1
|
Deberneh HM, Taylor ME, Borowik AK, Miyagi M, Miller BF, Sadygov RG. Numbers of Exchangeable Hydrogens from LC-MS Data of Heavy Water Metabolically Labeled Samples. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024. [PMID: 39057601 DOI: 10.1021/jasms.4c00157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Abstract
Labeling with deuterium oxide (D2O) has emerged as one of the preferred approaches for measuring the synthesis of individual proteins in vivo. In these experiments, the synthesis rates of proteins are determined by modeling mass shifts in peptides during the labeling period. This modeling depends on a theoretical maximum enrichment determined by the number of labeling sites (NEH) of each amino acid in the peptide sequence. Currently, NEH is determined from one set of published values. However, it has been demonstrated that NEH can differ between species and potentially tissues. The goal of this work was to determine the number of NEH for each amino acid within a given experiment to capture the conditions unique to that experiment. We used four methods to compute the NEH values. To test these approaches, we used two publicly available data sets. In a de novo approach, we compute NEH values and the label enrichment from the abundances of three mass isotopomers. The other three methods use the complete isotope profiles and body water enrichment in deuterium as an input parameter. They determine the NEH values by (1) minimizing the residual sum of squares, (2) from the mole percent excess of labeling, and (3) the time course profile of the depletion of the relative isotope abundance of monoisotope. In the test samples, the method using residual sum of squares performed the best. The methods are implemented in a tool for determining the NEH for each amino acid within a given experiment to use in the determination of protein synthesis rates using D2O.
Collapse
Affiliation(s)
- Henock M Deberneh
- Department of Biochemistry and Molecular Biology The University of Texas Medical Branch 301 University of Blvd, Galveston, Texas 77555, United States
| | - Michael E Taylor
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation 825 NE 13th Street Oklahoma City, Oklahoma 73104, United States
| | - Agnieszka K Borowik
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation 825 NE 13th Street Oklahoma City, Oklahoma 73104, United States
| | - Masaru Miyagi
- Department of Pharmacology Case Western Reserve University 10900 Euclid Avenue Cleveland, Ohio 44106, United States
| | - Benjamin F Miller
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation 825 NE 13th Street Oklahoma City, Oklahoma 73104, United States
- Oklahoma City VA, Oklahoma City, Oklahoma 73104, United States
| | - Rovshan G Sadygov
- Department of Biochemistry and Molecular Biology The University of Texas Medical Branch 301 University of Blvd, Galveston, Texas 77555, United States
| |
Collapse
|
2
|
Currie J, Ng DCM, Pandi B, Black A, Manda V, Pavelka J, Lam MPY, Lau E. Improved determination of protein turnover rate with heavy water labeling by mass isotopomer ratio selection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597043. [PMID: 38895333 PMCID: PMC11185681 DOI: 10.1101/2024.06.04.597043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
The synthesis and degradation rates of proteins form an essential component of gene expression control. Heavy water labeling has been used in conjunction with mass spectrometry to measure protein turnover rates, but the optimal analytical approaches to derive turnover rates from the isotopomer patterns of deuterium labeled peptides continue to be a subject of research. Here we describe a method, which comprises a reverse lookup of numerically approximated peptide isotope envelopes, coupled to the selection of optimal isotopomer pairs based on peptide sequence, to calculate the molar fraction of new peptide synthesis in heavy water labeling mass spectrometry experiments. We validated this approach using an experimental calibration curve comprising mixtures of fully unlabeled and fully labeled proteomes. We then re-analyzed 17 proteome-wide turnover experiments from four mouse organs, and showed that the method increases the coverage of well-fitted peptides in protein turnover experiments by 25-82%. The method is implemented in the Riana software tool for protein turnover analysis, and may avail ongoing efforts to study the synthesis and degradation kinetics of proteins in animals on a proteome-wide scale. What’s new We describe a reverse lookup method to calculate the molar fraction of new synthesis from numerically approximated peptide isotopomer profiles in heavy water labeling mass spectrometry experiments. Using an experimental calibration curve comprising mixtures of fully unlabeled and fully labeled proteomes at various proportions, we show that this method provides a straightforward way to calculate the proportion of new proteins in a protein pool from arbitrarily chosen isotopomer ratios. We next analyzed which of the isotopomer pairs within the peptide isotope envelope yielded isotopomer time courses that fit most closely to kinetic models, and found that the identity of the isotopomer pair depends partially on the number of deuterium accessible labeling sites of the peptide. We next derived a strategy to automatically select the isotopomer pairs to calculate turnover rates based on peptide sequence, and showed that this increases the coverage of existing proteome-wide turnover experiments in multiple data sets of the mouse heart, liver, kidney, and skeletal muscle by up to 25-82%.
Collapse
|
3
|
Verschuren L, Mak AL, van Koppen A, Özsezen S, Difrancesco S, Caspers MPM, Snabel J, van der Meer D, van Dijk AM, Rashu EB, Nabilou P, Werge MP, van Son K, Kleemann R, Kiliaan AJ, Hazebroek EJ, Boonstra A, Brouwer WP, Doukas M, Gupta S, Kluft C, Nieuwdorp M, Verheij J, Gluud LL, Holleboom AG, Tushuizen ME, Hanemaaijer R. Development of a novel non-invasive biomarker panel for hepatic fibrosis in MASLD. Nat Commun 2024; 15:4564. [PMID: 38811591 PMCID: PMC11137090 DOI: 10.1038/s41467-024-48956-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 05/20/2024] [Indexed: 05/31/2024] Open
Abstract
Accurate non-invasive biomarkers to diagnose metabolic dysfunction-associated steatotic liver disease (MASLD)-related fibrosis are urgently needed. This study applies a translational approach to develop a blood-based biomarker panel for fibrosis detection in MASLD. A molecular gene expression signature identified from a diet-induced MASLD mouse model (LDLr-/-.Leiden) is translated into human blood-based biomarkers based on liver biopsy transcriptomic profiles and protein levels in MASLD patient serum samples. The resulting biomarker panel consists of IGFBP7, SSc5D and Sema4D. LightGBM modeling using this panel demonstrates high accuracy in predicting MASLD fibrosis stage (F0/F1: AUC = 0.82; F2: AUC = 0.89; F3/F4: AUC = 0.87), which is replicated in an independent validation cohort. The overall accuracy of the model outperforms predictions by the existing markers Fib-4, APRI and FibroScan. In conclusion, here we show a disease mechanism-related blood-based biomarker panel with three biomarkers which is able to identify MASLD patients with mild or advanced hepatic fibrosis with high accuracy.
Collapse
Affiliation(s)
| | - Anne Linde Mak
- Department of Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | | | | | | | | | | | | | - Anne-Marieke van Dijk
- Department of Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Elias Badal Rashu
- Gastro Unit, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark and Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Puria Nabilou
- Gastro Unit, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark and Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel Parsberg Werge
- Gastro Unit, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark and Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Koen van Son
- Department of Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | | | - Amanda J Kiliaan
- Department of Medical Imaging, Anatomy, and Radboud Alzheimer Center, Radboud University Medical Center, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, the Netherlands
| | - Eric J Hazebroek
- Department of Bariatric Surgery, Vitalys, Rijnstate Hospital, Arnhem, the Netherlands and Division of Human Nutrition and Health, Wageningen University, Wageningen, The Netherlands
| | - André Boonstra
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Willem P Brouwer
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Michail Doukas
- Department of Pathology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Saurabh Gupta
- Translational Medicine, Bristol Meyers Squibb, Princeton Pike, NJ, USA
| | | | - Max Nieuwdorp
- Department of Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Joanne Verheij
- Department of Pathology, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Lise Lotte Gluud
- Gastro Unit, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark and Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Adriaan G Holleboom
- Department of Vascular Medicine, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Maarten E Tushuizen
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | | |
Collapse
|
4
|
Wilkinson DJ, Crossland H, Atherton PJ. Metabolomic and proteomic applications to exercise biomedicine. TRANSLATIONAL EXERCISE BIOMEDICINE 2024; 1:9-22. [PMID: 38660119 PMCID: PMC11036890 DOI: 10.1515/teb-2024-2006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 03/07/2024] [Indexed: 04/26/2024]
Abstract
Objectives 'OMICs encapsulates study of scaled data acquisition, at the levels of DNA, RNA, protein, and metabolite species. The broad objectives of OMICs in biomedical exercise research are multifarious, but commonly relate to biomarker development and understanding features of exercise adaptation in health, ageing and metabolic diseases. Methods This field is one of exponential technical (i.e., depth of feature coverage) and scientific (i.e., in health, metabolic conditions and ageing, multi-OMICs) progress adopting targeted and untargeted approaches. Results Key findings in exercise biomedicine have led to the identification of OMIC features linking to heritability or adaptive responses to exercise e.g., the forging of GWAS/proteome/metabolome links to cardiovascular fitness and metabolic health adaptations. The recent addition of stable isotope tracing to proteomics ('dynamic proteomics') and metabolomics ('fluxomics') represents the next phase of state-of-the-art in 'OMICS. Conclusions These methods overcome limitations associated with point-in-time 'OMICs and can be achieved using substrate-specific tracers or deuterium oxide (D2O), depending on the question; these methods could help identify how individual protein turnover and metabolite flux may explain exercise responses. We contend application of these methods will shed new light in translational exercise biomedicine.
Collapse
Affiliation(s)
- Daniel J. Wilkinson
- Centre of Metabolism, Ageing & Physiology (CoMAP), Medical Research Council/Versus Arthritis UK Centre of Excellence for Musculoskeletal Ageing Research (CMAR), School of Medicine, University of Nottingham, Royal Derby Hospital, Derby, UK
| | - Hannah Crossland
- Centre of Metabolism, Ageing & Physiology (CoMAP), Medical Research Council/Versus Arthritis UK Centre of Excellence for Musculoskeletal Ageing Research (CMAR), School of Medicine, University of Nottingham, Royal Derby Hospital, Derby, UK
| | - Philip J. Atherton
- Centre of Metabolism, Ageing & Physiology (CoMAP), Medical Research Council/Versus Arthritis UK Centre of Excellence for Musculoskeletal Ageing Research (CMAR), School of Medicine, University of Nottingham, Royal Derby Hospital, Derby, UK
| |
Collapse
|
5
|
Ziari N, Hellerstein MK. PyMIDA: A Graphical User Interface for Mass Isotopomer Distribution Analysis. Anal Chem 2024; 96:2303-2308. [PMID: 38306584 DOI: 10.1021/acs.analchem.3c02211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2024]
Abstract
Mass isotopomer distribution analysis (MIDA) is an analytical technique that measures the synthesis rate of biological polymers using combinatorial probabilities and stable isotope labeling. Over the past few decades, this method has been developed and applied to a wide range of uses that have increased our understanding of metabolism and the etiology and monitoring of disease. There is currently no publicly available piece of software for performing MIDA calculations in a targeted manner without its functionality being limited to a specific use case. We present a cross-platform Python graphical user interface implementation for research to obtain kinetic parameters easily from stable-isotope labeling studies and provide the code and user manual on GitHub.
Collapse
Affiliation(s)
- Naveed Ziari
- Department of Nutritional Sciences & Toxicology, College of Natural Resources, University of California, Berkeley, 94720 California, United States
| | - Marc K Hellerstein
- Department of Nutritional Sciences & Toxicology, College of Natural Resources, University of California, Berkeley, 94720 California, United States
| |
Collapse
|
6
|
Ziari N, Hellerstein M. Measurement of gluconeogenesis by 2H 2O labeling and mass isotopomer distribution analysis. J Biol Chem 2023; 299:105206. [PMID: 37660907 PMCID: PMC10539955 DOI: 10.1016/j.jbc.2023.105206] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/05/2023] Open
Abstract
The gluconeogenesis pathway, which converts nonsugar molecules into glucose, is critical for maintaining glucose homeostasis. Techniques that measure flux through this pathway are invaluable for studying metabolic diseases such as diabetes that are associated with dysregulation of this pathway. We introduce a new method that measures fractional gluconeogenesis by heavy water labeling and gas chromatographic-mass spectrometric analysis. This technique circumvents cumbersome benchwork or inference of positionality from mass spectra. The enrichment and pattern of deuterium label on glucose is quantified by use of mass isotopomer distribution analysis, which informs on how much of glucose-6-phosphate-derived glucose comes from the gluconeogenesis (GNG) pathway. We use an in vivo model of the GNG pathway that is based on previously published models but offers a new approach to calculating GNG pathway and subpathway contributions using combinatorial probabilities. We demonstrated that this method accurately quantifies fractional GNG through experiments that perturb flux through the pathway and by probing analytical sensitivity. While this method was developed in mice, the results suggest that it is translatable to humans in a clinical setting.
Collapse
Affiliation(s)
- Naveed Ziari
- Department of Nutritional Sciences & Toxicology, University of California, Berkeley, California, USA
| | - Marc Hellerstein
- Department of Nutritional Sciences & Toxicology, University of California, Berkeley, California, USA.
| |
Collapse
|
7
|
Nishimura Y, Bittel AJ, Stead CA, Chen YW, Burniston JG. Facioscapulohumeral Muscular Dystrophy is Associated With Altered Myoblast Proteome Dynamics. Mol Cell Proteomics 2023; 22:100605. [PMID: 37353005 PMCID: PMC10392138 DOI: 10.1016/j.mcpro.2023.100605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 05/31/2023] [Accepted: 06/20/2023] [Indexed: 06/25/2023] Open
Abstract
Proteomic studies in facioscapulohumeral muscular dystrophy (FSHD) could offer new insight into disease mechanisms underpinned by post-transcriptional processes. We used stable isotope (deuterium oxide; D2O) labeling and peptide mass spectrometry to investigate the abundance and turnover rates of proteins in cultured muscle cells from two individuals affected by FSHD and their unaffected siblings (UASb). We measured the abundance of 4420 proteins and the turnover rate of 2324 proteins in each (n = 4) myoblast sample. FSHD myoblasts exhibited a greater abundance but slower turnover rate of subunits of mitochondrial respiratory complexes and mitochondrial ribosomal proteins, which may indicate an accumulation of "older" less viable mitochondrial proteins in myoblasts from individuals affected by FSHD. Treatment with a 2'-O-methoxyethyl modified antisense oligonucleotide targeting exon 3 of the double homeobox 4 (DUX4) transcript tended to reverse mitochondrial protein dysregulation in FSHD myoblasts, indicating the effect on mitochondrial proteins may be a DUX4-dependent mechanism. Our results highlight the importance of post-transcriptional processes and protein turnover in FSHD pathology and provide a resource for the FSHD research community to explore this burgeoning aspect of FSHD.
Collapse
Affiliation(s)
- Yusuke Nishimura
- Research Institute for Sport & Exercise Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Adam J Bittel
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, District of Columbia, USA
| | - Connor A Stead
- Research Institute for Sport & Exercise Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Yi-Wen Chen
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, District of Columbia, USA.
| | - Jatin G Burniston
- Research Institute for Sport & Exercise Sciences, Liverpool John Moores University, Liverpool, United Kingdom.
| |
Collapse
|
8
|
Peinado-Izaguerri J, Zarzuela E, McLaughlin M, Small AC, Riva F, McKeegan DEF, Bain M, Muñoz J, Bhide M, Preston T. A novel dynamic proteomics approach for the measurement of broiler chicken protein fractional synthesis rate. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023; 37:e9497. [PMID: 36851885 DOI: 10.1002/rcm.9497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/13/2023] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
RATIONALE The study of protein synthesis in farm animals is uncommon despite its potential to increase knowledge about metabolism and discover new biomarkers of health and growth status. The present study describes a novel dynamic proteomics approach for the measurement of protein fractional synthesis rate (FSR) in broiler chickens. METHODS Chickens received a 10 g/kg oral dose of 2 H2 O at day 21 of their life. Body water 2 H abundance was measured in plasma samples using a portable Fourier transform infrared spectrometer. Free and protein-bound amino acids (AAs) were isolated and had their 2 H enrichment measured by gas chromatography with mass spectrometry (GC/MS). Peptide 2 H enrichment was measured by proteomics analysis of plasma and muscle samples. Albumin, fibrinogen and muscle protein FSR were calculated from GC/MS and proteomics data. RESULTS Ala appeared to be more enriched at the site of protein synthesis than in the AA free pools. Glu was found to be the AA closest to isotopic equilibrium between the different AA pools. Glu was used as an anchor to calculate n(AA) values necessary for chicken protein FSR calculation in dynamic proteomics studies. FSR values calculated using proteomics data and GC/MS data showed good agreement as evidenced by a Bland-Altman residual plot. CONCLUSIONS A new dynamic proteomics approach for the measurement of broiler chicken individual protein FSR based on the administration of a single 2 H2 O oral bolus has been developed and validated. The proposed approach could facilitate new immunological and nutritional studies on free-living animals.
Collapse
Affiliation(s)
- Jorge Peinado-Izaguerri
- University of Glasgow, Glasgow, UK
- University of Veterinary Medicine and Pharmacy in Košice, Košice, Slovakia
| | - Eduardo Zarzuela
- Proteomics Unit, Spanish National Cancer Research Center, Madrid, Spain
| | | | | | - Francesca Riva
- University of Glasgow, Glasgow, UK
- University of Zagreb, Zagreb, Croatia
| | | | | | - Javier Muñoz
- Proteomics Unit, Spanish National Cancer Research Center, Madrid, Spain
- Cell Signalling and Clinical Proteomics Group, Biocruces Bizkaia Health Research Institute, Biocruces Bizkaia, Barakaldo, Spain
| | - Mangesh Bhide
- University of Veterinary Medicine and Pharmacy in Košice, Košice, Slovakia
| | | |
Collapse
|
9
|
Dandan M, Han J, Mann S, Kim R, Li K, Mohammed H, Chuang JC, Zhu K, Billin AN, Huss RS, Chung C, Myers RP, Hellerstein M. Acetyl-CoA carboxylase inhibitor increases LDL-apoB production rate in NASH with cirrhosis: prevention by fenofibrate. J Lipid Res 2023; 64:100339. [PMID: 36737040 PMCID: PMC10017426 DOI: 10.1016/j.jlr.2023.100339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 01/27/2023] [Accepted: 01/28/2023] [Indexed: 02/04/2023] Open
Abstract
Treatment with acetyl-CoA carboxylase inhibitors (ACCi) in nonalcoholic steatohepatitis (NASH) may increase plasma triglycerides (TGs), with variable changes in apoB concentrations. ACC is rate limiting in de novo lipogenesis and regulates fatty acid oxidation, making it an attractive therapeutic target in NASH. Our objectives were to determine the effects of the ACCi, firsocostat, on production rates of plasma LDL-apoB in NASH and the effects of combined therapy with fenofibrate. Metabolic labeling with heavy water and tandem mass spectrometric analysis of LDL-apoB enrichments was performed in 16 NASH patients treated with firsocostat for 12 weeks and in 29 NASH subjects treated with firsocostat and fenofibrate for 12 weeks. In NASH on firsocostat, plasma TG increased significantly by 17% from baseline to week 12 (P = 0.0056). Significant increases were also observed in LDL-apoB fractional replacement rate (baseline to week 12: 31 ± 20.2 to 46 ± 22.6%/day, P = 0.03) and absolute synthesis rate (ASR) (30.4-45.2 mg/dl/day, P = 0.016) but not plasma apoB concentrations. The effect of firsocostat on LDL-apoB ASR was restricted to patients with cirrhosis (21.0 ± 9.6 at baseline and 44.2 ± 17 mg/dl/day at week 12, P = 0.002, N = 8); noncirrhotic patients did not change (39.8 ± 20.8 and 46.3 ± 14.8 mg/dl/day, respectively, P = 0.51, N = 8). Combination treatment with fenofibrate and firsocostat prevented increases in plasma TG, LDL-apoB fractional replacement rate, and ASR. In summary, in NASH with cirrhosis, ACCi treatment increases LDL-apoB100 production rate and this effect can be prevented by concurrent fenofibrate therapy.
Collapse
Affiliation(s)
- Mohamad Dandan
- Department of Nutritional Sciences and Toxicology, Graduate Program in Metabolic Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Julia Han
- Department of Nutritional Sciences and Toxicology, Graduate Program in Metabolic Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Sabrina Mann
- Department of Nutritional Sciences and Toxicology, Graduate Program in Metabolic Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Rachael Kim
- Department of Nutritional Sciences and Toxicology, Graduate Program in Metabolic Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Kelvin Li
- Department of Nutritional Sciences and Toxicology, Graduate Program in Metabolic Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Hussein Mohammed
- Department of Nutritional Sciences and Toxicology, Graduate Program in Metabolic Biology, University of California at Berkeley, Berkeley, CA, USA
| | | | - Kaiyi Zhu
- Gilead Sciences, Inc, Foster City, CA, USA
| | | | | | | | | | - Marc Hellerstein
- Department of Nutritional Sciences and Toxicology, Graduate Program in Metabolic Biology, University of California at Berkeley, Berkeley, CA, USA.
| |
Collapse
|
10
|
Fornasiero EF, Savas JN. Determining and interpreting protein lifetimes in mammalian tissues. Trends Biochem Sci 2023; 48:106-118. [PMID: 36163144 PMCID: PMC9868050 DOI: 10.1016/j.tibs.2022.08.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 01/26/2023]
Abstract
The orchestration of protein production and degradation, and the regulation of protein lifetimes, play a central role in the majority of biological processes. Recent advances in proteomics have enabled the estimation of protein half-lives for thousands of proteins in vivo. What is the utility of these measurements, and how can they be leveraged to interpret the proteome changes occurring during development, aging, and disease? This opinion article summarizes leading technical approaches and highlights their strengths and weaknesses. We also disambiguate frequently used terminology, illustrate recent mechanistic insights, and provide guidance for interpreting and validating protein turnover measurements. Overall, protein lifetimes, coupled to estimates of protein levels, are essential for obtaining a deep understanding of mammalian biology and the basic processes defining life itself.
Collapse
Affiliation(s)
- Eugenio F Fornasiero
- Department of Neuro-Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany.
| | - Jeffrey N Savas
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
| |
Collapse
|
11
|
Shi Y, Weng N, Jian W. Measurement of protein in vivo turnover rate with metabolic labeling using LC-MS. Biomed Chromatogr 2023:e5583. [PMID: 36634055 DOI: 10.1002/bmc.5583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/04/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023]
Abstract
Understanding the protein dynamics of a drug target is important for pharmaceutical research because it provides insight into drug design, target engagement, pharmacodynamics and drug efficacy. Nonradioactive isotope labeling has been the method of choice for protein turnover measurement thanks to the advancement of high-resolution mass spectrometry. While the changes in proteome in cell cultures can be monitored precisely, as the culture media can be completely replaced with 2 H-, 15 N- or 13 C-labeled essential amino acids, quantifying rates of protein synthesis in vivo is more challenging. The amount of isotope tracer that can be administered into the body is relatively small compared with the existing protein, thus requiring more sensitive detection, and the precursor-product labeling relationship is more complicated to interpret. The purpose of this review is to provide an overview of the principles of in vivo protein turnover studies using deuterium water (2 H2 O) with an emphasis on targeted protein analysis by hybrid LC-MS assay platforms. The pursuit of these opportunities will facilitate drug discovery and research in preclinical and clinical stages.
Collapse
Affiliation(s)
- Yifan Shi
- Bioanalytical Discovery and Development Sciences, Janssen Research and Development, Spring House, PA, USA
| | - Naidong Weng
- Bioanalytical Discovery and Development Sciences, Janssen Research and Development, Spring House, PA, USA
| | - Wenying Jian
- Bioanalytical Discovery and Development Sciences, Janssen Research and Development, Spring House, PA, USA
| |
Collapse
|
12
|
Naylor B, Anderson CNK, Hadfield M, Parkinson DH, Ahlstrom A, Hannemann A, Quilling CR, Cutler KJ, Denton RL, Adamson R, Angel TE, Burlett RS, Hafen PS, Dallon JC, Transtrum MK, Hyldahl RD, Price JC. Utilizing Nonequilibrium Isotope Enrichments to Dramatically Increase Turnover Measurement Ranges in Single Biopsy Samples from Humans. J Proteome Res 2022; 21:2703-2714. [PMID: 36099490 PMCID: PMC9639613 DOI: 10.1021/acs.jproteome.2c00380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Indexed: 11/30/2022]
Abstract
The synthesis of new proteins and the degradation of old proteins in vivo can be quantified in serial samples using metabolic isotope labeling to measure turnover. Because serial biopsies in humans are impractical, we set out to develop a method to calculate the turnover rates of proteins from single human biopsies. This method involved a new metabolic labeling approach and adjustments to the calculations used in previous work to calculate protein turnover. We demonstrate that using a nonequilibrium isotope enrichment strategy avoids the time dependent bias caused by variable lag in label delivery to different tissues observed in traditional metabolic labeling methods. Turnover rates are consistent for the same subject in biopsies from different labeling periods, and turnover rates calculated in this study are consistent with previously reported values. We also demonstrate that by measuring protein turnover we can determine where proteins are synthesized. In human subjects a significant difference in turnover rates differentiated proteins synthesized in the salivary glands versus those imported from the serum. We also provide a data analysis tool, DeuteRater-H, to calculate protein turnover using this nonequilibrium metabolic 2H2O method.
Collapse
Affiliation(s)
- Bradley
C. Naylor
- Department
of Chemistry and Biochemistry, Brigham Young
University, Provo, Utah 84602, United States
| | | | - Marcus Hadfield
- Department
of Chemistry and Biochemistry, Brigham Young
University, Provo, Utah 84602, United States
| | - David H. Parkinson
- Department
of Chemistry and Biochemistry, Brigham Young
University, Provo, Utah 84602, United States
| | - Austin Ahlstrom
- Department
of Chemistry and Biochemistry, Brigham Young
University, Provo, Utah 84602, United States
| | - Austin Hannemann
- Department
of Chemistry and Biochemistry, Brigham Young
University, Provo, Utah 84602, United States
| | - Chad R. Quilling
- Department
of Chemistry and Biochemistry, Brigham Young
University, Provo, Utah 84602, United States
| | - Kyle J. Cutler
- Department
of Chemistry and Biochemistry, Brigham Young
University, Provo, Utah 84602, United States
| | - Russell L. Denton
- Department
of Chemistry and Biochemistry, Brigham Young
University, Provo, Utah 84602, United States
| | - Robert Adamson
- Department
of Chemistry and Biochemistry, Brigham Young
University, Provo, Utah 84602, United States
| | - Thomas E. Angel
- In-vitro/In-vivo
Translation Platform Group, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Rebecca S. Burlett
- Department
of Chemistry and Biochemistry, Brigham Young
University, Provo, Utah 84602, United States
| | - Paul S. Hafen
- Department
of Exercise Sciences, Brigham Young University, Provo, Utah 84602, United States
| | - John. C. Dallon
- Department
of Mathematics, Brigham Young University, Provo, Utah 84602, United States
| | - Mark K. Transtrum
- Department
of Physics and Astronomy, Brigham Young
University, Provo, Utah 84602, United States
| | - Robert D. Hyldahl
- Department
of Exercise Sciences, Brigham Young University, Provo, Utah 84602, United States
| | - John C. Price
- Department
of Chemistry and Biochemistry, Brigham Young
University, Provo, Utah 84602, United States
| |
Collapse
|
13
|
Howard EE, Shankaran M, Evans WJ, Berryman CE, Margolis LM, Lieberman HR, Karl JP, Young AJ, Montano MA, Matthews MD, Bizieff A, Nyangao E, Mohammed H, Harris MN, Hellerstein MK, Rood JC, Pasiakos SM. Effects of Testosterone on Mixed-Muscle Protein Synthesis and Proteome Dynamics During Energy Deficit. J Clin Endocrinol Metab 2022; 107:e3254-e3263. [PMID: 35532889 DOI: 10.1210/clinem/dgac295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Indexed: 11/19/2022]
Abstract
CONTEXT Effects of testosterone on integrated muscle protein metabolism and muscle mass during energy deficit are undetermined. OBJECTIVE The objective was to determine the effects of testosterone on mixed-muscle protein synthesis (MPS), proteome-wide fractional synthesis rates (FSR), and skeletal muscle mass during energy deficit. DESIGN This was a randomized, double-blind, placebo-controlled trial. SETTING The study was conducted at Pennington Biomedical Research Center. PARTICIPANTS Fifty healthy men. INTERVENTION The study consisted of 14 days of weight maintenance, followed by a 28-day 55% energy deficit with 200 mg testosterone enanthate (TEST, n = 24) or placebo (PLA, n = 26) weekly, and up to 42 days of ad libitum recovery feeding. MAIN OUTCOME MEASURES Mixed-MPS and proteome-wide FSR before (Pre), during (Mid), and after (Post) the energy deficit were determined using heavy water (days 1-42) and muscle biopsies. Muscle mass was determined using the D3-creatine dilution method. RESULTS Mixed-MPS was lower than Pre at Mid and Post (P < 0.0005), with no difference between TEST and PLA. The proportion of individual proteins with numerically higher FSR in TEST than PLA was significant by 2-tailed binomial test at Post (52/67; P < 0.05), but not Mid (32/67; P > 0.05). Muscle mass was unchanged during energy deficit but was greater in TEST than PLA during recovery (P < 0.05). CONCLUSIONS The high proportion of individual proteins with greater FSR in TEST than PLA at Post suggests exogenous testosterone exerted a delayed but broad stimulatory effect on synthesis rates across the muscle proteome during energy deficit, resulting in muscle mass accretion during subsequent recovery.
Collapse
Affiliation(s)
- Emily E Howard
- Military Nutrit ion Division, U.S. Army Research Institute of Environmental Medicine, Natick, MA 01760, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, TN 37830, USA
| | - Mahalakshmi Shankaran
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720, USA
| | - Willian J Evans
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720, USA
| | - Claire E Berryman
- Military Nutrit ion Division, U.S. Army Research Institute of Environmental Medicine, Natick, MA 01760, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, TN 37830, USA
- Department of Nutrition, Food, and Exercise Sciences, Florida State University, Tallahassee, FL 32306, USA
| | - Lee M Margolis
- Military Nutrit ion Division, U.S. Army Research Institute of Environmental Medicine, Natick, MA 01760, USA
| | - Harris R Lieberman
- Military Nutrit ion Division, U.S. Army Research Institute of Environmental Medicine, Natick, MA 01760, USA
| | - J Philip Karl
- Military Nutrit ion Division, U.S. Army Research Institute of Environmental Medicine, Natick, MA 01760, USA
| | - Andrew J Young
- Military Nutrit ion Division, U.S. Army Research Institute of Environmental Medicine, Natick, MA 01760, USA
| | - Monty A Montano
- MyoSyntax Corporation, Worcester, MA 01605, USA
- Harvard Medical School, Boston, MA 02115, USA
- Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Marcy D Matthews
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720, USA
| | - Alec Bizieff
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720, USA
| | - Edna Nyangao
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720, USA
| | - Hussein Mohammed
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720, USA
| | - Melissa N Harris
- Pennington Biomedical Research Center, Baton Rouge, LA 70808, USA
| | - Marc K Hellerstein
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720, USA
| | - Jennifer C Rood
- Pennington Biomedical Research Center, Baton Rouge, LA 70808, USA
| | - Stefan M Pasiakos
- Military Performance Division, U.S. Army Research Institute of Environmental Medicine, Natick, MA 01760, USA
| |
Collapse
|
14
|
Duncan O, Millar AH. Day and night isotope labelling reveal metabolic pathway specific regulation of protein synthesis rates in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:745-763. [PMID: 34997626 DOI: 10.1111/tpj.15661] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 12/14/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
Plants have a diurnal separation of metabolic fluxes and a need for differential maintenance of protein machinery in the day and night. To directly assess the output of the translation process and to estimate the ATP investment involved, the individual rates of protein synthesis and degradation of hundreds of different proteins need to be measured simultaneously. We quantified protein synthesis and degradation through pulse labelling with heavy hydrogen in Arabidopsis thaliana rosettes to allow such an assessment of ATP investment in leaf proteome homeostasis on a gene-by-gene basis. Light-harvesting complex proteins were synthesised and degraded much faster in the day (approximately 10:1), while carbon metabolism and vesicle trafficking components were translated at similar rates day or night. Few leaf proteins changed in abundance between the day and the night despite reduced protein synthesis rates at night, indicating that protein degradation rates are tightly coordinated. The data reveal how the pausing of photosystem synthesis and degradation at night allows the redirection of a decreased energy budget to a selective night-time maintenance schedule.
Collapse
Affiliation(s)
- Owen Duncan
- ARC Centre of Excellence in Plant Energy Biology, Perth, WA, Australia
- Western Australian Proteomics, The University Western Australia, Perth, WA, Australia
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, Perth, WA, Australia
- Western Australian Proteomics, The University Western Australia, Perth, WA, Australia
- School of Molecular Sciences, The University of Western Australia, Perth, WA, Australia
| |
Collapse
|
15
|
Dandan M, Han J, Mann S, Kim R, Mohammed H, Nyangau E, Hellerstein M. Turnover Rates of the Low-Density Lipoprotein Receptor and PCSK9: Added Dimension to the Cholesterol Homeostasis Model. Arterioscler Thromb Vasc Biol 2021; 41:2866-2876. [PMID: 34615375 DOI: 10.1161/atvbaha.121.316764] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVE We measured the turnover rates of the LDLR (low-density lipoprotein receptor) and PCSK9 (proprotein convertase subtilisin/kexin type 9) in mice by metabolic labeling with heavy water and mass spectrometry. Approach and Results: In liver of mice fed high-cholesterol diets, LDLR mRNA levels and synthesis rates were markedly lower with complete suppression of cholesterol synthesis and higher cholesterol content, consistent with the Brown-Goldstein model of tissue cholesterol homeostasis. We observed markedly lower PCSK9 mRNA levels and synthesis rates in liver and lower concentrations and synthesis rates in plasma. Hepatic LDLR half-life (t½) was prolonged, consistent with an effect of reduced PCSK9, and resulted in no reduction in hepatic LDLR content despite reduced mRNA levels and LDLR synthesis rates. These changes in PCSK9 synthesis complement and expand the well-established model of tissue cholesterol homeostasis in mouse liver, in that reduced synthesis and levels of PCSK9 counterbalance lower LDLR synthesis by promoting less LDLR catabolism, thereby maintaining uptake of LDL cholesterol into liver despite high intracellular cholesterol concentrations. CONCLUSIONS Lower hepatic synthesis and secretion of PCSK9, an SREBP2 (sterol response element binding protein) target gene, results in longer hepatic LDLR t½ in response to cholesterol feeding in mice in the face of high intracellular cholesterol content. PCSK9 modulation opposes the canonical lowering of LDLR mRNA and synthesis by cholesterol surplus and preserves LDLR levels. The physiological and therapeutic implications of these opposing control mechanisms over liver LDLR are of interest and may reflect subservience of hepatic cholesterol homeostasis to whole body cholesterol needs.
Collapse
Affiliation(s)
- Mohamad Dandan
- Graduate Program in Metabolic Biology, Department of Nutritional Sciences and Toxicology, University of California, Berkeley
| | - Julia Han
- Graduate Program in Metabolic Biology, Department of Nutritional Sciences and Toxicology, University of California, Berkeley
| | - Sabrina Mann
- Graduate Program in Metabolic Biology, Department of Nutritional Sciences and Toxicology, University of California, Berkeley
| | - Rachael Kim
- Graduate Program in Metabolic Biology, Department of Nutritional Sciences and Toxicology, University of California, Berkeley
| | - Hussein Mohammed
- Graduate Program in Metabolic Biology, Department of Nutritional Sciences and Toxicology, University of California, Berkeley
| | - Edna Nyangau
- Graduate Program in Metabolic Biology, Department of Nutritional Sciences and Toxicology, University of California, Berkeley
| | - Marc Hellerstein
- Graduate Program in Metabolic Biology, Department of Nutritional Sciences and Toxicology, University of California, Berkeley
| |
Collapse
|
16
|
Rolfs Z, Frey BL, Shi X, Kawai Y, Smith LM, Welham NV. An atlas of protein turnover rates in mouse tissues. Nat Commun 2021; 12:6778. [PMID: 34836951 PMCID: PMC8626426 DOI: 10.1038/s41467-021-26842-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/25/2021] [Indexed: 01/25/2023] Open
Abstract
Protein turnover is critical to cellular physiology as well as to the growth and maintenance of tissues. The unique synthesis and degradation rates of each protein help to define tissue phenotype, and knowledge of tissue- and protein-specific half-lives is directly relevant to protein-related drug development as well as the administration of medical therapies. Using stable isotope labeling and mass spectrometry, we determine the in vivo turnover rates of thousands of proteins-including those of the extracellular matrix-in a set of biologically important mouse tissues. We additionally develop a data visualization platform, named ApplE Turnover, that enables facile searching for any protein of interest in a tissue of interest and then displays its half-life, confidence interval, and supporting measurements. This extensive dataset and the corresponding visualization software provide a reference to guide future studies of mammalian protein turnover in response to physiologic perturbation, disease, or therapeutic intervention.
Collapse
Affiliation(s)
- Zach Rolfs
- grid.14003.360000 0001 2167 3675Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Brian L. Frey
- grid.14003.360000 0001 2167 3675Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Xudong Shi
- grid.14003.360000 0001 2167 3675Division of Otolaryngology–Head and Neck Surgery, Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792 USA
| | - Yoshitaka Kawai
- grid.14003.360000 0001 2167 3675Division of Otolaryngology–Head and Neck Surgery, Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792 USA ,grid.258799.80000 0004 0372 2033Present Address: Department of Otolaryngology–Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto, 606-8507 Japan
| | - Lloyd M. Smith
- grid.14003.360000 0001 2167 3675Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Nathan V. Welham
- grid.14003.360000 0001 2167 3675Division of Otolaryngology–Head and Neck Surgery, Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792 USA
| |
Collapse
|
17
|
Gabisonia K, Burjanadze G, Woitek F, Keles A, Seki M, Gorgodze N, Carlucci L, Ilchenko S, Kurishima C, Walsh K, Piontkivska H, Recchia FA, Kasumov T. Proteome dynasmics and bioinformatics reveal major alterations in the turnover rate of functionally related cardiac and plasma proteins in a dog model of congestive heart failure. J Card Fail 2021; 28:588-600. [PMID: 34785403 DOI: 10.1016/j.cardfail.2021.11.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 11/05/2021] [Accepted: 11/05/2021] [Indexed: 11/26/2022]
Abstract
Protein pool turnover is a critically important cellular homeostatic component, yet it has been little explored in the context of heart failure (HF) pathophysiology. We employed in vivo 2H labeling/ proteome dynamics for non-biased discovery of turnover alterations involving functionally linked cardiac and plasma proteins in canine tachypacing-induced HF, an established preclinical model of dilated cardiomyopathy. Compared to control, dogs with congestive HF displayed bidirectional turnover changes of 28 cardiac proteins, i.e. reduced half-life of several key enzymes involved in glycolysis, homocysteine metabolism and glycogenesis, and increased half-life of proteins involved in proteolysis. Changes in plasma proteins were more modest: only 5 proteins, involved in various functions including proteolysis inhibition, hemoglobin, calcium and ferric-iron binding, displayed increased or decreased turnover rates. In other dogs undergoing cardiac tachypacing, we infused for 2 weeks the myokine Follistatin-like protein 1 (FSTL1), known for its ameliorative effects on HF-induced alterations. Proteome dynamics proved very sensitive in detecting the partial or complete prevention, by FSTL1, of cardiac and plasma protein turnover alterations. In conclusion, our study unveiled, for the first time in a large mammal, numerous HF-related alterations that may serve as the basis for future mechanistic research and/or as conceptually new molecular markers.
Collapse
Key Words
- ATIC, 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase /IMP cyclohydrolase
- BNP, brain natriuretic peptide
- CLTC, Clathrin heavy chain
- CRP, Pentraxin
- CYB5R3, NADH-cytochrome b5 reductase
- DPYSL2, Dihydropyrimidinase Like 2
- FDR, false discovery rate
- FSTL1, Follistatin-like protein 1
- GAPDHS, Glyceraldehyde-3-phosphate dehydrogenase
- GYS1, Glycogen synthase
- HF, Heart failure
- HSP90, Heat shock protein 90
- HSP90AB1, Heat shock protein 90 alpha family class B member 1
- HSPA1A, Heat Shock Protein A1
- LC-MS, liquid chromatography-mass spectrometry
- LFQ, Label-free quantification
- LOC479668, Haptoglobin
- LTAH4, Leukotriene A (4) hydrolase
- LV, Left ventricle
- PCA, Principal Component Analysis
- PDHA1, Pyruvate dehydrogenase E1 component subunit alpha
- PDHB, Pyruvate dehydrogenase E1 component subunit beta
- PGM, Phosphoglucomutase 1
- PSMD2, Proteasome 26S subunit, non-ATPase 2
- STIP1, Stress induced phosphoprotein
- TF, Transferrin
- proteome dynamics, bioinformatics, cardiac disease, heart failure, List of abbreviations: ANP, atrial natriuretic peptide
Collapse
Affiliation(s)
- Khatia Gabisonia
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa; Fondazione Gabriele Monasterio, Pisa, Italy
| | - Gia Burjanadze
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa; Fondazione Gabriele Monasterio, Pisa, Italy
| | - Felix Woitek
- Heart Center Dresden-University Clinic, Technical University Dresden, Dresden, Germany
| | - Ayse Keles
- Northeast Ohio Medical University, Rootstown, OH, USA
| | - Mitsuru Seki
- Cardiovascular Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Nikoloz Gorgodze
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa; Fondazione Gabriele Monasterio, Pisa, Italy
| | - Lucia Carlucci
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa; Fondazione Gabriele Monasterio, Pisa, Italy
| | - Serguei Ilchenko
- Cardiovascular Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Clara Kurishima
- Cardiovascular Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Kenneth Walsh
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Helen Piontkivska
- Department of Biological Sciences and Brain Health Research Institute, Kent State University, Kent, OH, USA
| | - Fabio A Recchia
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa; Fondazione Gabriele Monasterio, Pisa, Italy; Cardiovascular Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA.
| | | |
Collapse
|
18
|
Jameson TSO, Kilroe SP, Fulford J, Abdelrahman DR, Murton AJ, Dirks ML, Stephens FB, Wall BT. Muscle damaging eccentric exercise attenuates disuse-induced declines in daily myofibrillar protein synthesis and transiently prevents muscle atrophy in healthy men. Am J Physiol Endocrinol Metab 2021; 321:E674-E688. [PMID: 34632796 PMCID: PMC8791791 DOI: 10.1152/ajpendo.00294.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Short-term disuse leads to muscle loss driven by lowered daily myofibrillar protein synthesis (MyoPS). However, disuse commonly results from muscle damage, and its influence on muscle deconditioning during disuse is unknown. Twenty-one males [20 ± 1 yr, BMI = 24 ± 1 kg·m-2 (± SE)] underwent 7 days of unilateral leg immobilization immediately preceded by 300 bilateral, maximal, muscle-damaging eccentric quadriceps contractions (DAM; subjects n = 10) or no exercise (CON; subjects n = 11). Participants ingested deuterated water and underwent temporal bilateral thigh MRI scans and vastus lateralis muscle biopsies of immobilized (IMM) and nonimmobilized (N-IMM) legs. N-IMM quadriceps muscle volume remained unchanged throughout both groups. IMM quadriceps muscle volume declined after 2 days by 1.7 ± 0.5% in CON (P = 0.031; and by 1.3 ± 0.6% when corrected to N-IMM; P = 0.06) but did not change in DAM, and declined equivalently in CON [by 6.4 ± 1.1% (5.0 ± 1.6% when corrected to N-IMM)] and DAM [by 2.6 ± 1.8% (4.0 ± 1.9% when corrected to N-IMM)] after 7 days. Immobilization began to decrease MyoPS compared with N-IMM in both groups after 2 days (P = 0.109), albeit with higher MyoPS rates in DAM compared with CON (P = 0.035). Frank suppression of MyoPS was observed between days 2 and 7 in CON (IMM = 1.04 ± 0.12, N-IMM = 1.86 ± 0.10%·day-1; P = 0.002) but not DAM (IMM = 1.49 ± 0.29, N-IMM = 1.90 ± 0.30%·day-1; P > 0.05). Declines in MyoPS and quadriceps volume after 7 days correlated positively in CON (r2 = 0.403; P = 0.035) but negatively in DAM (r2 = 0.483; P = 0.037). Quadriceps strength declined following immobilization in both groups, but to a greater extent in DAM. Prior muscle-damaging eccentric exercise increases MyoPS and prevents loss of quadriceps muscle volume after 2 (but not 7) days of disuse.NEW & NOTEWORTHY We investigated the impact of prior muscle-damaging eccentric exercise on disuse-induced muscle deconditioning. Two and 7 days of muscle disuse per se lowered quadriceps muscle volume in association with lowered daily myofibrillar protein synthesis (MyoPS). Prior eccentric exercise prevented the decline in muscle volume after 2 days and attenuated the decline in MyoPS after 2 and 7 days. These data indicate eccentric exercise increases MyoPS and transiently prevents quadriceps muscle atrophy during muscle disuse.
Collapse
Affiliation(s)
- Tom S O Jameson
- Nutritional Physiology Group, Department of Sport and Health Sciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Sean P Kilroe
- Department of Nutrition and Metabolism, Center for Recovery, Physical Activity and Nutrition, University of Texas Medical Branch, Galveston, Texas
| | - Jonathan Fulford
- Peninsula NIHR Clinical Research Facility, College of Medicine and Health, University of Exeter, Exeter, United Kingdom
| | - Doaa R Abdelrahman
- Department of Surgery, University of Texas Medical Branch, Galveston, Texas
| | - Andrew J Murton
- Department of Surgery, University of Texas Medical Branch, Galveston, Texas
- Sealy Center of Aging, University of Texas Medical Branch, Galveston, Texas
| | - Marlou L Dirks
- Nutritional Physiology Group, Department of Sport and Health Sciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Francis B Stephens
- Nutritional Physiology Group, Department of Sport and Health Sciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Benjamin T Wall
- Nutritional Physiology Group, Department of Sport and Health Sciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| |
Collapse
|
19
|
Nallasamy S, Palacios HH, Setlem R, Caraballo MC, Li K, Cao E, Shankaran M, Hellerstein M, Mahendroo M. Transcriptome and proteome dynamics of cervical remodeling in the mouse during pregnancy. Biol Reprod 2021; 105:1257-1271. [PMID: 34309663 DOI: 10.1093/biolre/ioab144] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/02/2021] [Accepted: 07/20/2021] [Indexed: 11/14/2022] Open
Abstract
During gestation, the female reproductive tract must maintain pregnancy while concurrently preparing for parturition. Here, we explore the transitions in gene expression and protein turnover (fractional synthesis rates [FSR]) by which the cervix implements a transition from rigid to compliant. Shifts in gene transcription to achieve immune tolerance and alter epithelial cell programs begin in early pregnancy. Subsequently, in mid-to-late pregnancy transcriptional programs emerge that promote structural reorganization of the extracellular matrix (ECM). Stable isotope labeling revealed a striking slowdown of overall FSRs across the proteome on gestation day 6 that reverses in mid-to-late pregnancy. An exception was soluble fibrillar collagens and proteins of collagen assembly, which exhibit high turnover in non-pregnant cervix compared to other tissues and FSRs that continue throughout pregnancy. This finding provides a mechanism to explain how cross-linked collagen is replaced by newly synthesized, less-cross-linked collagens, which allows increased tissue compliance during parturition. The rapid transition requires a reservoir of newly synthesized, less cross-linked collagens, which is assured by the high FSR of soluble collagens in the cervix. These findings suggest a previously unrecognized form of "metabolic flexibility" for ECM in the cervix that underlies rapid transformation in compliance to allow parturition.
Collapse
Affiliation(s)
- Shanmugasundaram Nallasamy
- Department of Ob/Gyn and Cecil H. and Ida Green Center for Reproductive Biological Science, The University of Texas Southwestern Medical Center, Dallas, TX
| | - Hector H Palacios
- Department of Nutritional Sciences & Toxicology, University of California Berkeley, Berkeley, CA
| | - Rohit Setlem
- Department of Ob/Gyn and Cecil H. and Ida Green Center for Reproductive Biological Science, The University of Texas Southwestern Medical Center, Dallas, TX
| | - Mariano Colon Caraballo
- Department of Ob/Gyn and Cecil H. and Ida Green Center for Reproductive Biological Science, The University of Texas Southwestern Medical Center, Dallas, TX
| | - Kelvin Li
- Department of Nutritional Sciences & Toxicology, University of California Berkeley, Berkeley, CA
| | - Edward Cao
- Department of Nutritional Sciences & Toxicology, University of California Berkeley, Berkeley, CA
| | - Mahalakshmi Shankaran
- Department of Nutritional Sciences & Toxicology, University of California Berkeley, Berkeley, CA
| | - Marc Hellerstein
- Department of Nutritional Sciences & Toxicology, University of California Berkeley, Berkeley, CA
| | - Mala Mahendroo
- Department of Ob/Gyn and Cecil H. and Ida Green Center for Reproductive Biological Science, The University of Texas Southwestern Medical Center, Dallas, TX
| |
Collapse
|
20
|
Wilkinson DJ, Brook MS, Smith K. Principles of stable isotope research - with special reference to protein metabolism. CLINICAL NUTRITION OPEN SCIENCE 2021; 36:111-125. [PMID: 33969338 PMCID: PMC8083121 DOI: 10.1016/j.nutos.2021.02.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 02/06/2021] [Indexed: 12/13/2022] Open
Abstract
The key to understanding the mechanisms regulating disease stems from the ability to accurately quantify the dynamic nature of the metabolism underlying the physiological and pathological changes occurring as a result of the disease. Stable isotope tracer technologies have been at the forefront of this for almost 80 years now, and through a combination of both intense theoretical and technological development over these decades, it is now possible to utilise stable isotope tracers to investigate the complexities of in vivo human metabolism from a whole body perspective, down to the regulation of sub-nanometer cellular components (i.e organelles, nucleotides and individual proteins). This review therefore aims to highlight; 1) the advances made in these stable isotope tracer approaches - with special reference given to their role in understanding the nutritional regulation of protein metabolism, 2) some considerations required for the appropriate application of these stable isotope techniques to study protein metabolism, 3) and finally how new stable isotopes approaches and instrument/technical developments will help to deliver greater clinical insight in the near future.
Collapse
Key Words
- A-V, Arterial Venous
- AA, Amino Acids
- AP(E), Atom percent (excess)
- FBR, Fractional Breakdown Rate
- FSR, Fractional Synthesis Rate
- GC-MS, Gas Chromatography Mass Spectrometry
- LC-MS, Liquid Chromatography Mass Spectrometry
- MPS, Muscle Protein Synthesis
- Muscle
- Protein turnover
- Ra, Rate of Appearance
- Rd, Rate of Disappearance
- Stable isotope tracers
Collapse
Affiliation(s)
- Daniel J. Wilkinson
- MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research, NIHR Nottingham BRC, UK
- Division of Health Sciences and Graduate Entry Medicine, School of Medicine, University of Nottingham, Royal Derby Hospital Centre, Derby, UK
| | - Matthew S. Brook
- MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research, NIHR Nottingham BRC, UK
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Ken Smith
- MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research, NIHR Nottingham BRC, UK
- Division of Health Sciences and Graduate Entry Medicine, School of Medicine, University of Nottingham, Royal Derby Hospital Centre, Derby, UK
| |
Collapse
|
21
|
Sadygov RG. Using Heavy Mass Isotopomers for Protein Turnover in Heavy Water Metabolic Labeling. J Proteome Res 2021; 20:2035-2041. [PMID: 33661639 DOI: 10.1021/acs.jproteome.0c00873] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metabolic labeling followed by LC-MS-based proteomics is a powerful tool to study proteome dynamics in high-throughput experiments both in vivo and in vitro. High mass resolution and accuracy allow differentiation in isotope profiles and the quantification of partially labeled peptide species. Metabolic labeling duration introduces a time domain in which the gradual incorporation of labeled isotopes is recorded. Different stable isotopes are used for labeling. Labeling with heavy water has advantages because it is cost-effective and easy to use. The protein degradation rate constant has been modeled using exponential decay models for the relative abundances of mass isotopomers. The recently developed closed-form equations were applied to study the analytic behavior of the heavy mass isotopomers in the time domain of metabolic labeling. The predictions from the closed-form equations are compared with the practices that have been used to extract degradation rate constants from the time-course profiles of heavy mass isotopomers. It is shown that all mass isotopomers, except for the monoisotope, require data transformations to obtain the exponential depletion, which serves as a basis for the rate constant model. Heavy mass isotopomers may be preferable choices for modeling high-mass peptides or peptides with a high number of labeling sites. The results are also applicable to stable isotope labeling with other atom-based labeling agents.
Collapse
Affiliation(s)
- Rovshan G Sadygov
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555, United States
| |
Collapse
|
22
|
Singh SA, Andraski AB, Higashi H, Lee LH, Ramsaroop A, Sacks FM, Aikawa M. Metabolism of PLTP, CETP, and LCAT on multiple HDL sizes using the Orbitrap Fusion Lumos. JCI Insight 2021; 6:143526. [PMID: 33351780 PMCID: PMC7934878 DOI: 10.1172/jci.insight.143526] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/16/2020] [Indexed: 11/18/2022] Open
Abstract
Recent in vivo tracer studies demonstrated that targeted mass spectrometry (MS) on the Q Exactive Orbitrap could determine the metabolism of HDL proteins 100s-fold less abundant than apolipoprotein A1 (APOA1). In this study, we demonstrate that the Orbitrap Lumos can measure tracer in proteins whose abundances are 1000s-fold less than APOA1, specifically the lipid transfer proteins phospholipid transfer protein (PLTP), cholesterol ester transfer protein (CETP), and lecithin-cholesterol acyl transferase (LCAT). Relative to the Q Exactive, the Lumos improved tracer detection by reducing tracer enrichment compression, thereby providing consistent enrichment data across multiple HDL sizes from 6 participants. We determined by compartmental modeling that PLTP is secreted in medium and large HDL (alpha2, alpha1, and alpha0) and is transferred from medium to larger sizes during circulation from where it is catabolized. CETP is secreted mainly in alpha1 and alpha2 and remains in these sizes during circulation. LCAT is secreted mainly in medium and small HDL (alpha2, alpha3, prebeta). Unlike PLTP and CETP, LCAT’s appearance on HDL is markedly delayed, indicating that LCAT may reside for a time outside of systemic circulation before attaching to HDL in plasma. The determination of these lipid transfer proteins’ unique metabolic structures was possible due to advances in MS technologies.
Collapse
Affiliation(s)
- Sasha A Singh
- Center for Interdisciplinary Cardiovascular Sciences, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Allison B Andraski
- Department of Nutrition and Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Hideyuki Higashi
- Center for Interdisciplinary Cardiovascular Sciences, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Lang Ho Lee
- Center for Interdisciplinary Cardiovascular Sciences, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ashisha Ramsaroop
- Center for Interdisciplinary Cardiovascular Sciences, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Frank M Sacks
- Department of Nutrition and Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.,Channing Division of Network Medicine, Department of Medicine, and
| | - Masanori Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Channing Division of Network Medicine, Department of Medicine, and.,Center for Excellence in Vascular Biology, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
23
|
Sadygov RG. Partial Isotope Profiles Are Sufficient for Protein Turnover Analysis Using Closed-Form Equations of Mass Isotopomer Dynamics. Anal Chem 2020; 92:14747-14753. [PMID: 33084301 DOI: 10.1021/acs.analchem.0c03343] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Metabolic labeling with atom-based heavy isotopes, followed by liquid chromatography coupled with mass spectrometry (LC-MS), has been a powerful technique for studies of proteome and metabolome. In proteomics, the protein turnover of thousands of proteins can be estimated from the gradual incorporation of 2H or 15N in the diet. Software tools have been developed to automate the estimation of protein turnover. Traditionally, the turnover has been estimated using the time course of the depletion of the normalized abundance of monoisotopes. While the bioinformatic aspects of peak detection and integration, time course modeling, and uncertainty estimation have progressed, mass isotopomer dynamics during label incorporation has only been modeled from approximate approaches or numerical simulations. We derive closed-form equations that describe the dynamics of mass isotopomers during metabolic labeling with an atom-based stable isotope. The derived equations create an alternative method for estimating label incorporation. They also provide opportunities for estimation of precursor-product relationships in species or systems where they are unknown. The equations are useful in bioinformatic tools for analyzing mass spectral data from metabolic labeling.
Collapse
Affiliation(s)
- Rovshan G Sadygov
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, 301 University of Blvd, Galveston, Texas 77555, United States
| |
Collapse
|
24
|
Kelly KL, Reagan WJ, Sonnenberg GE, Clasquin M, Hales K, Asano S, Amor PA, Carvajal-Gonzalez S, Shirai N, Matthews MD, Li KW, Hellerstein MK, Vera NB, Ross TT, Cappon G, Bergman A, Buckeridge C, Sun Z, Qejvanaj EZ, Schmahai T, Beebe D, Pfefferkorn JA, Esler WP. De novo lipogenesis is essential for platelet production in humans. Nat Metab 2020; 2:1163-1178. [PMID: 32929234 DOI: 10.1038/s42255-020-00272-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 08/06/2020] [Indexed: 02/08/2023]
Abstract
Acetyl-CoA carboxylase (ACC) catalyses the first step of de novo lipogenesis (DNL). Pharmacologic inhibition of ACC has been of interest for therapeutic intervention in a wide range of diseases. We demonstrate here that ACC and DNL are essential for platelet production in humans and monkeys, but in not rodents or dogs. During clinical evaluation of a systemically distributed ACC inhibitor, unexpected dose-dependent reductions in platelet count were observed. While platelet count reductions were not observed in rat and dog toxicology studies, subsequent studies in cynomolgus monkeys recapitulated these platelet count reductions with a similar concentration response to that in humans. These studies, along with ex vivo human megakaryocyte maturation studies, demonstrate that platelet lowering is a consequence of DNL inhibition likely to result in impaired megakaryocyte demarcation membrane formation. These observations demonstrate that while DNL is a minor quantitative contributor to global lipid balance in humans, DNL is essential to specific lipid pools of physiological importance.
Collapse
Affiliation(s)
- Kenneth L Kelly
- Internal Medicine Research Unit, Pfizer Worldwide Research and Development, Cambridge, MA, USA
| | - William J Reagan
- Drug Safety Research and Development, Pfizer Inc., Groton, CT, USA
| | - Gabriele E Sonnenberg
- Early Clinical Development, Pfizer Worldwide Research and Development, Cambridge, MA, USA
| | - Michelle Clasquin
- Internal Medicine Research Unit, Pfizer Worldwide Research and Development, Cambridge, MA, USA
| | - Katherine Hales
- Internal Medicine Research Unit, Pfizer Worldwide Research and Development, Cambridge, MA, USA
| | - Shoh Asano
- Internal Medicine Research Unit, Pfizer Worldwide Research and Development, Cambridge, MA, USA
| | - Paul A Amor
- Internal Medicine Research Unit, Pfizer Worldwide Research and Development, Cambridge, MA, USA
| | | | - Norimitsu Shirai
- Drug Safety Research and Development, Pfizer Inc., Groton, CT, USA
| | - Marcy D Matthews
- Department of Nutritional Sciences and Toxicology, University of California at Berkeley, Berkeley, CA, USA
| | - Kelvin W Li
- Department of Nutritional Sciences and Toxicology, University of California at Berkeley, Berkeley, CA, USA
| | - Marc K Hellerstein
- Department of Nutritional Sciences and Toxicology, University of California at Berkeley, Berkeley, CA, USA
| | - Nicholas B Vera
- Internal Medicine Research Unit, Pfizer Worldwide Research and Development, Cambridge, MA, USA
| | - Trenton T Ross
- Internal Medicine Research Unit, Pfizer Worldwide Research and Development, Cambridge, MA, USA
| | - Gregg Cappon
- Drug Safety Research and Development, Pfizer Inc., Groton, CT, USA
| | - Arthur Bergman
- Early Clinical Development, Pfizer Worldwide Research and Development, Cambridge, MA, USA
| | - Clare Buckeridge
- Internal Medicine Research Unit, Pfizer Worldwide Research and Development, Cambridge, MA, USA
| | - Zhongyuan Sun
- Internal Medicine Research Unit, Pfizer Worldwide Research and Development, Cambridge, MA, USA
| | - Enida Ziso Qejvanaj
- Internal Medicine Research Unit, Pfizer Worldwide Research and Development, Cambridge, MA, USA
| | | | - David Beebe
- Internal Medicine Research Unit, Pfizer Worldwide Research and Development, Cambridge, MA, USA
| | - Jeffrey A Pfefferkorn
- Internal Medicine Research Unit, Pfizer Worldwide Research and Development, Cambridge, MA, USA
| | - William P Esler
- Internal Medicine Research Unit, Pfizer Worldwide Research and Development, Cambridge, MA, USA.
| |
Collapse
|
25
|
Miller BF, Reid JJ, Price JC, Lin HJL, Atherton PJ, Smith K. CORP: The use of deuterated water for the measurement of protein synthesis. J Appl Physiol (1985) 2020; 128:1163-1176. [PMID: 32213116 DOI: 10.1152/japplphysiol.00855.2019] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The use of deuterium oxide (D2O) has greatly expanded the scope of what is possible for the measurement of protein synthesis. The greatest asset of D2O labeling is that it facilitates the measurement of synthesis rates over prolonged periods of time from single proteins through integrated tissue-based measurements. Because the ease of administration, the method is amenable for use in a variety of models and conditions. Although the method adheres to the same rules as other isotope methods, the flexibility can create conditions that are not the same as other approaches and thus requires careful execution to maintain validity and reliability. For this CORP article, we provide a history that gave rise to the method and discuss the advantages and disadvantages of the method, the critical assumptions, guidelines, and best practices based on instrumentation, models, and experimental design. The goal of this CORP article is to propagate additional use of D2O in a manner that produces reliable and valid data.
Collapse
Affiliation(s)
- Benjamin F Miller
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
| | - Justin J Reid
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
| | - John C Price
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah
| | - Hsien-Jung L Lin
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah
| | - Philip J Atherton
- MRC-ARUK Center for Musculoskeletal Ageing Research, School of Medicine, University of Nottingham, Derby, United Kingdom
| | - Kenneth Smith
- MRC-ARUK Center for Musculoskeletal Ageing Research, School of Medicine, University of Nottingham, Derby, United Kingdom
| |
Collapse
|
26
|
Srisawat K, Hesketh K, Cocks M, Strauss J, Edwards BJ, Lisboa PJ, Shepherd S, Burniston JG. Reliability of Protein Abundance and Synthesis Measurements in Human Skeletal Muscle. Proteomics 2020; 20:e1900194. [DOI: 10.1002/pmic.201900194] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 09/05/2019] [Indexed: 12/31/2022]
Affiliation(s)
- Kanchana Srisawat
- Research Institute for Sport & Exercise SciencesLiverpool John Moores University Liverpool L3 3AF UK
| | - Katie Hesketh
- Research Institute for Sport & Exercise SciencesLiverpool John Moores University Liverpool L3 3AF UK
| | - Matt Cocks
- Research Institute for Sport & Exercise SciencesLiverpool John Moores University Liverpool L3 3AF UK
| | - Juliette Strauss
- Research Institute for Sport & Exercise SciencesLiverpool John Moores University Liverpool L3 3AF UK
| | - Ben J. Edwards
- Research Institute for Sport & Exercise SciencesLiverpool John Moores University Liverpool L3 3AF UK
| | - Paulo J. Lisboa
- Department of Applied MathematicsLiverpool John Moores University Liverpool L3 3AF UK
| | - Sam Shepherd
- Research Institute for Sport & Exercise SciencesLiverpool John Moores University Liverpool L3 3AF UK
| | - Jatin G. Burniston
- Research Institute for Sport & Exercise SciencesLiverpool John Moores University Liverpool L3 3AF UK
| |
Collapse
|
27
|
Lehmann S, Hirtz C, Vialaret J, Ory M, Combes GG, Corre ML, Badiou S, Cristol JP, Hanon O, Cornillot E, Bauchet L, Gabelle A, Colinge J. In Vivo Large-Scale Mapping of Protein Turnover in Human Cerebrospinal Fluid. Anal Chem 2019; 91:15500-15508. [PMID: 31730336 DOI: 10.1021/acs.analchem.9b03328] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The extraction of accurate physiological parameters from clinical samples provides a unique perspective to understand disease etiology and evolution, including under therapy. We introduce a new methodologic framework to map patient proteome dynamics in vivo, either proteome-wide or in large targeted panels. We applied it to ventricular cerebrospinal fluid (CSF) and could determine the turnover parameters of almost 200 proteins, whereas a handful were known previously. We covered a large number of neuron biology- and immune system-related proteins, including many biomarkers and drug targets. This first large data set unraveled a significant relationship between turnover and protein origin that relates to our ability to investigate organ physiology with protein-labeling strategy specifics. Our data constitute the first draft of CSF proteome dynamics as well as a repertoire of peptides for the community to design new analyses. The disclosed methods apply to other fluids or tissues provided sequential sample collection can be performed. We show that the proposed mathematical modeling applies to other analytical methods in the field.
Collapse
Affiliation(s)
- Sylvain Lehmann
- CHU de Montpellier , 34295 Montpellier , France.,IRMB, INSERM, Laboratoire de Biochimie Protéomique Clinique , 34295 Montpellier , France.,Université de Montpellier , 34090 Montpellier , France
| | - Christophe Hirtz
- CHU de Montpellier , 34295 Montpellier , France.,IRMB, INSERM, Laboratoire de Biochimie Protéomique Clinique , 34295 Montpellier , France.,Université de Montpellier , 34090 Montpellier , France
| | - Jérôme Vialaret
- CHU de Montpellier , 34295 Montpellier , France.,IRMB, INSERM, Laboratoire de Biochimie Protéomique Clinique , 34295 Montpellier , France
| | - Maxence Ory
- Institut de Recherche en Cancérologie de Montpellier, INSERM , 34298 Montpellier , France
| | - Guillaume Gras Combes
- Université de Montpellier , 34090 Montpellier , France.,Hôpital Gui de Chauliac, Service de Neurochirurgie , CHU de Montpellier , 34295 Montpellier , France.,INSERM U1051 , 34295 Montpellier , France
| | - Marine Le Corre
- Université de Montpellier , 34090 Montpellier , France.,Hôpital Gui de Chauliac, Service de Neurochirurgie , CHU de Montpellier , 34295 Montpellier , France.,INSERM U1051 , 34295 Montpellier , France
| | - Stéphanie Badiou
- Université de Montpellier , 34090 Montpellier , France.,Département de Biochimie et Hormonologie , CHU de Montpellier , 34295 Montpellier , France.,PhyMedExp , Université de Montpellier, INSERM, CNRS , 34090 Montpellier , France
| | - Jean-Paul Cristol
- Université de Montpellier , 34090 Montpellier , France.,Département de Biochimie et Hormonologie , CHU de Montpellier , 34295 Montpellier , France.,PhyMedExp , Université de Montpellier, INSERM, CNRS , 34090 Montpellier , France
| | - Olivier Hanon
- Service de Gériatrie , Hôpital Broca (AP-HP) , 75013 Paris , France.,Université Paris Descartes, Sorbonne Paris Cité , 75006 Paris , France
| | - Emmanuel Cornillot
- Université de Montpellier , 34090 Montpellier , France.,Institut de Recherche en Cancérologie de Montpellier, INSERM , 34298 Montpellier , France
| | - Luc Bauchet
- Université de Montpellier , 34090 Montpellier , France.,Hôpital Gui de Chauliac, Service de Neurochirurgie , CHU de Montpellier , 34295 Montpellier , France.,INSERM U1051 , 34295 Montpellier , France
| | - Audrey Gabelle
- Université de Montpellier , 34090 Montpellier , France.,Centre Mémoire de Ressources et de Recherche Languedoc-Roussillon , 34295 Montpellier , France.,Hôpital Gui de Chauliac , CHU de Montpellier , 34295 Montpellier , France
| | - Jacques Colinge
- Université de Montpellier , 34090 Montpellier , France.,Institut de Recherche en Cancérologie de Montpellier, INSERM , 34298 Montpellier , France.,Institut Régional du Cancer de Montpellier , 34298 Montpellier , France
| |
Collapse
|
28
|
Ilchenko S, Haddad A, Sadana P, Recchia FA, Sadygov RG, Kasumov T. Calculation of the Protein Turnover Rate Using the Number of Incorporated 2H Atoms and Proteomics Analysis of a Single Labeled Sample. Anal Chem 2019; 91:14340-14351. [PMID: 31638786 DOI: 10.1021/acs.analchem.9b02757] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Rate constant estimation with heavy water requires a long-term experiment with data collection at multiple time points (3-4 weeks for mitochondrial proteome dynamics in mice and much longer in other species). When tissue proteins are analyzed, this approach requires euthanizing animals at each time point or multiple tissue biopsies in humans. Although short-term protocols are available, they require knowledge of the maximum number of isotope labels (N) and accurate quantification of observed 2H-enrichment in the peptide. The high-resolution accurate mass spectrometers used for proteome dynamics studies are characterized by a systematic spectral error that compromises these measurements. To circumvent these issues, we developed a simple algorithm for the rate constant calculation based on a single labeled sample and comparable unlabeled (time 0) sample. The algorithm determines N for all proteogenic amino acids from a long-term experiment to calculate the predicted plateau 2H-labeling of peptides for a short-term protocol and estimates the rate constant based on the measured baseline and the predicted plateau 2H-labeling of peptides. The method was validated based on the rate constant estimation in a long-term experiment in mice and dogs. The improved 2 time-point method enables the rate constant calculation with less than 10% relative error compared to the bench-marked multi-point method in mice and dogs and allows us to detect diet-induced subtle changes in ApoAI turnover in mice. In conclusion, we have developed and validated a new algorithm for protein rate constant calculation based on 2-time point measurements that could also be applied to other biomolecules.
Collapse
Affiliation(s)
- Serguei Ilchenko
- Northeast Ohio Medical University , Rootstown , Ohio 44272 , United States
| | - Andrew Haddad
- Northeast Ohio Medical University , Rootstown , Ohio 44272 , United States
| | - Prabodh Sadana
- Northeast Ohio Medical University , Rootstown , Ohio 44272 , United States
| | - Fabio A Recchia
- Institute of Life Sciences , Scuola Superiore Sant'Anna, Pisa, Fondazione Gabriele Monasterio , 56100 Pisa , Italy.,Cardiovascular Research Center , Lewis Katz School of Medicine at Temple University , Philadelphia , Pennsylvania 19140 , United States
| | - Rovshan G Sadygov
- University of Texas Medical Branch , Galveston , Texas 77555 , United States
| | - Takhar Kasumov
- Northeast Ohio Medical University , Rootstown , Ohio 44272 , United States
| |
Collapse
|
29
|
Borzou A, Sadygov VR, Zhang W, Sadygov RG. Proteome Dynamics from Heavy Water Metabolic Labeling and Peptide Tandem Mass Spectrometry. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2019; 445:10.1016/j.ijms.2019.116194. [PMID: 32055233 PMCID: PMC7017751 DOI: 10.1016/j.ijms.2019.116194] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Protein homeostasis (proteostasis) is a result of a dynamic equilibrium between protein synthesis and degradation. It is important for healthy cell/organ functioning and is often associated with diseases such as neurodegenerative diseases and non-Alcoholic Fatty Liver disease. Heavy water metabolic labeling, combined with liquid-chromatography and mass spectrometry (LC-MS), is a powerful approach to study proteostasis in vivo in high throughput. Traditionally, intact peptide signals are used to estimate stable isotope incorporation in time-course experiments. The time-course of label incorporation is used to extract protein decay rate constant (DRC). Intact peptide signals, computed from integration in chromatographic time and mass-to-charge ratio (m/z) domains, usually, provide an accurate estimate of label incorporation. However, sample complexity (co-elution), limited dynamic range, and low signal-to-noise ratio (S/N) may adversely interfere with the peptide signals. These artifacts complicate the DRC estimations by distorting peak shape in chromatographic time and m/z domains. Fragment ions, on the other hand, are less prone to these artifacts and are potentially well suited in aiding DRC estimations. Here, we show that the label incorporation encoded into the isotope distributions of fragment ions reflect the isotope enrichment during the metabolic labeling with heavy water. We explore the label incorporation statistics for devising practical approaches for DRC estimations.
Collapse
Affiliation(s)
- Ahmad Borzou
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, 301 University of Blvd, Galveston, TX 77555
| | - Vugar R. Sadygov
- Clear Creek High School, 2305 E. Main St., League City, TX 77573
| | - William Zhang
- Clear Lake High School, 2929 Bay Area Blvd, Houston, TX, 77058
| | - Rovshan G. Sadygov
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, 301 University of Blvd, Galveston, TX 77555
| |
Collapse
|
30
|
Angel TE, Naylor BC, Price JC, Evans C, Szapacs M. Improved Sensitivity for Protein Turnover Quantification by Monitoring Immonium Ion Isotopologue Abundance. Anal Chem 2019; 91:9732-9740. [PMID: 31259532 DOI: 10.1021/acs.analchem.9b01329] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe an analytical strategy allowing for the direct quantification of stable isotope label incorporation in newly synthesized proteins following administration of the stable isotope tracer deuterium oxide. We present a demonstration of coupling high-resolution mass spectrometry, metabolic stable isotope labeling, and MS/MS-based isotopologue quantification for the measurement of protein turnover. Stable isotope labeling with deuterium oxide, followed by immonium ion isotopologue quantification, is a more sensitive strategy for determining protein fractional synthesis rates compared to peptide centric mass isotopomer distribution analysis approaches when labeling time and/or stable isotope tracer exposure is limited and, as such, offers a great advantage for human studies.
Collapse
Affiliation(s)
- Thomas E Angel
- In-vitro/In-vivo Translation Platform Group , GlaxoSmithKline , 1250 S Collegeville Road , Collegeville , Pennsylvania 19426 , United States
| | - Bradley C Naylor
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84604 , United States
| | - John C Price
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84604 , United States
| | - Christopher Evans
- In-vitro/In-vivo Translation Platform Group , GlaxoSmithKline , 1250 S Collegeville Road , Collegeville , Pennsylvania 19426 , United States
| | - Matthew Szapacs
- In-vitro/In-vivo Translation Platform Group , GlaxoSmithKline , 1250 S Collegeville Road , Collegeville , Pennsylvania 19426 , United States
| |
Collapse
|
31
|
Morrison MC, Verschuren L, Salic K, Verheij J, Menke A, Wielinga PY, Iruarrizaga‐Lejarreta M, Gole L, Yu W, Turner S, Caspers MP, Martínez‐Arranz I, Pieterman E, Stoop R, van Koppen A, van den Hoek AM, Mato JM, Hanemaaijer R, Alonso C, Kleemann R. Obeticholic Acid Modulates Serum Metabolites and Gene Signatures Characteristic of Human NASH and Attenuates Inflammation and Fibrosis Progression in Ldlr-/-.Leiden Mice. Hepatol Commun 2018; 2:1513-1532. [PMID: 30556039 PMCID: PMC6287481 DOI: 10.1002/hep4.1270] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 09/17/2018] [Indexed: 02/06/2023] Open
Abstract
Concerns have been raised about whether preclinical models sufficiently mimic molecular disease processes observed in nonalcoholic steatohepatitis (NASH) patients, bringing into question their translational value in studies of therapeutic interventions in the process of NASH/fibrosis. We investigated the representation of molecular disease patterns characteristic for human NASH in high-fat diet (HFD)-fed Ldlr-/-.Leiden mice and studied the effects of obeticholic acid (OCA) on these disease profiles. Multiplatform serum metabolomic profiles and genome-wide liver transcriptome from HFD-fed Ldlr-/-.Leiden mice were compared with those of NASH patients. Mice were profiled at the stage of mild (24 weeks HFD) and severe (34 weeks HFD) fibrosis, and after OCA intervention (24-34 weeks; 10 mg/kg/day). Effects of OCA were analyzed histologically, biochemically, by immunohistochemistry, using deuterated water technology (de novo collagen formation), and by its effect on the human-based transcriptomics and metabolomics signatures. The transcriptomics and metabolomics profile of Ldlr-/-.Leiden mice largely reflected the molecular signature of NASH patients. OCA modulated the expression of these molecular profiles and quenched specific proinflammatory-profibrotic pathways. OCA attenuated specific facets of cellular inflammation in liver (F4/80-positive cells) and reduced crown-like structures in adipose tissue. OCA reduced de novo collagen formation and attenuated further progression of liver fibrosis, but did not reduce fibrosis below the level before intervention. Conclusion: HFD-fed Ldlr-/-.Leiden mice recapitulate molecular transcriptomic and metabolomic profiles of NASH patients, and these signatures are modulated by OCA. Intervention with OCA in developing fibrosis reduces collagen deposition and de novo synthesis but does not resolve already manifest fibrosis in the period studied. These data show that human molecular signatures can be used to evaluate the translational character of preclinical models for NASH.
Collapse
Affiliation(s)
- Martine C. Morrison
- Department of Metabolic Health ResearchNetherlands Organization for Applied Scientific ResearchLeidenThe Netherlands
| | - Lars Verschuren
- Department of Microbiology and Systems BiologyNetherlands Organisation for Applied Scientific ResearchZeistThe Netherlands
| | - Kanita Salic
- Department of Metabolic Health ResearchNetherlands Organization for Applied Scientific ResearchLeidenThe Netherlands
| | - Joanne Verheij
- Department of PathologyAmsterdam Medical CenterAmsterdamThe Netherlands
| | - Aswin Menke
- Department of PathologyTriskelion B.V.ZeistThe Netherlands
| | - Peter Y. Wielinga
- Department of Metabolic Health ResearchNetherlands Organization for Applied Scientific ResearchLeidenThe Netherlands
| | | | - Laurent Gole
- Computational BioImage Analysis Unit, Agency of Science, Technology and Research (A*STAR), Institute of Molecular and Cell BiologySingapore
| | - Wei‐Miao Yu
- Computational BioImage Analysis Unit, Agency of Science, Technology and Research (A*STAR), Institute of Molecular and Cell BiologySingapore
| | | | - Martien P.M. Caspers
- Department of Microbiology and Systems BiologyNetherlands Organisation for Applied Scientific ResearchZeistThe Netherlands
| | | | - Elsbet Pieterman
- Department of Metabolic Health ResearchNetherlands Organization for Applied Scientific ResearchLeidenThe Netherlands
| | - Reinout Stoop
- Department of Metabolic Health ResearchNetherlands Organization for Applied Scientific ResearchLeidenThe Netherlands
| | - Arianne van Koppen
- Department of Metabolic Health ResearchNetherlands Organization for Applied Scientific ResearchLeidenThe Netherlands
| | - Anita M. van den Hoek
- Department of Metabolic Health ResearchNetherlands Organization for Applied Scientific ResearchLeidenThe Netherlands
| | | | - Roeland Hanemaaijer
- Department of Metabolic Health ResearchNetherlands Organization for Applied Scientific ResearchLeidenThe Netherlands
| | | | - Robert Kleemann
- Department of Metabolic Health ResearchNetherlands Organization for Applied Scientific ResearchLeidenThe Netherlands
| |
Collapse
|
32
|
Lee K, Haddad A, Osme A, Kim C, Borzou A, Ilchenko S, Allende D, Dasarathy S, McCullough A, Sadygov RG, Kasumov T. Hepatic Mitochondrial Defects in a Nonalcoholic Fatty Liver Disease Mouse Model Are Associated with Increased Degradation of Oxidative Phosphorylation Subunits. Mol Cell Proteomics 2018; 17:2371-2386. [PMID: 30171159 DOI: 10.1074/mcp.ra118.000961] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 08/21/2018] [Indexed: 12/11/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is associated with hepatic mitochondrial dysfunction characterized by reduced ATP synthesis. We applied the 2H2O-metabolic labeling approach to test the hypothesis that the reduced stability of oxidative phosphorylation proteins contributes to mitochondrial dysfunction in a diet-induced mouse model of NAFLD. A high fat diet containing cholesterol (a so-called Western diet (WD)) led to hepatic oxidative stress, steatosis, inflammation and mild fibrosis, all markers of NAFLD, in low density cholesterol (LDL) receptor deficient (LDLR-/-) mice. In addition, compared with controls (LDLR-/- mice on normal diet), livers from NAFLD mice had reduced citrate synthase activity and ATP content, suggesting mitochondrial impairment. Proteome dynamics study revealed that mitochondrial defects are associated with reduced average half-lives of mitochondrial proteins in NAFLD mice (5.41 ± 0.46 versus 5.15 ± 0.49 day, p < 0.05). In particular, the WD reduced stability of oxidative phosphorylation subunits, including cytochrome b-c1 complex subunit 1 (5.9 ± 0.1 versus 3.4 ± 0.8 day), ATP synthase subunit α (6.3 ± 0.4 versus 5.5 ± 0.4 day) and ATP synthase F(0) complex subunit B1 of complex V (8.5 ± 0.6 versus 6.5 ± 0.2 day) (p < 0.05). These changes were associated with impaired complex III and F0F1-ATP synthase activities. Markers of mitophagy were increased, but proteasomal degradation activity were reduced in NAFLD mice liver, suggesting that ATP deficiency because of reduced stability of oxidative phosphorylation complex subunits contributed to inhibition of ubiquitin-proteasome and activation of mitophagy. In conclusion, the 2H2O-metabolic labeling approach shows that increased degradation of hepatic oxidative phosphorylation subunits contributed to mitochondrial impairment in NAFLD mice.
Collapse
Affiliation(s)
- Kwangwon Lee
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, Ohio 44272
| | - Andrew Haddad
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, Ohio 44272
| | - Abdullah Osme
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, Ohio 44272
| | - Chunki Kim
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, Ohio 44272
| | - Ahmad Borzou
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas 77555
| | - Sergei Ilchenko
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, Ohio 44272
| | - Daniela Allende
- Department of Pathology, Cleveland Clinic Foundation, Cleveland, Ohio 44195
| | | | - Arthur McCullough
- Department of Hepatology, Cleveland Clinic Foundation, Cleveland, Ohio 44195
| | - Rovshan G Sadygov
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas 77555
| | - Takhar Kasumov
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, Ohio 44272; Department of Hepatology, Cleveland Clinic Foundation, Cleveland, Ohio 44195.
| |
Collapse
|
33
|
Farrokhi V, Chabot JR, Neubert H, Yang Z. Assessing the Feasibility of Neutralizing Osteopontin with Various Therapeutic Antibody Modalities. Sci Rep 2018; 8:7781. [PMID: 29773891 PMCID: PMC5958109 DOI: 10.1038/s41598-018-26187-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 05/08/2018] [Indexed: 12/14/2022] Open
Abstract
Osteopontin is a secreted glycophosphoprotein that is highly implicated in many physiological and pathological processes such as biomineralization, cell-mediated immunity, inflammation, fibrosis, cell survival, tumorigenesis and metastasis. Antibodies against osteopontin have been actively pursued as potential therapeutics for various diseases by pharmaceutical companies and academic laboratories. Many studies have demonstrated the efficacy of osteopontin inhibition in a variety of preclinical models of diseases such as rheumatoid arthritis, cancer, nonalcoholic steatohepatitis, but clinical utility has not yet been demonstrated. To evaluate the feasibility of osteopontin neutralization with antibodies in a clinical setting, we measured its physiological turnover rate in humans, a sensitive parameter required for mechanistic pharmacokinetic and pharmacodynamic (PK/PD) modeling of biotherapeutics. Results from a stable isotope-labelled amino acid pulse-chase study in healthy human subjects followed by mass spectrometry showed that osteopontin undergoes very rapid turnover. PK/PD modeling and simulation of different theoretical scenarios reveal that achieving sufficient target coverage using antibodies can be very challenging mostly due to osteopontin’s fast turnover, as well as its relatively high plasma concentrations in human. Therapeutic antibodies against osteopontin would need to be engineered to have much extended PK than conventional antibodies, and be administered at high doses and with short dosing intervals.
Collapse
Affiliation(s)
- Vahid Farrokhi
- Biomedicine Design, Worldwide Research and Development, Pfizer Inc., Andover, Massachusetts, 01810, USA
| | - Jeffrey R Chabot
- Biomedicine Design, Worldwide Research and Development, Pfizer Inc., Cambridge, Massachusetts, 02139, USA
| | - Hendrik Neubert
- Biomedicine Design, Worldwide Research and Development, Pfizer Inc., Andover, Massachusetts, 01810, USA
| | - Zhiyong Yang
- Inflammation and Immunology Research Unit, Worldwide Research and Development, Pfizer Inc., Cambridge, Massachusetts, 02139, USA.
| |
Collapse
|
34
|
Goh B, Kim J, Seo S, Kim TY. High-Throughput Measurement of Lipid Turnover Rates Using Partial Metabolic Heavy Water Labeling. Anal Chem 2018; 90:6509-6518. [DOI: 10.1021/acs.analchem.7b05428] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
|
35
|
Murphy CH, Shankaran M, Churchward-Venne TA, Mitchell CJ, Kolar NM, Burke LM, Hawley JA, Kassis A, Karagounis LG, Li K, King C, Hellerstein M, Phillips SM. Effect of resistance training and protein intake pattern on myofibrillar protein synthesis and proteome kinetics in older men in energy restriction. J Physiol 2018. [PMID: 29532476 DOI: 10.1113/jp275246] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
KEY POINTS Strategies to enhance the loss of fat while preserving muscle mass during energy restriction are of great importance to prevent sarcopenia in overweight older adults. We show for the first time that the integrated rate of synthesis of numerous individual contractile, cytosolic and mitochondrial skeletal muscle proteins was increased by resistance training (RT) and unaffected by dietary protein intake pattern during energy restriction in free-living, obese older men. We observed a correlation between the synthetic rates of skeletal muscle-derived proteins obtained in serum (creatine kinase M-type, carbonic anhydrase 3) and the synthetic rates of proteins obtained via muscle sampling; and that the synthesis rates of these proteins in serum revealed the stimulatory effects of RT. These results have ramifications for understanding the influence of RT on skeletal muscle and are consistent with the role of RT in maintaining muscle protein synthesis and potentially supporting muscle mass preservation during weight loss. ABSTRACT We determined how the pattern of protein intake and resistance training (RT) influenced longer-term (2 weeks) integrated myofibrillar protein synthesis (MyoPS) during energy restriction (ER). MyoPS and proteome kinetics were measured during 2 weeks of ER alone and 2 weeks of ER plus RT (ER + RT) in overweight/obese older men. Participants were randomized to consume dietary protein in a balanced (BAL: 25% daily protein per meal × 4 meals) or skewed (SKEW: 7:17:72:4% daily protein per meal) pattern (n = 10 per group). Participants ingested deuterated water during the consecutive 2-week periods, and skeletal muscle biopsies and serum were obtained at the beginning and conclusion of ER and ER + RT. Bulk MyoPS (i.e. synthesis of the myofibrillar protein sub-fraction) and the synthetic rates of numerous individual skeletal muscle proteins were quantified. Bulk MyoPS was not affected by protein distribution during ER or ER + RT (ER: BAL = 1.24 ± 0.31%/day, SKEW = 1.26 ± 0.37%/day; ER + RT: BAL = 1.64 ± 0.48%/day, SKEW = 1.52 ± 0.66%/day) but was ∼26% higher during ER + RT than during ER (P = 0.023). The synthetic rates of 175 of 190 contractile, cytosolic and mitochondrial skeletal muscle proteins, as well as synthesis of muscle-derived proteins measured in serum, creatine kinase M-type (CK-M) and carbonic anhydrase 3 (CA-3), were higher during ER + RT than during ER (P < 0.05). In addition, the synthetic rates of CK-M and CA-3 measured in serum correlated with the synthetic rates of proteins obtained via muscle sampling (P < 0.05). This study provides novel data on the skeletal muscle adaptations to RT and dietary protein distribution.
Collapse
Affiliation(s)
| | - Mahalakshmi Shankaran
- KineMed, Inc., Emeryville, CA, USA.,Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA, USA
| | | | | | | | - Louise M Burke
- Department of Sports Nutrition, Australian Institute of Sport, Canberra, Australia
| | - John A Hawley
- Exercise and Nutrition Research Group, Mary MacKillop Institute for Health Research, Australian Catholic University, Victoria, Australia.,Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, UK
| | - Amira Kassis
- Nestlé Research Center, Nestec Ltd, Lausanne, Switzerland
| | | | - Kelvin Li
- KineMed, Inc., Emeryville, CA, USA.,Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA, USA
| | | | - Marc Hellerstein
- KineMed, Inc., Emeryville, CA, USA.,Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA, USA
| | | |
Collapse
|
36
|
Farrokhi V, Chen X, Neubert H. Protein Turnover Measurements in Human Serum by Serial Immunoaffinity LC-MS/MS. Clin Chem 2018; 64:279-288. [DOI: 10.1373/clinchem.2017.272922] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 08/17/2017] [Indexed: 12/15/2022]
Abstract
Abstract
BACKGROUND
The half-life of target proteins is frequently an important parameter in mechanistic pharmacokinetic and pharmacodynamic (PK/PD) modeling of biotherapeutics. Clinical studies for accurate measurement of physiologically relevant protein turnover can reduce the uncertainty in PK/PD model-based predictions, for example, of the therapeutic dose and dosing regimen in first-in-human clinical trials.
METHODS
We used a targeted mass spectrometry work flow based on serial immunoaffinity enrichment ofmultiple human serum proteins from a [5,5,5-2H3]-L-leucine tracer pulse-chase study in healthy volunteers. To confirm the reproducibility of turnover measurements from serial immunoaffinity enrichment, multiple aliquots from the same sample set were subjected to protein turnover analysis in varying order. Tracer incorporation was measured by multiple–reaction-monitoring mass spectrometry and target turnover was calculated using a four-compartment pharmacokinetic model.
RESULTS
Five proteins of clinical or therapeutic relevance including soluble tumor necrosis factor receptor superfamily member 12A, tissue factor pathway inhibitor, soluble interleukin 1 receptor like 1, soluble mucosal addressin cell adhesion molecule 1, and muscle-specific creatine kinase were sequentially subjected to turnover analysis from the same human serum sample. Calculated half-lives ranged from 5–15 h; however, no tracer incorporation was observed for mucosal addressin cell adhesion molecule 1.
CONCLUSIONS
The utility of clinical pulse-chase studies to investigate protein turnover can be extended by serial immunoaffinity enrichment of target proteins. Turnover analysis from serum and subsequently from remaining supernatants provided analytical sensitivity and reproducibility for multiple human target proteins in the same sample set, irrespective of the order of analysis.
Collapse
Affiliation(s)
- Vahid Farrokhi
- Biomedicine Design, Worldwide Research & Development, Pfizer, Inc., Andover, MA
| | - Xiaoying Chen
- Clinical Pharmacology, Worldwide Research & Development, Pfizer, Inc., La Jolla, CA
| | - Hendrik Neubert
- Biomedicine Design, Worldwide Research & Development, Pfizer, Inc., Andover, MA
| |
Collapse
|
37
|
Zachleder V, Vítová M, Hlavová M, Moudříková Š, Mojzeš P, Heumann H, Becher JR, Bišová K. Stable isotope compounds - production, detection, and application. Biotechnol Adv 2018; 36:784-797. [PMID: 29355599 DOI: 10.1016/j.biotechadv.2018.01.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 01/12/2018] [Accepted: 01/15/2018] [Indexed: 12/14/2022]
Abstract
Stable isotopes are used in wide fields of application from natural tracers in biology, geology and archeology through studies of metabolic fluxes to their application as tracers in quantitative proteomics and structural biology. We review the use of stable isotopes of biogenic elements (H, C, N, O, S, Mg, Se) with the emphasis on hydrogen and its heavy isotope deuterium. We will discuss the limitations of enriching various compounds in stable isotopes when produced in living organisms. Finally, we overview methods for measuring stable isotopes, focusing on methods for detection in single cells in situ and their exploitation in modern biotechnologies.
Collapse
Affiliation(s)
- Vilém Zachleder
- Institute of Microbiology, CAS, Centre Algatech, Laboratory of Cell Cycles of Algae, CZ-379 81 Třeboň, Czech Republic
| | - Milada Vítová
- Institute of Microbiology, CAS, Centre Algatech, Laboratory of Cell Cycles of Algae, CZ-379 81 Třeboň, Czech Republic
| | - Monika Hlavová
- Institute of Microbiology, CAS, Centre Algatech, Laboratory of Cell Cycles of Algae, CZ-379 81 Třeboň, Czech Republic
| | - Šárka Moudříková
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, CZ-121 16 Prague 2, Czech Republic
| | - Peter Mojzeš
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, CZ-121 16 Prague 2, Czech Republic
| | | | | | - Kateřina Bišová
- Institute of Microbiology, CAS, Centre Algatech, Laboratory of Cell Cycles of Algae, CZ-379 81 Třeboň, Czech Republic.
| |
Collapse
|
38
|
Atzrodt J, Derdau V, Kerr WJ, Reid M. Deuterium- und tritiummarkierte Verbindungen: Anwendungen in den modernen Biowissenschaften. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201704146] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Jens Atzrodt
- Isotope Chemistry and Metabolite Synthesis, Integrated Drug Discovery, Medicinal Chemistry; Industriepark Höchst, G876 65926 Frankfurt Deutschland
| | - Volker Derdau
- Isotope Chemistry and Metabolite Synthesis, Integrated Drug Discovery, Medicinal Chemistry; Industriepark Höchst, G876 65926 Frankfurt Deutschland
| | - William J. Kerr
- Department of Pure and Applied Chemistry, WestCHEM; University of Strathclyde; 295 Cathedral Street Glasgow Scotland G1 1XL Großbritannien
| | - Marc Reid
- Department of Pure and Applied Chemistry, WestCHEM; University of Strathclyde; 295 Cathedral Street Glasgow Scotland G1 1XL Großbritannien
| |
Collapse
|
39
|
Atzrodt J, Derdau V, Kerr WJ, Reid M. Deuterium- and Tritium-Labelled Compounds: Applications in the Life Sciences. Angew Chem Int Ed Engl 2018; 57:1758-1784. [PMID: 28815899 DOI: 10.1002/anie.201704146] [Citation(s) in RCA: 407] [Impact Index Per Article: 67.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 07/27/2017] [Indexed: 12/19/2022]
Abstract
Hydrogen isotopes are unique tools for identifying and understanding biological and chemical processes. Hydrogen isotope labelling allows for the traceless and direct incorporation of an additional mass or radioactive tag into an organic molecule with almost no changes in its chemical structure, physical properties, or biological activity. Using deuterium-labelled isotopologues to study the unique mass-spectrometric patterns generated from mixtures of biologically relevant molecules drastically simplifies analysis. Such methods are now providing unprecedented levels of insight in a wide and continuously growing range of applications in the life sciences and beyond. Tritium (3 H), in particular, has seen an increase in utilization, especially in pharmaceutical drug discovery. The efforts and costs associated with the synthesis of labelled compounds are more than compensated for by the enhanced molecular sensitivity during analysis and the high reliability of the data obtained. In this Review, advances in the application of hydrogen isotopes in the life sciences are described.
Collapse
Affiliation(s)
- Jens Atzrodt
- Isotope Chemistry and Metabolite Synthesis, Integrated Drug Discovery, Medicinal Chemistry, Industriepark Höchst, G876, 65926, Frankfurt, Germany
| | - Volker Derdau
- Isotope Chemistry and Metabolite Synthesis, Integrated Drug Discovery, Medicinal Chemistry, Industriepark Höchst, G876, 65926, Frankfurt, Germany
| | - William J Kerr
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde, 295 Cathedral Street, Glasgow, Scotland, G1 1XL, UK
| | - Marc Reid
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde, 295 Cathedral Street, Glasgow, Scotland, G1 1XL, UK
| |
Collapse
|
40
|
Wilkinson DJ. Historical and contemporary stable isotope tracer approaches to studying mammalian protein metabolism. MASS SPECTROMETRY REVIEWS 2018; 37:57-80. [PMID: 27182900 PMCID: PMC5763415 DOI: 10.1002/mas.21507] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 04/22/2016] [Indexed: 06/05/2023]
Abstract
Over a century ago, Frederick Soddy provided the first evidence for the existence of isotopes; elements that occupy the same position in the periodic table are essentially chemically identical but differ in mass due to a different number of neutrons within the atomic nucleus. Allied to the discovery of isotopes was the development of some of the first forms of mass spectrometers, driven forward by the Nobel laureates JJ Thomson and FW Aston, enabling the accurate separation, identification, and quantification of the relative abundance of these isotopes. As a result, within a few years, the number of known isotopes both stable and radioactive had greatly increased and there are now over 300 stable or radioisotopes presently known. Unknown at the time, however, was the potential utility of these isotopes within biological disciplines, it was soon discovered that these stable isotopes, particularly those of carbon (13 C), nitrogen (15 N), oxygen (18 O), and hydrogen (2 H) could be chemically introduced into organic compounds, such as fatty acids, amino acids, and sugars, and used to "trace" the metabolic fate of these compounds within biological systems. From this important breakthrough, the age of the isotope tracer was born. Over the following 80 yrs, stable isotopes would become a vital tool in not only the biological sciences, but also areas as diverse as forensics, geology, and art. This progress has been almost exclusively driven through the development of new and innovative mass spectrometry equipment from IRMS to GC-MS to LC-MS, which has allowed for the accurate quantitation of isotopic abundance within samples of complex matrices. This historical review details the development of stable isotope tracers as metabolic tools, with particular reference to their use in monitoring protein metabolism, highlighting the unique array of tools that are now available for the investigation of protein metabolism in vivo at a whole body down to a single protein level. Importantly, it will detail how this development has been closely aligned to the technological development within the area of mass spectrometry. Without the dedicated development provided by these mass spectrometrists over the past century, the use of stable isotope tracers within the field of protein metabolism would not be as widely applied as it is today, this relationship will no doubt continue to flourish in the future and stable isotope tracers will maintain their importance as a tool within the biological sciences for many years to come. © 2016 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc. Mass Spec Rev.
Collapse
Affiliation(s)
- Daniel James Wilkinson
- MRC‐ARUK Centre for Musculoskeletal Ageing Research, Clinical, Metabolic and Molecular PhysiologyUniversity of Nottingham, Royal Derby Hospital CentreDerbyUnited Kingdom
| |
Collapse
|
41
|
Chen X, Farrokhi V, Singh P, Ocana MF, Patel J, Lin LL, Neubert H, Brodfuehrer J. Biomeasures and mechanistic modeling highlight PK/PD risks for a monoclonal antibody targeting Fn14 in kidney disease. MAbs 2017; 10:62-70. [PMID: 29190188 DOI: 10.1080/19420862.2017.1398873] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Discovery of the upregulation of fibroblast growth factor-inducible-14 (Fn14) receptor following tissue injury has prompted investigation into biotherapeutic targeting of the Fn14 receptor for the treatment of conditions such as chronic kidney diseases. In the development of monoclonal antibody (mAb) therapeutics, there is an increasing trend to use biomeasures combined with mechanistic pharmacokinetic/pharmacodynamic (PK/PD) modeling to enable decision making in early discovery. With the aim of guiding preclinical efforts on designing an antibody with optimized properties, we developed a mechanistic site-of-action (SoA) PK/PD model for human application. This model incorporates experimental biomeasures, including concentration of soluble Fn14 (sFn14) in human plasma and membrane Fn14 (mFn14) in human kidney tissue, and turnover rate of human sFn14. Pulse-chase studies using stable isotope-labeled amino acids and mass spectrometry indicated the sFn14 half-life to be approximately 5 hours in healthy volunteers. The biomeasures (concentration, turnover) of sFn14 in plasma reveals a significant hurdle in designing an antibody against Fn14 with desired characteristics. The projected dose (>1 mg/kg/wk for 90% target coverage) derived from the human PK/PD model revealed potential high and frequent dosing requirements under certain conditions. The PK/PD model suggested a unique bell-shaped relationship between target coverage and antibody affinity for anti-Fn14 mAb, which could be applied to direct the antibody engineering towards an optimized affinity. This investigation highlighted potential applications, including assessment of PK/PD risks during early target validation, human dose prediction and drug candidate optimization.
Collapse
Affiliation(s)
- Xiaoying Chen
- a Department of Biomedicine Design , Pfizer Inc , Cambridge , MA , United States of America
| | - Vahid Farrokhi
- b Department of Biomedicine Design , Pfizer Inc , Andover , MA , United States of America
| | - Pratap Singh
- b Department of Biomedicine Design , Pfizer Inc , Andover , MA , United States of America
| | - Mireia Fernandez Ocana
- b Department of Biomedicine Design , Pfizer Inc , Andover , MA , United States of America
| | - Jenil Patel
- b Department of Biomedicine Design , Pfizer Inc , Andover , MA , United States of America
| | - Lih-Ling Lin
- c Inflammation and Immunology Research Unit , Pfizer Inc. , Cambridge , MA , United States of America
| | - Hendrik Neubert
- b Department of Biomedicine Design , Pfizer Inc , Andover , MA , United States of America
| | - Joanne Brodfuehrer
- a Department of Biomedicine Design , Pfizer Inc , Cambridge , MA , United States of America
| |
Collapse
|
42
|
Eisen A, Greenberg BM, Bowen JD, Arnold DL, Caggiano AO. A double-blind, placebo-controlled, single ascending-dose study of remyelinating antibody rHIgM22 in people with multiple sclerosis. Mult Scler J Exp Transl Clin 2017; 3:2055217317743097. [PMID: 29348926 PMCID: PMC5768281 DOI: 10.1177/2055217317743097] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 09/12/2017] [Accepted: 10/09/2017] [Indexed: 11/15/2022] Open
Abstract
Objective The objective of this paper is to assess, in individuals with clinically stable multiple sclerosis (MS), the safety, tolerability, pharmacokinetics (PK) and exploratory pharmacodynamics of the monoclonal recombinant human antibody IgM22 (rHIgM22). Methods Seventy-two adults with stable MS were enrolled in a double-blind, randomized, placebo-controlled, single ascending-dose, Phase 1 trial examining rHIgM22 from 0.025 to 2.0 mg/kg. Assessments included MRI, MR spectroscopy, plasma PK, and changes in clinical status, laboratory values and adverse events for three months. The final cohort had additional clinical, ophthalmologic, CSF collection and exploratory biomarker evaluations. Participants were monitored for six months. Results rHIgM22 was well tolerated with no clinically significant safety signals. Noncompartmental PK modeling demonstrated linear dose-proportionality both of Cmax and AUC0–Last. The steady-state apparent volume of distribution of approximately 58 ml/kg suggested primarily vascular compartmentalization. CSF:plasma rHIgM22 concentration increased from 0.003% on Day 2 for both 1.0 and 2.0 mg/kg to 0.056% and 0.586% for 1.0 and 2.0 mg/kg, respectively, on Day 29. No statistically significant treatment-related changes were observed in exploratory pharmacodynamic outcome measures included for the 21 participants of the extension cohort. Conclusions Single doses of rHIgM22 were well tolerated and exhibited linear PK, and antibody was detected in the CSF.
Collapse
Affiliation(s)
| | | | | | - Douglas L Arnold
- NeuroRx Research, Montreal, QC, Canada.,Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | | |
Collapse
|
43
|
van Koppen A, Verschuren L, van den Hoek AM, Verheij J, Morrison MC, Li K, Nagabukuro H, Costessi A, Caspers MP, van den Broek TJ, Sagartz J, Kluft C, Beysen C, Emson C, van Gool AJ, Goldschmeding R, Stoop R, Bobeldijk-Pastorova I, Turner SM, Hanauer G, Hanemaaijer R. Uncovering a Predictive Molecular Signature for the Onset of NASH-Related Fibrosis in a Translational NASH Mouse Model. Cell Mol Gastroenterol Hepatol 2017; 5:83-98.e10. [PMID: 29276754 PMCID: PMC5738456 DOI: 10.1016/j.jcmgh.2017.10.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 10/06/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS The incidence of nonalcoholic steatohepatitis (NASH) is increasing. The pathophysiological mechanisms of NASH and the sequence of events leading to hepatic fibrosis are incompletely understood. The aim of this study was to gain insight into the dynamics of key molecular processes involved in NASH and to rank early markers for hepatic fibrosis. METHODS A time-course study in low-density lipoprotein-receptor knockout. Leiden mice on a high-fat diet was performed to identify the temporal dynamics of key processes contributing to NASH and fibrosis. An integrative systems biology approach was used to elucidate candidate markers linked to the active fibrosis process by combining transcriptomics, dynamic proteomics, and histopathology. The translational value of these findings were confirmed using human NASH data sets. RESULTS High-fat-diet feeding resulted in obesity, hyperlipidemia, insulin resistance, and NASH with fibrosis in a time-dependent manner. Temporal dynamics of key molecular processes involved in the development of NASH were identified, including lipid metabolism, inflammation, oxidative stress, and fibrosis. A data-integrative approach enabled identification of the active fibrotic process preceding histopathologic detection using a novel molecular fibrosis signature. Human studies were used to identify overlap of genes and processes and to perform a network biology-based prioritization to rank top candidate markers representing the early manifestation of fibrosis. CONCLUSIONS An early predictive molecular signature was identified that marked the active profibrotic process before histopathologic fibrosis becomes manifest. Early detection of the onset of NASH and fibrosis enables identification of novel blood-based biomarkers to stratify patients at risk, development of new therapeutics, and help shorten (pre)clinical experimental time frames.
Collapse
Key Words
- ALT, alanine aminotransferase
- AST, aspartate aminotransferase
- DEG, differentially expressed genes
- Diagnosis
- ECM, extracellular matrix
- HFD, high-fat diet
- IPA, Ingenuity Pathway Analysis
- LDLr-/-, low-density lipoprotein receptor knock out
- Liver Disease
- Metabolic Syndrome
- NAFLD, nonalcoholic fatty liver disease
- NASH, nonalcoholic steatohepatitis
- Systems Biology
- THBS1, thrombospontin-1
Collapse
Affiliation(s)
- Arianne van Koppen
- Department of Metabolic Health Research, TNO, Leiden, The Netherlands
- University Medical Center Utrecht, Utrecht, The Netherlands
| | - Lars Verschuren
- Department of Microbiology and Systems Biology, TNO, Zeist, The Netherlands
| | | | - Joanne Verheij
- Department of Pathology, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | | | - Kelvin Li
- Kinemed, Inc, Emeryville, California
| | | | | | | | | | | | | | | | | | - Alain J. van Gool
- Department of Microbiology and Systems Biology, TNO, Zeist, The Netherlands
- Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Reinout Stoop
- Department of Metabolic Health Research, TNO, Leiden, The Netherlands
| | | | | | | | | |
Collapse
|
44
|
Holwerda AM, Paulussen KJM, Overkamp M, Smeets JSJ, Gijsen AP, Goessens JPB, Verdijk LB, van Loon LJC. Daily resistance-type exercise stimulates muscle protein synthesis in vivo in young men. J Appl Physiol (1985) 2017; 124:66-75. [PMID: 28935828 DOI: 10.1152/japplphysiol.00610.2017] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Resistance-type exercise increases muscle protein synthesis rates during acute postexercise recovery. The impact of resistance-type exercise training on (local) muscle protein synthesis rates under free-living conditions on a day-to-day basis remains unclear. We determined the impact of daily unilateral resistance-type exercise on local myofibrillar protein synthesis rates during a 3-day period. Twelve healthy young men (22 ± 1 yr) were recruited to participate in this study where they performed daily, unilateral resistance-type exercise during a 3-day intervention period. Two days before the exercise training subjects ingested 400 ml deuterated water (2H2O). Additional 50-ml doses of deuterated water were ingested daily during the training period. Saliva and blood samples were collected daily to assess body water and amino acid precursor deuterium enrichments, respectively. Muscle tissue biopsies were collected before and after the 3 days of unilateral resistance-type exercise training from both the exercised and the nonexercised, control leg for the assessment of muscle protein synthesis rates. Deuterated water dosing resulted in a steady-state body water enrichment of 0.70 ± 0.03%. Intramuscular free [2H]alanine enrichment increased up to 1.84 ± 0.06 mole percent excess (MPE) before the exercise training and did not change in both the exercised and control leg during the 3 subsequent exercise training days (2.11 ± 0.11 and 2.19 ± 0.12 MPE, respectively; P > 0.05). Muscle protein synthesis rates averaged 1.984 ± 0.118 and 1.642 ± 0.089%/day in the exercised vs. nonexercised, control leg when assessed over the entire 3-day period ( P < 0.05). Daily resistance-type exercise stimulates (local) muscle protein synthesis in vivo in humans. NEW & NOTEWORTHY This study demonstrates that daily resistance-type exercise stimulates muscle protein synthesis rates in vivo in humans over multiple days. Whereas acute studies have shown that resistance-type exercise increases muscle protein synthesis rates by 50-100%, we observed a lower impact of resistance-type exercise under free-living conditions. We also compared precursor tracer selection for the calculation of muscle protein synthesis rates and observed that saliva deuterium enrichment serves as an appropriate and practical choice of precursor.
Collapse
Affiliation(s)
- Andrew M Holwerda
- NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+ (MUMC+) , Maastricht , The Netherlands
| | - Kevin J M Paulussen
- NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+ (MUMC+) , Maastricht , The Netherlands
| | - Maarten Overkamp
- NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+ (MUMC+) , Maastricht , The Netherlands
| | - Joey S J Smeets
- NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+ (MUMC+) , Maastricht , The Netherlands
| | - Annemie P Gijsen
- NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+ (MUMC+) , Maastricht , The Netherlands.,Stable Isotope Research Center (SIRC), Maastricht University Medical Center+ (MUMC+) , Maastricht , The Netherlands
| | - Joy P B Goessens
- NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+ (MUMC+) , Maastricht , The Netherlands.,Stable Isotope Research Center (SIRC), Maastricht University Medical Center+ (MUMC+) , Maastricht , The Netherlands
| | - Lex B Verdijk
- NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+ (MUMC+) , Maastricht , The Netherlands
| | - Luc J C van Loon
- NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+ (MUMC+) , Maastricht , The Netherlands
| |
Collapse
|
45
|
Carson RH, Lewis CR, Erickson MN, Zagieboylo AP, Naylor BC, Li KW, Farnsworth PB, Price JC. Imaging regiospecific lipid turnover in mouse brain with desorption electrospray ionization mass spectrometry. J Lipid Res 2017; 58:1884-1892. [PMID: 28743728 DOI: 10.1194/jlr.m078170] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 07/16/2017] [Indexed: 12/31/2022] Open
Abstract
Compartmentalization of metabolism into specific regions of the cell, tissue, and organ is critical to life for all organisms. Mass spectrometric imaging techniques have been valuable in identifying and quantifying concentrations of metabolites in specific locations of cells and tissues, but a true understanding of metabolism requires measurement of metabolite flux on a spatially resolved basis. Here, we utilize desorption ESI-MS (DESI-MS) to measure lipid turnover in the brains of mice. We show that anatomically distinct regions of the brain have distinct lipid turnover rates. These turnover measurements, in conjunction with relative concentration, will enable calculation of regiospecific synthesis rates for individual lipid species in vivo. Monitoring spatially dependent changes in metabolism has the potential to significantly facilitate research in many areas, such as brain development, cancer, and neurodegeneration.
Collapse
Affiliation(s)
- Richard H Carson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 86402
| | - Charlotte R Lewis
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 86402
| | - Mercede N Erickson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 86402
| | | | - Bradley C Naylor
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 86402
| | - Kelvin W Li
- Independent Researcher Brigham Young University, Provo, UT 86402
| | - Paul B Farnsworth
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 86402
| | - John C Price
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 86402
| |
Collapse
|
46
|
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.
Collapse
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
| |
Collapse
|
47
|
Decaris ML, Li KW, Emson CL, Gatmaitan M, Liu S, Wang Y, Nyangau E, Colangelo M, Angel TE, Beysen C, Cui J, Hernandez C, Lazaro L, Brenner DA, Turner SM, Hellerstein MK, Loomba R. Identifying nonalcoholic fatty liver disease patients with active fibrosis by measuring extracellular matrix remodeling rates in tissue and blood. Hepatology 2017; 65:78-88. [PMID: 27706836 PMCID: PMC5516243 DOI: 10.1002/hep.28860] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Revised: 08/02/2016] [Accepted: 09/26/2016] [Indexed: 12/12/2022]
Abstract
UNLABELLED Excess collagen synthesis (fibrogenesis) in the liver plays a causal role in the progression of nonalcoholic fatty liver disease (NAFLD). Methods are needed to identify patients with more rapidly progressing disease and to demonstrate early response to treatment. We describe here a novel method to quantify hepatic fibrogenesis flux rates both directly in liver tissue and noninvasively in blood. Twenty-one patients with suspected NAFLD ingested heavy water (2 H2 O, 50-mL aliquots) two to three times daily for 3-5 weeks prior to a clinically indicated liver biopsy. Liver collagen fractional synthesis rate (FSR) and plasma lumican FSR were measured based on 2 H labeling using tandem mass spectrometry. Patients were classified by histology for fibrosis stage (F0-F4) and as having nonalcoholic fatty liver or nonalcoholic steatohepatitis (NASH). Magnetic resonance elastography measurements of liver stiffness were also performed. Hepatic collagen FSR in NAFLD increased with advancing disease stage (e.g., higher in NASH than nonalcoholic fatty liver, positive correlation with fibrosis score and liver stiffness) and correlated with hemoglobin A1C. In addition, plasma lumican FSR demonstrated a significant correlation with hepatic collagen FSR. CONCLUSION Using a well-characterized cohort of patients with biopsy-proven NAFLD, this study demonstrates that hepatic scar in NASH is actively remodeled even in advanced fibrosis, a disease that is generally regarded as static and slowly progressive. Moreover, hepatic collagen FSR correlates with established risks for fibrotic disease progression in NASH, and plasma lumican FSR correlates with hepatic collagen FSR, suggesting applications as direct or surrogate markers, respectively, of hepatic fibrogenesis in humans. (Hepatology 2017;65:78-88).
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Jeffrey Cui
- NAFLD Research CenterDivision of GastroenterologyDepartment of MedicineUniversity of California at San DiegoLa JollaCA
| | - Carolyn Hernandez
- NAFLD Research CenterDivision of GastroenterologyDepartment of MedicineUniversity of California at San DiegoLa JollaCA
| | - Len Lazaro
- NAFLD Research CenterDivision of GastroenterologyDepartment of MedicineUniversity of California at San DiegoLa JollaCA
| | - David A. Brenner
- NAFLD Research CenterDivision of GastroenterologyDepartment of MedicineUniversity of California at San DiegoLa JollaCA
| | | | - Marc K. Hellerstein
- KineMed, IncEmeryvilleCA,Department of Nutritional Sciences and ToxicologyUniversity of California at BerkeleyBerkeleyCA
| | - Rohit Loomba
- NAFLD Research CenterDivision of GastroenterologyDepartment of MedicineUniversity of California at San DiegoLa JollaCA
| |
Collapse
|
48
|
Lam MPY, Ping P, Murphy E. Proteomics Research in Cardiovascular Medicine and Biomarker Discovery. J Am Coll Cardiol 2016; 68:2819-2830. [PMID: 28007144 PMCID: PMC5189682 DOI: 10.1016/j.jacc.2016.10.031] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/20/2016] [Accepted: 10/21/2016] [Indexed: 11/21/2022]
Abstract
Proteomics is a systems physiology discipline to address the large-scale characterization of protein species within a biological system, be it a cell, a tissue, a body biofluid, an organism, or a cohort population. Building on advances from chemical analytical platforms (e.g., mass spectrometry and other technologies), proteomics approaches have contributed powerful applications in cardiovascular biomedicine, most notably in: 1) the discovery of circulating protein biomarkers of heart diseases from plasma samples; and 2) the identification of disease mechanisms and potential therapeutic targets in cardiovascular tissues, in both preclinical models and translational studies. Contemporary proteomics investigations offer powerful means to simultaneously examine tens of thousands of proteins in various samples, and understand their molecular phenotypes in health and disease. This concise review introduces study design considerations, example applications and use cases, as well as interpretation and analysis of proteomics data in cardiovascular biomedicine.
Collapse
Affiliation(s)
- Maggie P Y Lam
- NIH BD2K Center of Excellence and Department of Physiology, Medicine and Bioinformatics, University of California, Los Angeles, California.
| | - Peipei Ping
- NIH BD2K Center of Excellence and Department of Physiology, Medicine and Bioinformatics, University of California, Los Angeles, California
| | - Elizabeth Murphy
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland.
| |
Collapse
|
49
|
Mathis AD, Naylor BC, Carson RH, Evans E, Harwell J, Knecht J, Hexem E, Peelor FF, Miller BF, Hamilton KL, Transtrum MK, Bikman BT, Price JC. Mechanisms of In Vivo Ribosome Maintenance Change in Response to Nutrient Signals. Mol Cell Proteomics 2016; 16:243-254. [PMID: 27932527 PMCID: PMC5294211 DOI: 10.1074/mcp.m116.063255] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 11/10/2016] [Indexed: 01/01/2023] Open
Abstract
Control of protein homeostasis is fundamental to the health and longevity of all organisms. Because the rate of protein synthesis by ribosomes is a central control point in this process, regulation, and maintenance of ribosome function could have amplified importance in the overall regulatory circuit. Indeed, ribosomal defects are commonly associated with loss of protein homeostasis, aging, and disease (1–4), whereas improved protein homeostasis, implying optimal ribosomal function, is associated with disease resistance and increased lifespan (5–7). To maintain a high-quality ribosome population within the cell, dysfunctional ribosomes are targeted for autophagic degradation. It is not known if complete degradation is the only mechanism for eukaryotic ribosome maintenance or if they might also be repaired by replacement of defective components. We used stable-isotope feeding and protein mass spectrometry to measure the kinetics of turnover of ribosomal RNA (rRNA) and 71 ribosomal proteins (r-proteins) in mice. The results indicate that exchange of individual proteins and whole ribosome degradation both contribute to ribosome maintenance in vivo. In general, peripheral r-proteins and those with more direct roles in peptide-bond formation are replaced multiple times during the lifespan of the assembled structure, presumably by exchange with a free cytoplasmic pool, whereas the majority of r-proteins are stably incorporated for the lifetime of the ribosome. Dietary signals impact the rates of both new ribosome assembly and component exchange. Signal-specific modulation of ribosomal repair and degradation could provide a mechanistic link in the frequently observed associations among diminished rates of protein synthesis, increased autophagy, and greater longevity (5, 6, 8, 9).
Collapse
Affiliation(s)
| | | | | | - Eric Evans
- From the ‡Department of Chemistry and Biochemistry
| | | | - Jared Knecht
- From the ‡Department of Chemistry and Biochemistry
| | - Eric Hexem
- From the ‡Department of Chemistry and Biochemistry
| | - Fredrick F Peelor
- §Department of Health and Exercise Science, Colorado State University, Fort Collins, Colorado 80523
| | - Benjamin F Miller
- §Department of Health and Exercise Science, Colorado State University, Fort Collins, Colorado 80523
| | - Karyn L Hamilton
- §Department of Health and Exercise Science, Colorado State University, Fort Collins, Colorado 80523
| | | | - Benjamin T Bikman
- ‖Department of Physiology and Developmental Biology, Brigham Young University, Provo, Utah 84602
| | - John C Price
- From the ‡Department of Chemistry and Biochemistry,
| |
Collapse
|
50
|
Miyagi M, Kasumov T. Monitoring the synthesis of biomolecules using mass spectrometry. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2015.0378. [PMID: 27644976 PMCID: PMC5031643 DOI: 10.1098/rsta.2015.0378] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/07/2016] [Indexed: 06/01/2023]
Abstract
The controlled and selective synthesis/clearance of biomolecules is critical for most cellular processes. In most high-throughput 'omics' studies, we measure the static quantities of only one class of biomolecules (e.g. DNA, mRNA, proteins or metabolites). It is, however, important to recognize that biological systems are highly dynamic in which biomolecules are continuously renewed and different classes of biomolecules interact and affect each other's production/clearance. Therefore, it is necessary to measure the turnover of diverse classes of biomolecules to understand the dynamic nature of biological systems. Herein, we explain why the kinetic analysis of a diverse range of biomolecules is important and how such an analysis can be done. We argue that heavy water ((2)H2O) could be a universal tracer for monitoring the synthesis of biomolecules on a global scale.This article is part of the themed issue 'Quantitative mass spectrometry'.
Collapse
Affiliation(s)
- Masaru Miyagi
- Center for Proteomics and Bioinformatics, Department of Nutrition, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Takhar Kasumov
- Mass Spectrometry Laboratory, Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH 44272, USA
| |
Collapse
|