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Andraski AB, Sacks FM, Aikawa M, Singh SA. Understanding HDL Metabolism and Biology Through In Vivo Tracer Kinetics. Arterioscler Thromb Vasc Biol 2024; 44:76-88. [PMID: 38031838 PMCID: PMC10842918 DOI: 10.1161/atvbaha.123.319742] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 11/07/2023] [Indexed: 12/01/2023]
Abstract
HDL (high-density lipoprotein), owing to its high protein content and small size, is the densest circulating lipoprotein. In contrast to lipid-laden VLDL (very-low-density lipoprotein) and LDL (low-density lipoprotein) that promote atherosclerosis, HDL is hypothesized to mitigate atherosclerosis via reverse cholesterol transport, a process that entails the uptake and clearance of excess cholesterol from peripheral tissues. This process is mediated by APOA1 (apolipoprotein A-I), the primary structural protein of HDL, as well as by the activities of additional HDL proteins. Tracer-dependent kinetic studies are an invaluable tool to study HDL-mediated reverse cholesterol transport and overall HDL metabolism in humans when a cardiovascular disease therapy is investigated. Unfortunately, HDL cholesterol-raising therapies have not been successful at reducing cardiovascular events suggesting an incomplete picture of HDL biology. However, as HDL tracer studies have evolved from radioactive isotope- to stable isotope-based strategies that in turn are reliant on mass spectrometry technologies, the complexity of the HDL proteome and its metabolism can be more readily addressed. In this review, we outline the motivations, timelines, advantages, and disadvantages of the various tracer kinetics strategies. We also feature the metabolic properties of select HDL proteins known to regulate reverse cholesterol transport, which in turn underscore that HDL lipoproteins comprise a heterogeneous particle population whose distinct protein constituents and kinetics likely determine its function and potential contribution to cholesterol clearance.
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Affiliation(s)
- Allison B. Andraski
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Frank M. Sacks
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Masanori Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Sasha A. Singh
- Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
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2
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Sadygov RG. Protein turnover models for LC-MS data of heavy water metabolic labeling. Brief Bioinform 2022; 23:6513431. [PMID: 35062023 PMCID: PMC8921656 DOI: 10.1093/bib/bbab598] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 12/12/2021] [Accepted: 12/26/2021] [Indexed: 01/23/2023] Open
Abstract
Protein turnover is vital for cellular functioning and is often associated with the pathophysiology of a variety of diseases. Metabolic labeling with heavy water followed by liquid chromatography coupled to mass spectrometry is a powerful tool to study in vivo protein turnover in high throughput and large scale. Heavy water is a cost-effective and easy to use labeling agent. It labels all nonessential amino acids. Due to its toxicity in high concentrations (20% or higher), small enrichments (8% or smaller) of heavy water are used with most organisms. The low concentration results in incomplete labeling of peptides/proteins. Therefore, the data processing is more challenging and requires accurate quantification of labeled and unlabeled forms of a peptide from overlapping mass isotopomer distributions. The work describes the bioinformatics aspects of the analysis of heavy water labeled mass spectral data, available software tools and current challenges and opportunities.
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Affiliation(s)
- Rovshan G Sadygov
- Corresponding author: Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555, USA. Tel.: (409)772-3287; E-mail:
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3
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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.
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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
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4
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Lassman ME, Chappell DL, McAvoy T, Cheng A, de Alwis DP, Pruitt SK, Laterza OF, Li C, Stoch A, Mayawala K. Experimental Medicine Study to Measure Immune Checkpoint Receptors PD-1 and GITR Turnover Rates In Vivo in Humans. Clin Pharmacol Ther 2020; 109:1575-1582. [PMID: 33280089 DOI: 10.1002/cpt.2129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 11/12/2020] [Indexed: 11/12/2022]
Abstract
Development of monoclonal antibodies (mAbs) targeting immune-checkpoint receptors (IMRs) for the treatment of cancer is one of the most active areas of investment in the biopharmaceutical industry. A key decision in the clinical development of anti-IMR mAbs is dose selection. Dose selection can be challenging because the traditional oncology paradigm of administering the maximum tolerated dose is not applicable to anti-IMR mAbs. Instead, dose selection should be informed by the pharmacology of immune signaling. Engaging an IMR is a key initial step to triggering pharmacologic effects, and turnover (i.e., the rate of protein synthesis) of the IMR is a key property to determining the dose level needed to engage the IMR. Here, we applied the stable isotope labeling mass spectrometry technique using 13 C6 -leucine to measure the in vivo turnover rates of IMRs in humans. The 13 C6 -leucine was administered to 10 study participants over 15 hours to measure 13 C6 -leucine enrichment kinetics in 2 IMR targets that have been clinically pursued in oncology: GITR and PD-1. We report the first measurements of GITR and PD-1 median half-lives associated with turnover to be 55.6 and ≥ 49.5 hours, respectively. The approach outlined here can be applied to other IMRs and, more generally, to protein targets.
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Affiliation(s)
- Michael E Lassman
- Translational Molecular Biomarkers, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Derek L Chappell
- Translational Molecular Biomarkers, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Thomas McAvoy
- Translational Molecular Biomarkers, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Amy Cheng
- Translational Medicine Clinical Operations, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Dinesh P de Alwis
- Quantitative Pharmacology and Pharmacometrics, PPDM, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Scott K Pruitt
- Oncology Clinical Research, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Omar F Laterza
- Translational Molecular Biomarkers, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Claire Li
- Quantitative Pharmacology and Pharmacometrics, PPDM, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | | | - Kapil Mayawala
- Quantitative Pharmacology and Pharmacometrics, PPDM, Merck & Co., Inc., Kenilworth, New Jersey, USA
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5
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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.
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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
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Rafiq S, Yeku OO, Jackson HJ, Purdon TJ, van Leeuwen DG, Drakes DJ, Song M, Miele MM, Li Z, Wang P, Yan S, Xiang J, Ma X, Seshan VE, Henderickson RC, Liu C, Brentjens RJ. Targeted delivery of a PD-1-blocking scFv by CAR-T cells enhances anti-tumor efficacy in vivo. Nat Biotechnol 2018; 36:847-856. [PMID: 30102295 PMCID: PMC6126939 DOI: 10.1038/nbt.4195] [Citation(s) in RCA: 519] [Impact Index Per Article: 86.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 06/21/2018] [Indexed: 12/13/2022]
Abstract
The efficacy of chimeric antigen receptor (CAR) T cell therapy against poorly responding tumors can be enhanced by administering the cells in combination with immune checkpoint blockade inhibitors. Alternatively, the CAR construct has been engineered to coexpress factors that boost CAR-T cell function in the tumor microenvironment. We modified CAR-T cells to secrete PD-1-blocking single-chain variable fragments (scFv). These scFv-secreting CAR-T cells acted in both a paracrine and autocrine manner to improve the anti-tumor activity of CAR-T cells and bystander tumor-specific T cells in clinically relevant syngeneic and xenogeneic mouse models of PD-L1+ hematologic and solid tumors. The efficacy was similar to or better than that achieved by combination therapy with CAR-T cells and a checkpoint inhibitor. This approach may improve safety, as the secreted scFvs remained localized to the tumor, protecting CAR-T cells from PD-1 inhibition, which could potentially avoid toxicities associated with systemic checkpoint inhibition.
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Affiliation(s)
- Sarwish Rafiq
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Cellular Therapeutics Center, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Oladapo O. Yeku
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Hollie J. Jackson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Terence J. Purdon
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | - Dylan J. Drakes
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Mei Song
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York, USA
| | - Matthew M. Miele
- Proteomics Core Laboratory, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Zhuoning Li
- Proteomics Core Laboratory, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Pei Wang
- Eureka Therapeutics Inc., Emeryville, California, USA
| | - Su Yan
- Eureka Therapeutics Inc., Emeryville, California, USA
| | - Jingyi Xiang
- Eureka Therapeutics Inc., Emeryville, California, USA
| | - Xiaojing Ma
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York, USA
| | - Venkatraman E. Seshan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Ronald C. Henderickson
- Proteomics Core Laboratory, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Molecular Pharmacology & Chemistry Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Cheng Liu
- Eureka Therapeutics Inc., Emeryville, California, USA
| | - Renier J. Brentjens
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Cellular Therapeutics Center, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Molecular Pharmacology & Chemistry Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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7
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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.
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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
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Mourino-Alvarez L, Baldan-Martin M, Rincon R, Martin-Rojas T, Corbacho-Alonso N, Sastre-Oliva T, Barderas MG. Recent advances and clinical insights into the use of proteomics in the study of atherosclerosis. Expert Rev Proteomics 2017; 14:701-713. [PMID: 28689450 DOI: 10.1080/14789450.2017.1353912] [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: 12/11/2022]
Abstract
INTRODUCTION The application of new proteomics methods may help to identify new diagnostic/predictive molecular markers in an attempt to improve the clinical management of atherosclerosis. Areas covered: Technological advances in proteomics have enhanced its sensitivity and multiplexing capacity, as well as the possibility of studying protein interactions and tissue structure. These advances will help us better understand the molecular mechanisms at play in atherosclerosis as a biological system. Moreover, this should help identify new predictive/diagnostic biomarkers and therapeutic targets that may facilitate effective risk stratification and early diagnosis, with the ensuing rapid implementation of treatment. This review provides a comprehensive overview of the novel methods in proteomics, including state-of-the-art techniques, novel biological samples and applications for the study of atherosclerosis. Expert commentary: Collaboration between clinicians and researchers is crucial to further validate and introduce new molecular markers to manage atherosclerosis that are identified using the most up to date proteomic approaches.
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Affiliation(s)
- Laura Mourino-Alvarez
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos , Toledo , Spain
| | | | - Raul Rincon
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos , Toledo , Spain
| | - Tatiana Martin-Rojas
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos , Toledo , Spain
| | - Nerea Corbacho-Alonso
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos , Toledo , Spain
| | - Tamara Sastre-Oliva
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos , Toledo , Spain
| | - Maria G Barderas
- a Department of Vascular Physiopathology , Hospital Nacional de Paraplejicos , Toledo , Spain
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9
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Baig F, Joshi A, Mayr M. High-density lipoproteins in high resolution: Will proteomics solve the paradox for cardiovascular risk? Proteomics 2017; 17. [DOI: 10.1002/pmic.201600426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 01/05/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Ferheen Baig
- King's British Heart Foundation Centre; King's College London; London UK
| | - Abhishek Joshi
- King's British Heart Foundation Centre; King's College London; London UK
| | - Manuel Mayr
- King's British Heart Foundation Centre; King's College London; London UK
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Abstract
PURPOSE OF REVIEW Mass spectrometry is an ever evolving technology that is equipped with a variety of tools for protein research. Some lipoprotein studies, especially those pertaining to HDL biology, have been exploiting the versatility of mass spectrometry to understand HDL function through its proteome. Despite the role of mass spectrometry in advancing research as a whole, however, the technology remains obscure to those without hands on experience, but still wishing to understand it. In this review, we walk the reader through the coevolution of common mass spectrometry workflows and HDL research, starting from the basic unbiased mass spectrometry methods used to profile the HDL proteome to the most recent targeted methods that have enabled an unprecedented view of HDL metabolism. RECENT FINDINGS Unbiased global proteomics have demonstrated that the HDL proteome is organized into subgroups across the HDL size fractions providing further evidence that HDL functional heterogeneity is in part governed by its varying protein constituents. Parallel reaction monitoring, a novel targeted mass spectrometry method, was used to monitor the metabolism of HDL apolipoproteins in humans and revealed that apolipoproteins contained within the same HDL size fraction exhibit diverse metabolic properties. SUMMARY Mass spectrometry provides a variety of tools and strategies to facilitate understanding, through its proteins, the complex biology of HDL.
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Affiliation(s)
- Sasha A. Singh
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Masanori Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Center for Excellence in Vascular Biology, Cardiovascular Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
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11
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Plasma PCSK9 measurement by liquid chromatography-Tandem mass spectrometry and comparison with conventional ELISA. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1044-1045:24-29. [PMID: 28064066 DOI: 10.1016/j.jchromb.2016.12.040] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 12/21/2016] [Accepted: 12/30/2016] [Indexed: 11/22/2022]
Abstract
The combination of liquid chromatography-tandem mass spectrometry (LC-MS/MS) and trypsin proteolysis is an effective tool for accurate quantitation of multiple proteins in a single run. However, expensive samples pre-treatment as immunoenrichment are often required to analyze low abundant proteins. Plasma proprotein convertase subtilisin/kexin type 9 (PCSK9), a circulating regulator of low-density lipoprotein metabolism, was studied as an example of a low abundant plasma protein. We investigated post-proteolysis solid-phase extraction (SPE) as an alternative strategy to improve its detection. After optimization of pretreatment, including denaturation, reduction, alkylation, tryptic digestion and selective SPE concentration, 91±7% of PCSK9 was recovered from human plasma samples and coefficients of variation were less than 13.2% with a lower limit of quantification of 37.5ng/ml. This LC-MS/MS method was compared with standard enzyme-linked immunosorbent assay in 30 human plasma samples with a broad range of PCSK9 concentrations. Both methods were significantly correlated (r=0.936, p<0.001) with less than 7% of the values out of the 95% confidence interval and similar concentrations were measured using either LC-MS/MS or ELISA methods (514.2±217.2 vs. 504.2±231.0ng/ml, respectively- p=NS). This method involving SPE is an effective measurement tool for low abundant plasma protein analysis that could be easily included in multiplexed assays.
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12
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SRM-based measurements of proprotein convertase subtilisin/kexin type 9 and lipoprotein(a) kinetics in nonhuman primate serum. Bioanalysis 2016; 8:2551-2563. [DOI: 10.4155/bio-2016-0146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Aim: PCSK9 and Lp(a) have been identified as potential biomarkers for cardiovascular disease. The ability to measure protein turnover rates will provide insights into the dynamic properties of these proteins and lead to better understanding of their biological roles. We aimed to implement the stable isotope-labeled tracers ([2H3]-leucine) and develop a novel LC-selected reaction monitoring (SRM) mass spectrometry (MS) method to study the kinetics of PCSK9 and Lp(a). Results: A sensitive method using immunoaffinity enrichment coupled with LC-SRM MS was developed to measure the production and degradation rates of PCSK9 and Lp(a) in naive nonhuman primate serum. Comparable results were obtained from two different routes of tracer administration. Conclusion: Immunoaffinity enrichment coupled with LC-SRM MS demonstrated success in in vivo kinetic measurements of proteins with relatively slow turnover rate (Lp[a]) or low abundance (PCSK9) in serum.
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13
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Holman SW, Hammond DE, Simpson DM, Waters J, Hurst JL, Beynon RJ. Protein turnover measurement using selected reaction monitoring-mass spectrometry (SRM-MS). PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2015.0362. [PMID: 27644981 PMCID: PMC5031629 DOI: 10.1098/rsta.2015.0362] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/23/2016] [Indexed: 05/28/2023]
Abstract
Protein turnover represents an important mechanism in the functioning of cells, with deregulated synthesis and degradation of proteins implicated in many diseased states. Therefore, proteomics strategies to measure turnover rates with high confidence are of vital importance to understanding many biological processes. In this study, the more widely used approach of non-targeted precursor ion signal intensity (MS1) quantification is compared with selected reaction monitoring (SRM), a data acquisition strategy that records data for specific peptides, to determine if improved quantitative data would be obtained using a targeted quantification approach. Using mouse liver as a model system, turnover measurement of four tricarboxylic acid cycle proteins was performed using both MS1 and SRM quantification strategies. SRM outperformed MS1 in terms of sensitivity and selectivity of measurement, allowing more confident determination of protein turnover rates. SRM data are acquired using cheaper and more widely available tandem quadrupole mass spectrometers, making the approach accessible to a larger number of researchers than MS1 quantification, which is best performed on high mass resolution instruments. SRM acquisition is ideally suited to focused studies where the turnover of tens of proteins is measured, making it applicable in determining the dynamics of proteins complexes and complete metabolic pathways.This article is part of the themed issue 'Quantitative mass spectrometry'.
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Affiliation(s)
- Stephen W Holman
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Dean E Hammond
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Crown Street, Liverpool L69 3BX, UK
| | - Deborah M Simpson
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - John Waters
- Mammalian Behaviour and Evolution Group, Department of Evolution, Ecology and Behaviour, Institute of Integrative Biology, University of Liverpool, Leahurst Campus, Neston CH64 7TE, UK
| | - Jane L Hurst
- Mammalian Behaviour and Evolution Group, Department of Evolution, Ecology and Behaviour, Institute of Integrative Biology, University of Liverpool, Leahurst Campus, Neston CH64 7TE, UK
| | - Robert J Beynon
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
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14
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Fernández-Fernández M, Rodríguez-González P, García Alonso JI. A simplified calculation procedure for mass isotopomer distribution analysis (MIDA) based on multiple linear regression. JOURNAL OF MASS SPECTROMETRY : JMS 2016; 51:980-987. [PMID: 27388533 DOI: 10.1002/jms.3809] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 06/16/2016] [Accepted: 07/05/2016] [Indexed: 06/06/2023]
Abstract
We have developed a novel, rapid and easy calculation procedure for Mass Isotopomer Distribution Analysis based on multiple linear regression which allows the simultaneous calculation of the precursor pool enrichment and the fraction of newly synthesized labelled proteins (fractional synthesis) using linear algebra. To test this approach, we used the peptide RGGGLK as a model tryptic peptide containing three subunits of glycine. We selected glycine labelled in two 13 C atoms (13 C2 -glycine) as labelled amino acid to demonstrate that spectral overlap is not a problem in the proposed methodology. The developed methodology was tested first in vitro by changing the precursor pool enrichment from 10 to 40% of 13 C2 -glycine. Secondly, a simulated in vivo synthesis of proteins was designed by combining the natural abundance RGGGLK peptide and 10 or 20% 13 C2 -glycine at 1 : 1, 1 : 3 and 3 : 1 ratios. Precursor pool enrichments and fractional synthesis values were calculated with satisfactory precision and accuracy using a simple spreadsheet. This novel approach can provide a relatively rapid and easy means to measure protein turnover based on stable isotope tracers. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Mario Fernández-Fernández
- Department of Physical and Analytical Chemistry Faculty of Chemistry, University of Oviedo, Julián Clavería 8, 33006, Oviedo, Spain
| | - Pablo Rodríguez-González
- Department of Physical and Analytical Chemistry Faculty of Chemistry, University of Oviedo, Julián Clavería 8, 33006, Oviedo, Spain
| | - J Ignacio García Alonso
- Department of Physical and Analytical Chemistry Faculty of Chemistry, University of Oviedo, Julián Clavería 8, 33006, Oviedo, Spain.
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15
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Singh SA, Aikawa E, Aikawa M. Current Trends and Future Perspectives of State-of-the-Art Proteomics Technologies Applied to Cardiovascular Disease Research. Circ J 2016; 80:1674-83. [PMID: 27430298 DOI: 10.1253/circj.cj-16-0499] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The use of mass spectrometry (MS)-dependent protein research is increasing in the cardiovascular sciences. A major reason for this is the versatility of and ability for MS technologies to accommodate a variety of biological questions such as those pertaining to basic research and clinical applications. In addition, mass spectrometers are becoming easier to operate, and require less expertise to run standard proteomics experiments. Nonetheless, despite the increasing interest in proteomics, many non-expert end users may not be as familiar with the variety of mass spectrometric tools and workflows available to them. We therefore review the major strategies used in unbiased and targeted MS, while providing specific applications in cardiovascular research. Because MS technologies are developing rapidly, it is important to understand the core concepts, strengths and weaknesses. Most importantly, we hope to inspire the further integration of this exciting technology into everyday research in the cardiovascular sciences. (Circ J 2016; 80: 1674-1683).
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Affiliation(s)
- Sasha A Singh
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School
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16
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An evaluation of an aptamer for use as an affinity reagent with MS: PCSK9 as an example protein. Bioanalysis 2016; 8:1557-1564. [PMID: 27397798 DOI: 10.4155/bio-2016-0046] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND For quantitative immunoaffinity IA-LC-MS, the utility of antibodies has been demonstrated many times but the utility of aptamers as affinity reagents is unproven. METHODS Immunoaffinity reagents including a monoclonal antibody and an aptamer were coupled to magnetic beads and used as part of an enrichment strategy for PCSK9 quantitation in plasma. RESULTS With limited method development, we have established a comparison of an anti-PCSK9 aptamer with an anti-PCSK9 monoclonal antibody. The background that results from a tryptic digest of affinity enrichment in plasma was demonstrated for each reagent using high-resolution full scan MS. The assay recovery was demonstrated for multiple concentrations of aptamer in plasma with different concentrations of PCSK9 protein. CONCLUSION The aptamer achieved comparable enrichment to the antibody, but with lower peptide background, thus demonstrating the potential use of aptamers for IA-LC-MS.
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17
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Singh SA, Andraski AB, Pieper B, Goh W, Mendivil CO, Sacks FM, Aikawa M. Multiple apolipoprotein kinetics measured in human HDL by high-resolution/accurate mass parallel reaction monitoring. J Lipid Res 2016; 57:714-28. [PMID: 26862155 DOI: 10.1194/jlr.d061432] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Indexed: 01/10/2023] Open
Abstract
Endogenous labeling with stable isotopes is used to study the metabolism of proteins in vivo. However, traditional detection methods such as GC/MS cannot measure tracer enrichment in multiple proteins simultaneously, and multiple reaction monitoring MS cannot measure precisely the low tracer enrichment in slowly turning-over proteins as in HDL. We exploited the versatility of the high-resolution/accurate mass (HR/AM) quadrupole Orbitrap for proteomic analysis of five HDL sizes. We identified 58 proteins in HDL that were shared among three humans and that were organized into five subproteomes according to HDL size. For seven of these proteins, apoA-I, apoA-II, apoA-IV, apoC-III, apoD, apoE, and apoM, we performed parallel reaction monitoring (PRM) to measure trideuterated leucine tracer enrichment between 0.03 to 1.0% in vivo, as required to study their metabolism. The results were suitable for multicompartmental modeling in all except apoD. These apolipoproteins in each HDL size mainly originated directly from the source compartment, presumably the liver and intestine. Flux of apolipoproteins from smaller to larger HDL or the reverse contributed only slightly to apolipoprotein metabolism. These novel findings on HDL apolipoprotein metabolism demonstrate the analytical breadth and scope of the HR/AM-PRM technology to perform metabolic research.
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Affiliation(s)
- Sasha A Singh
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Allison B Andraski
- Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA
| | - Brett Pieper
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Wilson Goh
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | | | - Frank M Sacks
- Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Masanori Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
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18
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Croyal M, Fall F, Ferchaud-Roucher V, Chétiveaux M, Zaïr Y, Ouguerram K, Krempf M, Nobécourt E. Multiplexed peptide analysis for kinetic measurements of major human apolipoproteins by LC/MS/MS. J Lipid Res 2016; 57:509-15. [PMID: 26773160 DOI: 10.1194/jlr.d064618] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Indexed: 11/20/2022] Open
Abstract
A multiplexed assay was developed by MS to analyze, in a single run, six major human Apos involved in lipoprotein metabolism: ApoA-I, ApoA-II, ApoB100, ApoC-II, ApoC-III, and ApoE. This method was validated in vivo in six subjects who received a 14 h constant infusion of [5,5,5-(2)H3]L-leucine at 10 μM/kg/h. Plasma lipoprotein fractions were isolated from collected blood samples and were digested with trypsin. Proteotypic peptides were subsequently analyzed by LC/MS/MS. Enrichment measurement data were compared with those obtained by the standard method using GC/MS. The required time to obtain the LC/MS/MS data was less than that needed for GC/MS. The enrichments from both methods were correlated for ApoA-I (r = 0.994; P < 0.0001) and ApoB100 (r = 0.999; P < 0.0001), and the Bland-Altman plot confirmed the similarity of the two methods. Intra- and inter-assay variability calculated for the six Apos of interest did not exceed 10.7 and 12.5%, respectively, and kinetic parameters were similar and/or in agreement with previously reported data. Therefore, LC/MS/MS can be considered as a useful tool for human Apo kinetic studies using stable isotopes.
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Affiliation(s)
- Mikaël Croyal
- INRA, UMR 1280, Physiologie des Adaptations Nutritionnelles, CHU Hôtel-Dieu, F-44000 Nantes, France CRNHO, West Human Nutrition Research Center, CHU, F-44093 Nantes, France
| | - Fanta Fall
- INRA, UMR 1280, Physiologie des Adaptations Nutritionnelles, CHU Hôtel-Dieu, F-44000 Nantes, France CRNHO, West Human Nutrition Research Center, CHU, F-44093 Nantes, France
| | - Véronique Ferchaud-Roucher
- INRA, UMR 1280, Physiologie des Adaptations Nutritionnelles, CHU Hôtel-Dieu, F-44000 Nantes, France CRNHO, West Human Nutrition Research Center, CHU, F-44093 Nantes, France
| | - Maud Chétiveaux
- CRNHO, West Human Nutrition Research Center, CHU, F-44093 Nantes, France
| | - Yassine Zaïr
- CRNHO, West Human Nutrition Research Center, CHU, F-44093 Nantes, France
| | - Khadija Ouguerram
- INRA, UMR 1280, Physiologie des Adaptations Nutritionnelles, CHU Hôtel-Dieu, F-44000 Nantes, France CRNHO, West Human Nutrition Research Center, CHU, F-44093 Nantes, France
| | - Michel Krempf
- INRA, UMR 1280, Physiologie des Adaptations Nutritionnelles, CHU Hôtel-Dieu, F-44000 Nantes, France CRNHO, West Human Nutrition Research Center, CHU, F-44093 Nantes, France Department of Endocrinology, Metabolic Diseases, and Nutrition, G and R Laennec Hospital, F-44093 Nantes, France
| | - Estelle Nobécourt
- INRA, UMR 1280, Physiologie des Adaptations Nutritionnelles, CHU Hôtel-Dieu, F-44000 Nantes, France CRNHO, West Human Nutrition Research Center, CHU, F-44093 Nantes, France Department of Endocrinology, Metabolic Diseases, and Nutrition, G and R Laennec Hospital, F-44093 Nantes, France
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19
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Shankaran M, King CL, Angel TE, Holmes WE, Li KW, Colangelo M, Price JC, Turner SM, Bell C, Hamilton KL, Miller BF, Hellerstein MK. Circulating protein synthesis rates reveal skeletal muscle proteome dynamics. J Clin Invest 2016; 126:288-302. [PMID: 26657858 PMCID: PMC4701543 DOI: 10.1172/jci79639] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 11/05/2015] [Indexed: 11/17/2022] Open
Abstract
Here, we have described and validated a strategy for monitoring skeletal muscle protein synthesis rates in rodents and humans over days or weeks from blood samples. We based this approach on label incorporation into proteins that are synthesized specifically in skeletal muscle and escape into the circulation. Heavy water labeling combined with sensitive tandem mass spectrometric analysis allowed integrated synthesis rates of proteins in muscle tissue across the proteome to be measured over several weeks. Fractional synthesis rate (FSR) of plasma creatine kinase M-type (CK-M) and carbonic anhydrase 3 (CA-3) in the blood, more than 90% of which is derived from skeletal muscle, correlated closely with FSR of CK-M, CA-3, and other proteins of various ontologies in skeletal muscle tissue in both rodents and humans. Protein synthesis rates across the muscle proteome generally changed in a coordinate manner in response to a sprint interval exercise training regimen in humans and to denervation or clenbuterol treatment in rodents. FSR of plasma CK-M and CA-3 revealed changes and interindividual differences in muscle tissue proteome dynamics. In human subjects, sprint interval training primarily stimulated synthesis of structural and glycolytic proteins. Together, our results indicate that this approach provides a virtual biopsy, sensitively revealing individualized changes in proteome-wide synthesis rates in skeletal muscle without a muscle biopsy. Accordingly, this approach has potential applications for the diagnosis, management, and treatment of muscle disorders.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Christopher Bell
- Department of Health and Exercise Science, Colorado State University, Fort Collins, Colorado, USA
| | - Karyn L. Hamilton
- Department of Health and Exercise Science, Colorado State University, Fort Collins, Colorado, USA
| | - Benjamin F. Miller
- Department of Health and Exercise Science, Colorado State University, Fort Collins, Colorado, USA
| | - Marc K. Hellerstein
- KineMed Inc., Emeryville, California, USA
- Department of Nutritional Sciences, University of California, Berkeley, California, USA
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20
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Singh SA, Miyosawa K, Aikawa M. Mass spectrometry meets the challenge of understanding the complexity of the lipoproteome: recent findings regarding proteins involved in dyslipidemia and cardiovascular disease. Expert Rev Proteomics 2015; 12:519-32. [PMID: 26325144 DOI: 10.1586/14789450.2015.1078731] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Despite the fact that link between dyslipidemia and atherosclerosis was made over 100 years ago, atherosclerosis remains a major cause of morbidity and mortality worldwide. Major efforts focus towards understanding lipid metabolism, particularly by studying its particle compartments in circulation: the lipoproteins. In recent years, mass spectrometry has played an integral role in the deep sequencing of the lipoproteome and in metabolism studies conducted in vivo. This review highlights the path of lipoprotein research towards state-of-the-art mass spectrometry with special emphasis on the method of selected reaction monitoring and its impact on apolipoprotein metabolism studies. Also presented is what is expected for the lipoprotein field with the recent advent of high resolution/accurate mass parallel reaction monitoring mass spectrometry. The benefits of high resolution/accurate mass measurements are demonstrated by example instrument workflows and by detailing a novel method to quantify very low levels of circulating proprotein convertase subtilisin-kexin type 9 in rabbit. It is anticipated that future clinical studies or clinical trials aimed to treat dyslipidemia by manipulating key regulatory proteins will benefit from the new and exciting opportunities afforded by the latest technologies in mass spectrometry.
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Affiliation(s)
- Sasha A Singh
- a 1 Department of Medicine, Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Katsutoshi Miyosawa
- a 1 Department of Medicine, Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Masanori Aikawa
- a 1 Department of Medicine, Center for Interdisciplinary Cardiovascular Sciences, Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,b 2 Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
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21
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Budha NR, Leabman M, Jin JY, Wada DR, Baruch A, Peng K, Tingley WG, Davis JD. Modeling and Simulation to Support Phase 2 Dose Selection for RG7652, a Fully Human Monoclonal Antibody Against Proprotein Convertase Subtilisin/Kexin Type 9. AAPS J 2015; 17:881-90. [PMID: 25823668 PMCID: PMC4476990 DOI: 10.1208/s12248-015-9750-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 02/17/2015] [Indexed: 12/12/2022] Open
Abstract
RG7652 is a fully humanized monoclonal antibody targeting human PCSK9, a regulator of serum low density lipoprotein cholesterol (LDLc) levels. RG7652 prevents degradation of the hepatic LDLc receptors by blocking PCSK9 binding and thereby resulting in efficient LDLc uptake by hepatocytes. The pharmacokinetics of RG7652 have been evaluated in healthy subjects after single and multiple subcutaneous doses. Pharmacokinetic (PK) and pharmacodynamic (PD) models were developed to explain the antibody PK and LDLc time course data. The PK and PD models based on data from healthy subjects were used to simulate the effects of RG7652 on LDLc levels for a range of potential dose regimens in patients with coronary heart disease. A one-compartment PK model combined with an indirect PD response model was able to adequately describe the PK and LDLc data. Simulations of 400 mg every 4 weeks or 800 mg every 8 weeks regimens show significant LDLc reduction and suggest that dosing RG7652 once every month or once every 2 months is predicted to be optimal for the treatment of hypercholesterolemia. The PK and PD model successfully described the PK and LDLc data from healthy subjects in a Phase 1 study, and the model-based simulations provided useful insights and quantitative understanding for the selection of Phase 2 study doses in patients with coronary heart disease. The approach used in the case study demonstrates the utility of modeling and simulation in designing dose-ranging studies.
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Affiliation(s)
- Nageshwar R. Budha
- />Clinical Pharmacology, Genentech Inc., 1 DNA Way, MS # 463a, S., San Francisco, California 94080 USA
| | - Maya Leabman
- />Development Sciences, Genentech Inc., South San Francisco, California USA
| | - Jin Y. Jin
- />Clinical Pharmacology, Genentech Inc., 1 DNA Way, MS # 463a, S., San Francisco, California 94080 USA
| | | | - Amos Baruch
- />Development Sciences, Genentech Inc., South San Francisco, California USA
| | - Kun Peng
- />Development Sciences, Genentech Inc., South San Francisco, California USA
| | | | - John D. Davis
- />BioAnalytical Sciences, Genentech Inc., South San Francisco, California USA
- />Clinical Pharmacology, Regeneron Pharmaceuticals, Tarrytown, NY USA
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22
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Kaboord B, Smith S, Patel B, Meier S. Enrichment of low-abundant protein targets by immunoprecipitation upstream of mass spectrometry. Methods Mol Biol 2015; 1295:135-151. [PMID: 25820720 DOI: 10.1007/978-1-4939-2550-6_12] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Immunoprecipitation (IP) is commonly used upstream of mass spectrometry (MS) as an enrichment tool for low-abundant protein targets. However, several aspects of the classical IP procedure such as nonspecific protein binding to the isolation matrix, detergents or high salt concentrations in wash and elution buffers, and antibody chain contamination in elution fractions render it incompatible with downstream mass spectrometry analysis. Here, we discuss two IP workflows that are designed to minimize or eliminate these contaminants: the first employs biotinylated antibodies and streptavidin magnetic beads while the second method utilizes a traditional antibody that is oriented and cross-linked to Protein AG magnetic beads. Both modified magnetic supports have low background binding and both antibody immobilization strategies significantly reduce or eliminate antibody heavy and light chain contamination in the eluent, minimizing potential ion suppression effects and thereby maximizing detection of target antigens and interacting proteins.
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Affiliation(s)
- Barbara Kaboord
- Research & Development, Thermo Fisher Scientific, 3747 N. Meridian Rd., Rockford, IL, 61101, USA,
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23
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Quantitation of human peptides and proteins via MS: review of analytically validated assays. Bioanalysis 2014; 6:1843-57. [DOI: 10.4155/bio.14.145] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Since the development of monoclonal antibodies in the 1970s, antibody-based assays have been used for the quantitation of proteins and peptides and, today, they are the most widely used technology in routine laboratory medicine and bioanalysis. However, in the last couple of decades, liquid chromatography-mass spectrometry/mass spectrometry (LC–MS/MS) techniques have been adopted in the quantitation of small molecules, and more recently have made significant contributions in the quantitation of proteins and peptides. In this article, we will review clinical MS-based assays for endogenous peptides, proteins, and therapeutic antibodies, for which validated methods exist. We will also cover the measurement of protein turnover and the unique solutions that MS can offer in this field.
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24
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Applications of low-flow LC–SRM for the analysis of large molecules in pharmaceutical R&D. Bioanalysis 2014; 6:1859-67. [DOI: 10.4155/bio.14.141] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Although ligand-binding assays are frequently employed to measure large molecules, the use of LC–SRM assays is increasingly popular due to the inherent selectivity advantage and the ability to operate without exquisitely selective antibodies. Until recently LC–SRM assays have been unable to compete with ligand-binding assays in terms of sensitivity. However, the use of low-flow chromatography prior to mass spectrometry has played a crucial role in increasing the sensitivity of LC–SRM platforms and enabling measurements of large molecules that had previously been unmeasurable. In this article, we highlight some technical advances, describe strategies for employing low-flow chromatography, and review recent literature that describes implementation of low-flow LC–SRM to support large-molecule analysis in pharmaceutical R&D.
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25
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Lassman ME, McAvoy T, Lee AYH, Chappell D, Wong O, Zhou H, Reyes-Soffer G, Ginsberg HN, Millar JS, Rader DJ, Gutstein DE, Laterza O. Practical immunoaffinity-enrichment LC-MS for measuring protein kinetics of low-abundance proteins. Clin Chem 2014; 60:1217-24. [PMID: 24751376 DOI: 10.1373/clinchem.2014.222455] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
BACKGROUND For a more complete understanding of pharmacodynamic, metabolic, and pathophysiologic effects, protein kinetics, such as production rate and fractional catabolic rate, can offer substantially more information than protein concentration alone. Kinetic experiments with stable isotope tracers typically require laborious sample preparation and are most often used for studying abundant proteins. Here we describe a practical methodology for measuring isotope enrichment into low-abundance proteins that uses an automated procedure and immunoaffinity enrichment (IA) with LC-MS. Low-abundance plasma proteins cholesteryl ester transfer protein (CETP) and proprotein convertase subtilisin/kexin type 9 (PCSK9) were studied as examples. METHODS Human participants (n = 39) were infused with [(2)H(3)]leucine, and blood samples were collected at multiple time points. Sample preparation and analysis were automated and multiplexed to increase throughput. Proteins were concentrated from plasma by use of IA and digested with trypsin to yield proteotypic peptides that were analyzed by microflow chromatography-mass spectrometry to measure isotope enrichment. RESULTS The IA procedure was optimized to provide the greatest signal intensity. Use of a gel-free method increased throughput while increasing the signal. The intra- and interassay CVs were <15% at all isotope enrichment levels studied. More than 1400 samples were analyzed in <3 weeks without the need for instrument stoppages or user interventions. CONCLUSIONS The use of automated gel-free methods to multiplex the measurement of isotope enrichment was applied to the low-abundance proteins CETP and PCSK9.
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Affiliation(s)
| | | | | | | | | | | | | | - Henry N Ginsberg
- Molecular Biomarkers and Diagnostics, Molecular Biomarkers-PPDM, and Clinical Pharmacology, Merck Sharp & Dohme Corp., a subsidiary of Merck & Co., Inc., Whitehouse Station, NJ; Columbia University Medical Center, New York, NY; Division of Translational Medicine and Human Genetics, University of Pennsylvania, Philadelphia, PA
| | - John S Millar
- Division of Translational Medicine and Human Genetics, University of Pennsylvania, Philadelphia, PA
| | - Daniel J Rader
- Division of Translational Medicine and Human Genetics, University of Pennsylvania, Philadelphia, PA
| | - David E Gutstein
- Clinical Pharmacology, Merck Sharp & Dohme Corp., a subsidiary of Merck & Co., Inc., Whitehouse Station, NJ
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26
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Claydon AJ, Beynon R. Proteome dynamics: revisiting turnover with a global perspective. Mol Cell Proteomics 2012; 11:1551-65. [PMID: 23125033 DOI: 10.1074/mcp.o112.022186] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Although bulk protein turnover has been measured with the use of stable isotope labeled tracers for over half a century, it is only recently that the same approach has become applicable to the level of the proteome, permitting analysis of the turnover of many proteins instead of single proteins or an aggregated protein pool. The optimal experimental design for turnover studies is dependent on the nature of the biological system under study, which dictates the choice of precursor label, protein pool sampling strategy, and treatment of data. In this review we discuss different approaches and, in particular, explore how complexity in experimental design and data processing increases as we shift from unicellular to multicellular systems, in particular animals.
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Affiliation(s)
- Amy J Claydon
- Protein Function Group, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
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