLR-/- mice (mouse model of nonalcoholic fatty liver disease), which contained 256 LC-MS experiments. The study revealed reduced stability of 40S ribosomal protein subunits in the Western diet-fed mice.
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Affiliation(s)
- Rovshan G Sadygov
- Department of Biochemistry and Molecular Biology, Sealy Center for Molecular Medicine , The University of Texas Medical Branch , 301 University Blvd. , Galveston , Texas 77555 , United States
| | - Jayant Avva
- Department of Biochemistry and Molecular Biology, Sealy Center for Molecular Medicine , The University of Texas Medical Branch , 301 University Blvd. , Galveston , Texas 77555 , United States
| | - Mahbubur Rahman
- Department of Biochemistry and Molecular Biology, Sealy Center for Molecular Medicine , The University of Texas Medical Branch , 301 University Blvd. , Galveston , Texas 77555 , United States
| | - Kwangwon Lee
- Department of Pharmaceutical Sciences , Northeast Ohio Medical University , Rootstown , Ohio 44272 , United States
| | - Sergei Ilchenko
- Department of Pharmaceutical Sciences , Northeast Ohio Medical University , Rootstown , Ohio 44272 , United States
| | - Takhar Kasumov
- Department of Pharmaceutical Sciences , Northeast Ohio Medical University , Rootstown , Ohio 44272 , United States
| | - Ahmad Borzou
- Department of Biochemistry and Molecular Biology, Sealy Center for Molecular Medicine , The University of Texas Medical Branch , 301 University Blvd. , Galveston , Texas 77555 , United States
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Farthing DE, Buxbaum NP, Lucas PJ, Maglakelidze N, Oliver B, Wang J, Hu K, Castro E, Bare CV, Gress RE. Comparing DNA enrichment of proliferating cells following administration of different stable isotopes of heavy water. Sci Rep 2017. [PMID: 28642474 PMCID: PMC5481421 DOI: 10.1038/s41598-017-04404-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Deuterated water (2H2O) is a label commonly used for safe quantitative measurement of deuterium enrichment into DNA of proliferating cells. More recently, it has been used for labeling proteins and other biomolecules. Our in vitro - in vivo research reports important stable isotopic labeling enrichment differences into the DNA nucleosides and their isotopologues (e.g. deoxyadenosine (dA) M + 1, dA M + 2, dA M + 3), as well as tumor cell proliferation effects for various forms of commercially available stable heavy water (2H2O, H218O, and 2H218O). Using an in vitro mouse thymus tumor cell line, we determined that H218O provides superior DNA labeling enrichment quantitation, as measured by GC-positive chemical ionization (PCI)-MS/MS. In addition, at higher but physiologically relevant doses, both 2H218O and 2H2O down modulated mouse thymus tumor cell proliferation, whereas H218O water had no observable effects on cell proliferation. The in vivo labeling studies, where normal mouse bone marrow cells (i.e. high turnover) were evaluated post labeling, demonstrated DNA enrichments concordant with measurements from the in vitro studies. Our research also reports a headspace-GC-NCI-MS method, which rapidly and quantitatively measures stable heavy water levels in total body water.
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Affiliation(s)
- Don E Farthing
- National Institutes of Health (NIH), National Cancer Institute (NCI), Experimental Transplantation and Immunology (ETIB), 10 Center Drive, Bethesda, MD, 20892, United States.
| | - Nataliya P Buxbaum
- National Institutes of Health (NIH), National Cancer Institute (NCI), Experimental Transplantation and Immunology (ETIB), 10 Center Drive, Bethesda, MD, 20892, United States
| | - Philip J Lucas
- National Institutes of Health (NIH), National Cancer Institute (NCI), Experimental Transplantation and Immunology (ETIB), 10 Center Drive, Bethesda, MD, 20892, United States
| | - Natella Maglakelidze
- National Institutes of Health (NIH), National Cancer Institute (NCI), Experimental Transplantation and Immunology (ETIB), 10 Center Drive, Bethesda, MD, 20892, United States
| | - Brittany Oliver
- OCRT&ME, 10 Center Drive, Bethesda, MD, 20814, United States
| | - Jiun Wang
- National Institutes of Health (NIH), National Cancer Institute (NCI), Experimental Transplantation and Immunology (ETIB), 10 Center Drive, Bethesda, MD, 20892, United States
| | - Kevin Hu
- National Institutes of Health (NIH), National Cancer Institute (NCI), Experimental Transplantation and Immunology (ETIB), 10 Center Drive, Bethesda, MD, 20892, United States
| | - Ehydel Castro
- National Institutes of Health (NIH), National Cancer Institute (NCI), Experimental Transplantation and Immunology (ETIB), 10 Center Drive, Bethesda, MD, 20892, United States
| | - Catherine V Bare
- National Institutes of Health (NIH), National Cancer Institute (NCI), Experimental Transplantation and Immunology (ETIB), 10 Center Drive, Bethesda, MD, 20892, United States
| | - Ronald E Gress
- National Institutes of Health (NIH), National Cancer Institute (NCI), Experimental Transplantation and Immunology (ETIB), 10 Center Drive, Bethesda, MD, 20892, United States
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Buxbaum NP, Farthing DE, Maglakelidze N, Lizak M, Merkle H, Carpenter AC, Oliver BU, Kapoor V, Castro E, Swan GA, Dos Santos LM, Bouladoux NJ, Bare CV, Flomerfelt FA, Eckhaus MA, Telford WG, Belkaid Y, Bosselut RJ, Gress RE. In vivo kinetics and nonradioactive imaging of rapidly proliferating cells in graft-versus-host disease. JCI Insight 2017; 2:92851. [PMID: 28614804 DOI: 10.1172/jci.insight.92851] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/16/2017] [Indexed: 12/25/2022] Open
Abstract
Hematopoietic stem cell transplantation (HSCT) offers a cure for cancers that are refractory to chemotherapy and radiation. Most HSCT recipients develop chronic graft-versus-host disease (cGVHD), a systemic alloimmune attack on host organs. Diagnosis is based on clinical signs and symptoms, as biopsies are risky. T cells are central to the biology of cGVHD. We found that a low Treg/CD4+ T effector memory (Tem) ratio in circulation, lymphoid, and target organs identified early and established mouse cGVHD. Using deuterated water labeling to measure multicompartment in vivo kinetics of these subsets, we show robust Tem and Treg proliferation in lymphoid and target organs, while Tregs undergo apoptosis in target organs. Since deuterium enrichment into DNA serves as a proxy for cell proliferation, we developed a whole-body clinically relevant deuterium MRI approach to nonradioactively detect cGVHD and potentially allow imaging of other diseases characterized by rapidly proliferating cells.
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Affiliation(s)
- Nataliya P Buxbaum
- Experimental Transplantation and Immunology Branch, National Cancer Institute
| | - Donald E Farthing
- Experimental Transplantation and Immunology Branch, National Cancer Institute
| | | | - Martin Lizak
- In Vivo NMR Center, National Institute of Neurological Disorders and Stroke
| | - Hellmut Merkle
- Laboratory of Functional and Molecular Imaging, National Institute of Neurological Disorders and Stroke
| | | | - Brittany U Oliver
- Experimental Transplantation and Immunology Branch, National Cancer Institute
| | - Veena Kapoor
- Experimental Transplantation and Immunology Branch, National Cancer Institute
| | - Ehydel Castro
- Experimental Transplantation and Immunology Branch, National Cancer Institute
| | - Gregory A Swan
- Experimental Transplantation and Immunology Branch, National Cancer Institute
| | - Liliane M Dos Santos
- Mucosal Immunology Section, National Institute of Allergy and Infectious Diseases, and
| | - Nicolas J Bouladoux
- Mucosal Immunology Section, National Institute of Allergy and Infectious Diseases, and
| | - Catherine V Bare
- Experimental Transplantation and Immunology Branch, National Cancer Institute
| | | | - Michael A Eckhaus
- Diagnostic and Research Services Branch, Office of the Director, NIH, Bethesda, Maryland, USA
| | - William G Telford
- Experimental Transplantation and Immunology Branch, National Cancer Institute
| | - Yasmine Belkaid
- Mucosal Immunology Section, National Institute of Allergy and Infectious Diseases, and
| | - Remy J Bosselut
- Laboratory of Immune Cell Biology, National Cancer Institute
| | - Ronald E Gress
- Experimental Transplantation and Immunology Branch, National Cancer Institute
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Wilkinson DJ, Cegielski J, Phillips BE, Boereboom C, Lund JN, Atherton PJ, Smith K. Internal comparison between deuterium oxide (D2O) and L-[ring-13C6] phenylalanine for acute measurement of muscle protein synthesis in humans. Physiol Rep 2015; 3:3/7/e12433. [PMID: 26149278 PMCID: PMC4552519 DOI: 10.14814/phy2.12433] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Stable isotope tracer methodologies are becoming increasingly widespread in metabolic research; yet a number of factors restrict their implementation, such as, i.v infusions, multiple cannulae, tissue samples, and significant cost. We recently validated the sensitivity of the orally administered stable isotope tracer deuterium oxide (D2O) for quantifying day-to-day changes in muscle protein synthesis (MPS). This method is less invasive, restrictive, and more cost-effective than traditional amino acid (AA) tracer techniques. In the present study, we hypothesized the sensitivity of our analytical techniques (GC-Pyrolysis-IRMS) would permit D2O-derived measurements of MPS over much shorter periods (i.e., hours) usually only possible using AA-tracer techniques. We recruited nine males (24 ± 3 year, BMI: 25 ± 3 kg·m−²) into an internally controlled comparison of D2O versus 13C AA-tracers. The day before the acute study subjects consumed 400 mL D2O, and on the study day, received a primed (0.3 mg·kg−1) continuous (0.6 mg·kg·h−1) i.v infusion of L-[ring-13C6]-phenylalanine to quantify MPS under both: (1) basal [postabsorptive] and; (2) stimulated [postprandial] that is, consumption of 20 g EAA, conditions. Measures of MPS yielded indistinguishable technique differences with respect to EAA, 13C: 0.065 ± 0.004 to 0.089 ± 0.006%·h−1 (P < 0.05) and D2O: 0.050 ± 0.007 to 0.088 ± 0.008%·h−1 (P < 0.05) with qualitatively similar increases. Our findings reveal that acute measurement of MPS, usually only possible using AA-tracers, are feasible over shorter periods with orally administered D2O when used in tandem with GC-Pyrolysis-IRMS. We conclude that this D2O approach provides a less invasive, cost-effective, and flexible means by which to quantify MPS acutely over several hours.
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Affiliation(s)
- Daniel J Wilkinson
- MRC-ARUK Centre of Excellence for Musculoskeletal Ageing Research School of Medicine University of Nottingham, Derby, UK
| | - Jessica Cegielski
- MRC-ARUK Centre of Excellence for Musculoskeletal Ageing Research School of Medicine University of Nottingham, Derby, UK
| | - Bethan E Phillips
- MRC-ARUK Centre of Excellence for Musculoskeletal Ageing Research School of Medicine University of Nottingham, Derby, UK
| | - Catherine Boereboom
- MRC-ARUK Centre of Excellence for Musculoskeletal Ageing Research School of Medicine University of Nottingham, Derby, UK
| | - Jonathan N Lund
- MRC-ARUK Centre of Excellence for Musculoskeletal Ageing Research School of Medicine University of Nottingham, Derby, UK
| | - Philip J Atherton
- MRC-ARUK Centre of Excellence for Musculoskeletal Ageing Research School of Medicine University of Nottingham, Derby, UK
| | - Kenneth Smith
- MRC-ARUK Centre of Excellence for Musculoskeletal Ageing Research School of Medicine University of Nottingham, Derby, UK
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De Boer RJ, Perelson AS. Quantifying T lymphocyte turnover. J Theor Biol 2013; 327:45-87. [PMID: 23313150 PMCID: PMC3640348 DOI: 10.1016/j.jtbi.2012.12.025] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 12/13/2012] [Accepted: 12/30/2012] [Indexed: 01/13/2023]
Abstract
Peripheral T cell populations are maintained by production of naive T cells in the thymus, clonal expansion of activated cells, cellular self-renewal (or homeostatic proliferation), and density dependent cell life spans. A variety of experimental techniques have been employed to quantify the relative contributions of these processes. In modern studies lymphocytes are typically labeled with 5-bromo-2'-deoxyuridine (BrdU), deuterium, or the fluorescent dye carboxy-fluorescein diacetate succinimidyl ester (CFSE), their division history has been studied by monitoring telomere shortening and the dilution of T cell receptor excision circles (TRECs) or the dye CFSE, and clonal expansion has been documented by recording changes in the population densities of antigen specific cells. Proper interpretation of such data in terms of the underlying rates of T cell production, division, and death has proven to be notoriously difficult and involves mathematical modeling. We review the various models that have been developed for each of these techniques, discuss which models seem most appropriate for what type of data, reveal open problems that require better models, and pinpoint how the assumptions underlying a mathematical model may influence the interpretation of data. Elaborating various successful cases where modeling has delivered new insights in T cell population dynamics, this review provides quantitative estimates of several processes involved in the maintenance of naive and memory, CD4(+) and CD8(+) T cell pools in mice and men.
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Affiliation(s)
- Rob J De Boer
- Theoretical Biology & Bioinformatics, Utrecht University, The Netherlands; Santa Fe Institute, Santa Fe, NM 87501, USA.
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De Boer RJ, Perelson AS, Ribeiro RM. Modelling deuterium labelling of lymphocytes with temporal and/or kinetic heterogeneity. J R Soc Interface 2012; 9:2191-200. [PMID: 22513720 PMCID: PMC3405764 DOI: 10.1098/rsif.2012.0149] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2012] [Accepted: 03/27/2012] [Indexed: 12/12/2022] Open
Abstract
To study the kinetics of lymphocytes, models have divided the cell population into subpopulations with different turnover rates. These have been called 'kinetic heterogeneity models' so as to distinguish them from 'temporal heterogeneity models', in which a cell population may have different turnover rates at different times, e.g. when resting versus when activated. We model labelling curves for temporally heterogeneous populations, and predict that they exhibit equal biphasic up- and downslopes. We show when cells divide only once upon activation, these slopes are dominated by the slowest exponent, yielding underestimates of the average turnover rate. When cells undergo more than one division, the labelling curves allow fitting of the two exponential slopes in the temporal heterogeneity model. The same data can also be described with a two-compartment kinetic heterogeneity model. In both instances, the average turnover rate is correctly estimated. Because both models assume a different cell biology but describe the data equally well, the parameters of either model have no simple biological interpretation, as each parameter could reflect a combination of parameters of another biological process. Thus, even if there are sufficient data to reliably estimate all exponentials, one can only accurately estimate an average turnover rate. We illustrate these issues by re-fitting labelling data from healthy and HIV-infected individuals.
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Affiliation(s)
- Rob J De Boer
- Department of Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, The Netherlands.
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