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Kobeissy F, Goli M, Yadikar H, Shakkour Z, Kurup M, Haidar MA, Alroumi S, Mondello S, Wang KK, Mechref Y. Advances in neuroproteomics for neurotrauma: unraveling insights for personalized medicine and future prospects. Front Neurol 2023; 14:1288740. [PMID: 38073638 PMCID: PMC10703396 DOI: 10.3389/fneur.2023.1288740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/01/2023] [Indexed: 02/12/2024] Open
Abstract
Neuroproteomics, an emerging field at the intersection of neuroscience and proteomics, has garnered significant attention in the context of neurotrauma research. Neuroproteomics involves the quantitative and qualitative analysis of nervous system components, essential for understanding the dynamic events involved in the vast areas of neuroscience, including, but not limited to, neuropsychiatric disorders, neurodegenerative disorders, mental illness, traumatic brain injury, chronic traumatic encephalopathy, and other neurodegenerative diseases. With advancements in mass spectrometry coupled with bioinformatics and systems biology, neuroproteomics has led to the development of innovative techniques such as microproteomics, single-cell proteomics, and imaging mass spectrometry, which have significantly impacted neuronal biomarker research. By analyzing the complex protein interactions and alterations that occur in the injured brain, neuroproteomics provides valuable insights into the pathophysiological mechanisms underlying neurotrauma. This review explores how such insights can be harnessed to advance personalized medicine (PM) approaches, tailoring treatments based on individual patient profiles. Additionally, we highlight the potential future prospects of neuroproteomics, such as identifying novel biomarkers and developing targeted therapies by employing artificial intelligence (AI) and machine learning (ML). By shedding light on neurotrauma's current state and future directions, this review aims to stimulate further research and collaboration in this promising and transformative field.
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Affiliation(s)
- Firas Kobeissy
- Department of Neurobiology, School of Medicine, Neuroscience Institute, Atlanta, GA, United States
| | - Mona Goli
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
| | - Hamad Yadikar
- Department of Biological Sciences Faculty of Science, Kuwait University, Safat, Kuwait
| | - Zaynab Shakkour
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, MO, United States
| | - Milin Kurup
- Alabama College of Osteopathic Medicine, Dothan, AL, United States
| | | | - Shahad Alroumi
- Department of Biological Sciences Faculty of Science, Kuwait University, Safat, Kuwait
| | - Stefania Mondello
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| | - Kevin K. Wang
- Department of Neurobiology, School of Medicine, Neuroscience Institute, Atlanta, GA, United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
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2
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Dowling P, Zweyer M, Sabir H, Henry M, Meleady P, Swandulla D, Ohlendieck K. Mass spectrometry-based proteomic characterization of the middle-aged mouse brain for animal model research of neuromuscular diseases. Eur J Transl Myol 2023; 33:11553. [PMID: 37545360 PMCID: PMC10583138 DOI: 10.4081/ejtm.2023.11553] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 07/28/2023] [Indexed: 08/08/2023] Open
Abstract
Neuromuscular diseases with primary muscle wasting symptoms may also display multi-systemic changes in the body and exhibit secondary pathophysiological alterations in various non-muscle tissues. In some cases, this includes proteome-wide alterations and/or adaptations in the central nervous system. Thus, in order to provide an improved bioanalytical basis for the comprehensive evaluation of animal models that are routinely used in muscle research, this report describes the mass spectrometry-based proteomic characterization of the mouse brain. Crude tissue extracts were examined by bottom-up proteomics and detected 4558 distinct protein species. The detailed analysis of the brain proteome revealed the presence of abundant cellular proteoforms in the neuronal cytoskeleton, as well as various brain region enriched proteins, including markers of the cerebral cortex, cerebellum, hippocampus and the olfactory bulb. Neuroproteomic markers of specific cell types in the brain were identified in association with various types of neurons and glia cells. Markers of subcellular structures were established for the plasmalemma, nucleus, endoplasmic reticulum, mitochondria and other crucial organelles, as well as synaptic components that are involved in presynaptic vesicle docking, neurotransmitter release and synapse remodelling.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland; Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare.
| | - Margit Zweyer
- Department of Neonatology and Paediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany; German Centre for Neurodegenerative Diseases, University of Bonn, Bonn.
| | - Hemmen Sabir
- Department of Neonatology and Paediatric Intensive Care, Children's Hospital, University of Bonn, Bonn, Germany; German Centre for Neurodegenerative Diseases, University of Bonn, Bonn.
| | - Michael Henry
- National Institute for Cellular Biotechnology, Dublin City University, Dublin.
| | - Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University, Dublin.
| | - Dieter Swandulla
- Institute of Physiology, Medical Faculty, University of Bonn, Bonn.
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland; Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare.
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3
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Targeted Quantification of Protein Phosphorylation and Its Contributions towards Mathematical Modeling of Signaling Pathways. Molecules 2023; 28:molecules28031143. [PMID: 36770810 PMCID: PMC9919559 DOI: 10.3390/molecules28031143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/12/2023] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
Post-translational modifications (PTMs) are key regulatory mechanisms that can control protein function. Of these, phosphorylation is the most common and widely studied. Because of its importance in regulating cell signaling, precise and accurate measurements of protein phosphorylation across wide dynamic ranges are crucial to understanding how signaling pathways function. Although immunological assays are commonly used to detect phosphoproteins, their lack of sensitivity, specificity, and selectivity often make them unreliable for quantitative measurements of complex biological samples. Recent advances in Mass Spectrometry (MS)-based targeted proteomics have made it a more useful approach than immunoassays for studying the dynamics of protein phosphorylation. Selected reaction monitoring (SRM)-also known as multiple reaction monitoring (MRM)-and parallel reaction monitoring (PRM) can quantify relative and absolute abundances of protein phosphorylation in multiplexed fashions targeting specific pathways. In addition, the refinement of these tools by enrichment and fractionation strategies has improved measurement of phosphorylation of low-abundance proteins. The quantitative data generated are particularly useful for building and parameterizing mathematical models of complex phospho-signaling pathways. Potentially, these models can provide a framework for linking analytical measurements of clinical samples to better diagnosis and treatment of disease.
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Aragoneses-Cazorla G, Machuca A, Buendia-Nacarino MP, Anunciação DS, Garcia-Calvo E, Luque-Garcia JL. Super-SILAC Quantitative Proteome Profiling of Zebrafish Larvae. Methods Mol Biol 2023; 2603:199-207. [PMID: 36370281 DOI: 10.1007/978-1-0716-2863-8_16] [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] [Indexed: 06/16/2023]
Abstract
The super-SILAC approach enables the quantitative proteome profiling of highly complex samples such as biological tissues or whole organisms. In this approach, a super-SILAC mix consisting of heavy isotope-labeled cells representative of the tissue or organism to be analyzed is mixed with the unlabeled samples of interest, such that the labeled proteins act as a spike-in standard, thus allowing the relative quantification of proteins between the samples of interest. In this chapter, we thoroughly describe the protocol to carry out the super-SILAC approach using a common in vivo model such as zebrafish larvae.
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Affiliation(s)
| | - Andres Machuca
- Analytical Chemistry Department, Faculty of Chemical Sciences, Complutense University of Madrid, Madrid, Spain
| | - M Pilar Buendia-Nacarino
- Analytical Chemistry Department, Faculty of Chemical Sciences, Complutense University of Madrid, Madrid, Spain
| | - Daniela S Anunciação
- Instituto de Química e Biotecnologia, Universidade Federal de Alagoas, Maceió, AL, Brazil
| | - Estefania Garcia-Calvo
- Analytical Chemistry Department, Faculty of Chemical Sciences, Complutense University of Madrid, Madrid, Spain.
| | - Jose L Luque-Garcia
- Analytical Chemistry Department, Faculty of Chemical Sciences, Complutense University of Madrid, Madrid, Spain.
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Hsiao JT, Chen KH, Sheu F. Determination of the soybean allergen Gly m 6 and its stability in food processing using liquid chromatography-tandem mass spectrometry coupled with stable-isotope dimethyl labelling. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2022; 39:1033-1046. [PMID: 35363120 DOI: 10.1080/19440049.2022.2056639] [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: 11/22/2021] [Revised: 03/04/2022] [Accepted: 03/11/2022] [Indexed: 10/18/2022]
Abstract
A cost-effective method using liquid chromatography-tandem mass spectrometry (LC-MS/MS) coupled with stable-isotope dimethyl labelling was used for the determination of Gly m 6. The validation results revealed that the recoveries and precisions obtained from five spiked levels were in the ranges of 88.8-113.0% and 8.3-22.0%, respectively. The content and stability of the major soybean allergen Gly m 6 in various food processing procedures were evaluated by the quantification results of its surrogate signature peptide. The Gly m 6 content in soybean decreased by 42% after natto fermentation, and by 31% and 35% in pasteurised soymilk and sterilised soymilk, respectively, relative to the raw soymilk. Only 19% of Gly m 6 in raw soymilk was retained in the soymilk film. This study extended the feasibility of dimethyl labelling to soy-based food samples and examined the proteolysis of Gly m 6 in natto fermentation and its thermal instability.
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Affiliation(s)
- Jhih-Ting Hsiao
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, Taiwan
| | - Kuan-Hong Chen
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, Taiwan
| | - Fuu Sheu
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, Taiwan
- Centre for Biotechnology, National Taiwan University, Taipei, Taiwan
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Abstract
Extracellular vesicles (EVs) play an important role in intercellular communication in normal cellular process and pathological conditions by facilitating the transport of cellular content from one cell to another. EVs as conveyors of various biological molecules with their ability to redirect effects on a target cell physiological function in cell type-specific manner makes EVs an excellent candidate for drug delivery vehicle in disease therapy. Moreover, unique characteristics and contents of EVs which differ depends on cellular origin and physiological state make them a valuable source of diagnostic biomarker. Herein, we review the current progress in extracellular vesicle (EV) analysis, its transition from biomedical research to advancing therapy, and recent pioneered approaches to characterize and quantify EVs' subclasses with an emphasis on the integration of advanced technologies for both qualitative and quantitative analysis of EVs in different clinical tissue/body fluid samples.
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Affiliation(s)
- Arada Vinaiphat
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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Hu X, Go YM, Jones DP. Omics Integration for Mitochondria Systems Biology. Antioxid Redox Signal 2020; 32:853-872. [PMID: 31891667 PMCID: PMC7074923 DOI: 10.1089/ars.2019.8006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 12/30/2019] [Indexed: 12/13/2022]
Abstract
Significance: Elucidation of the central importance of mitophagy in homeostasis of cells and organisms emphasizes that mitochondrial functions extend far beyond short-term needs for energy production. In mitochondria systems biology, the mitochondrial genome, proteome, and metabolome operate as a functional network in coordination of cell activities. Organization occurs through subnetworks that are interconnected by membrane potential, transport activities, allosteric and cooperative interactions, redox signaling mechanisms, rheostatic control by post-translational modifications, and metal ion homeostasis. These subnetworks enable use of varied energy precursors, defense against environmental stressors, and macromolecular rewiring to titrate energy production, biosynthesis, and detoxification according to cell-specific needs. Rewiring mechanisms, termed mitochondrial reprogramming, enhance fitness to respond to metabolic resources and challenges from the environment. Maladaptive responses can cause cell death. Maladaptive rewiring can cause disease. In cancer, adaptive rewiring can interfere with effective treatment. Recent Advances: Many recent advances have been facilitated by the development of new omics tools, which create opportunities to use data-driven analysis of omics data to address these complex adaptive and maladaptive mechanisms of mitochondrial reprogramming in human disease. Critical Issues: Application of omics integration to model systems reveals a critical role for metal ion homeostasis broadly impacting mitochondrial reprogramming. Importantly, data show that trans-omics associations are more robust and biologically relevant than single omics associations. Future Directions: Application of omics integration to mitophagy research creates new opportunities to link the complex, interactive functions of mitochondrial form and function in mitochondria systems biology.
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Affiliation(s)
- Xin Hu
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, Georgia
| | - Young-Mi Go
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, Georgia
| | - Dean P. Jones
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Emory University, Atlanta, Georgia
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Matthiesen R, Carvalho AS. Methods and Algorithms for Quantitative Proteomics by Mass Spectrometry. Methods Mol Biol 2020; 2051:161-197. [PMID: 31552629 DOI: 10.1007/978-1-4939-9744-2_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein quantitation by mass spectrometry has always been a resourceful technique in protein discovery, and more recently it has leveraged the advent of clinical proteomics. A single mass spectrometry analysis experiment provides identification and quantitation of proteins as well as information on posttranslational modifications landscape. By contrast, protein array technologies are restricted to quantitation of targeted proteins and their modifications. Currently, there are an overwhelming number of quantitative mass spectrometry methods for protein and peptide quantitation. The aim here is to provide an overview of the most common mass spectrometry methods and algorithms used in quantitative proteomics and discuss the computational aspects to obtain reliable quantitative measures of proteins, peptides and their posttranslational modifications. The development of a pipeline using commercial or freely available software is one of the main challenges in data analysis of many experimental projects. Recent developments of R statistical programming language make it attractive to fully develop pipelines for quantitative proteomics. We discuss concepts of quantitative proteomics that together with current R packages can be used to build highly customizable pipelines.
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Affiliation(s)
- Rune Matthiesen
- Computational and Experimental Biology Group, CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisboa, Portugal
| | - Ana Sofia Carvalho
- Computational and Experimental Biology Group, CEDOC, Chronic Diseases Research Centre, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, Lisboa, Portugal.
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9
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Benz C, Urbaniak MD. Organising the cell cycle in the absence of transcriptional control: Dynamic phosphorylation co-ordinates the Trypanosoma brucei cell cycle post-transcriptionally. PLoS Pathog 2019; 15:e1008129. [PMID: 31830130 PMCID: PMC6907760 DOI: 10.1371/journal.ppat.1008129] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 10/07/2019] [Indexed: 11/18/2022] Open
Abstract
The cell division cycle of the unicellular eukaryote Trypanosome brucei is tightly regulated despite the paucity of transcriptional control that results from the arrangement of genes in polycistronic units and lack of dynamically regulated transcription factors. To identify the contribution of dynamic phosphorylation to T. brucei cell cycle control we have combined cell cycle synchronisation by centrifugal elutriation with quantitative phosphoproteomic analysis. Cell cycle regulated changes in phosphorylation site abundance (917 sites, average 5-fold change) were more widespread and of a larger magnitude than changes in protein abundance (443 proteins, average 2-fold change) and were mostly independent of each other. Hierarchical clustering of co-regulated phosphorylation sites according to their cell cycle profile revealed that a bulk increase in phosphorylation occurs across the cell cycle, with a significant enrichment of known cell cycle regulators and RNA binding proteins (RBPs) within the largest clusters. Cell cycle regulated changes in essential cell cycle kinases are temporally co-ordinated with differential phosphorylation of components of the kinetochore and eukaryotic initiation factors, along with many RBPs not previously linked to the cell cycle such as eight PSP1-C terminal domain containing proteins. The temporal profiles demonstrate the importance of dynamic phosphorylation in co-ordinating progression through the cell cycle, and provide evidence that RBPs play a central role in post-transcriptional regulation of the T. brucei cell cycle. Data are available via ProteomeXchange with identifier PXD013488.
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Affiliation(s)
- Corinna Benz
- Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, United Kingdom
| | - Michael D. Urbaniak
- Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, United Kingdom
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Hoedt E, Zhang G, Neubert TA. Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) for Quantitative Proteomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1140:531-539. [PMID: 31347069 DOI: 10.1007/978-3-030-15950-4_31] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Stable isotope labeling by amino acids in cell culture (SILAC) is a powerful approach for high-throughput quantitative proteomics. SILAC allows highly accurate protein quantitation through metabolic encoding of whole cell proteomes using stable isotope labeled amino acids. Since its introduction in 2002, SILAC has become increasingly popular. In this chapter we review the methodology and application of SILAC, with an emphasis on three research areas: dynamics of posttranslational modifications, protein-protein interactions, and protein turnover.
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Affiliation(s)
- Esthelle Hoedt
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Guoan Zhang
- Proteomics and Metabolomics Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Thomas A Neubert
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Cell Biology, New York University School of Medicine, New York, NY, USA.
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11
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Frederick DW, Trefely S, Buas A, Goodspeed J, Singh J, Mesaros C, Baur JA, Snyder NW. Stable isotope labeling by essential nutrients in cell culture (SILEC) for accurate measurement of nicotinamide adenine dinucleotide metabolism. Analyst 2018; 142:4431-4437. [PMID: 29072717 DOI: 10.1039/c7an01378g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Nicotinamide adenine dinucleotide (NAD) and nicotinamide adenine dinucleotide phosphate (NADP) are conserved metabolic cofactors that mediate reduction-oxidation (redox) reactions throughout all domains of life. The diversity of synthetic routes and cellular processes involving the transfer of reducing equivalents to and from these cofactors makes the accurate quantitation and metabolic tracing of NAD(H) and NADP(H) of broad interest. However, current analytical techniques typically rely on standard curves that do not incorporate confounding effects of the sample matrix. We utilized the essential requirement of niacin and tryptophan for NAD synthesis in mammalian cells to devise a stable isotope labeling by essential nutrients in cell culture (SILEC) method for efficient labeling of intracellular NAD(H) and NADP(H) pools. Coupling this approach with detection by liquid chromatography-high resolution mass spectrometry (LC-HRMS), we demonstrate the utility of incorporating a [13C315N1]-nicotinamide moiety into a library of NAD-derived metabolites for use as internal standards in matrixed samples. Using a two-label system incorporating [13C315N1]-nicotinamide and [13C11]-tryptophan, we quantify the relative contribution of salvage and de novo NAD synthesis, respectively, in S. cerevisiae and HepG2 human hepatocellular carcinoma cells under basal conditions. As a further proof-of-principle, we demonstrate an improvement in the linear range for quantification of NAD and apply this method to analysis of NAD(H) in mouse liver. This method demonstrates the generalizability of SILEC, and provides a simple method for generating a library of stable isotope labeled internal standards for quantifying and tracing the metabolism of cellular and tissue NAD(H) and NADP(H).
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Affiliation(s)
- David W Frederick
- Department of Physiology and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Davis RG, Park HM, Kim K, Greer JB, Fellers RT, LeDuc RD, Romanova EV, Rubakhin SS, Zombeck JA, Wu C, Yau PM, Gao P, van Nispen AJ, Patrie SM, Thomas PM, Sweedler JV, Rhodes JS, Kelleher NL. Top-Down Proteomics Enables Comparative Analysis of Brain Proteoforms Between Mouse Strains. Anal Chem 2018; 90:3802-3810. [PMID: 29481055 DOI: 10.1021/acs.analchem.7b04108] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Over the past decade, advances in mass spectrometry-based proteomics have accelerated brain proteome research aimed at studying the expression, dynamic modification, interaction and function of proteins in the nervous system that are associated with physiological and behavioral processes. With the latest hardware and software improvements in top-down mass spectrometry, the technology has expanded from mere protein profiling to high-throughput identification and quantification of intact proteoforms. Murine systems are broadly used as models to study human diseases. Neuroscientists specifically study the mouse brain from inbred strains to help understand how strain-specific genotype and phenotype affect development, functioning, and disease progression. This work describes the first application of label-free quantitative top-down proteomics to the analysis of the mouse brain proteome. Operating in discovery mode, we determined physiochemical differences in brain tissue from four healthy inbred strains, C57BL/6J, DBA/2J, FVB/NJ, and BALB/cByJ, after probing their intact proteome in the 3.5-30 kDa mass range. We also disseminate these findings using a new tool for top-down proteomics, TDViewer and cataloged them in a newly established Mouse Brain Proteoform Atlas. The analysis of brain tissues from the four strains identified 131 gene products leading to the full characterization of 343 of the 593 proteoforms identified. Within the results, singly and doubly phosphorylated ARPP-21 proteoforms, known to inhibit calmodulin, were differentially expressed across the four strains. Gene ontology (GO) analysis for detected differentially expressed proteoforms also helps to illuminate the similarities and dissimilarities in phenotypes among these inbred strains.
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Affiliation(s)
- Roderick G Davis
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence , Northwestern University , 2145 North Sheridan Road , Evanston , Illinois 60208 , United States
| | - Hae-Min Park
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence , Northwestern University , 2145 North Sheridan Road , Evanston , Illinois 60208 , United States
| | - Kyunggon Kim
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence , Northwestern University , 2145 North Sheridan Road , Evanston , Illinois 60208 , United States
| | - Joseph B Greer
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence , Northwestern University , 2145 North Sheridan Road , Evanston , Illinois 60208 , United States
| | - Ryan T Fellers
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence , Northwestern University , 2145 North Sheridan Road , Evanston , Illinois 60208 , United States
| | - Richard D LeDuc
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence , Northwestern University , 2145 North Sheridan Road , Evanston , Illinois 60208 , United States
| | - Elena V Romanova
- Department of Chemistry , University of Illinois, Urbana-Champaign , 600 South Mathews Avenue , Urbana , Illinois 61801 , United States
| | - Stanislav S Rubakhin
- Department of Chemistry , University of Illinois, Urbana-Champaign , 600 South Mathews Avenue , Urbana , Illinois 61801 , United States
| | - Jonathan A Zombeck
- Department of Psychology , University of Illinois, Urbana-Champaign , 405 North Mathews Avenue , Urbana , Illinois 61801 , United States
| | - Cong Wu
- Department of Chemistry , University of Illinois, Urbana-Champaign , 600 South Mathews Avenue , Urbana , Illinois 61801 , United States
| | - Peter M Yau
- Roy J. Carver Biotechnology Center, Protein Sciences Facility , University of Illinois, Urbana-Champaign , 505 South Mathews Avenue , Urbana , Illinois 61801 , United States
| | - Peng Gao
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence , Northwestern University , 2145 North Sheridan Road , Evanston , Illinois 60208 , United States
| | - Alexandra J van Nispen
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence , Northwestern University , 2145 North Sheridan Road , Evanston , Illinois 60208 , United States
| | - Steven M Patrie
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence , Northwestern University , 2145 North Sheridan Road , Evanston , Illinois 60208 , United States
| | - Paul M Thomas
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence , Northwestern University , 2145 North Sheridan Road , Evanston , Illinois 60208 , United States
| | - Jonathan V Sweedler
- Department of Chemistry , University of Illinois, Urbana-Champaign , 600 South Mathews Avenue , Urbana , Illinois 61801 , United States
| | - Justin S Rhodes
- Department of Psychology , University of Illinois, Urbana-Champaign , 405 North Mathews Avenue , Urbana , Illinois 61801 , United States
| | - Neil L Kelleher
- Departments of Chemistry, Molecular Biosciences and the Proteomics Center of Excellence , Northwestern University , 2145 North Sheridan Road , Evanston , Illinois 60208 , United States
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13
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Yu C, Huang L. Cross-Linking Mass Spectrometry: An Emerging Technology for Interactomics and Structural Biology. Anal Chem 2018; 90:144-165. [PMID: 29160693 PMCID: PMC6022837 DOI: 10.1021/acs.analchem.7b04431] [Citation(s) in RCA: 222] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Clinton Yu
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA 92697
| | - Lan Huang
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA 92697
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14
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Chen B, Liu L, Ho H, Chen Y, Yang Z, Liang X, Payandeh J, Dean B, Hop CECA, Deng Y. Strategies of Drug Transporter Quantitation by LC-MS: Importance of Peptide Selection and Digestion Efficiency. AAPS JOURNAL 2017; 19:1469-1478. [PMID: 28589509 DOI: 10.1208/s12248-017-0106-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 05/24/2017] [Indexed: 12/18/2022]
Abstract
Huge variation of drug transporter abundance was seen in the literature, making PBPK prediction difficult when transporters play a major role. Among multiple factors such as membrane fraction, digestion, and peptide selection that contributed to such variation, peptide selection is the least discussed. Herein, a strategy was established by using a small amount of purified protein standard to select a peptide with near 100% digestion efficiency for quantitation of a transporter protein MDR1. The impact of native membrane protein's tertiary structure on the digestion efficiency of surrogate peptides of MDR1 was investigated. Peptides in more solvent accessible regions are found to be digested much more efficiently than those in large stretches of helical structures. The concentration of peptide EALDESIPPVSFWR(EAL) in the most solvent accessible linker region of MDR1 was found closest to the true protein concentration. When using EAL for MDR1 quantitation, the abundance is over 10 times higher than previously reported, indicating the importance of peptide selection for transporter quantitation. In addition, this study also proposes a screening strategy to select peptides appropriate for relative quantitation for in vitro-in vivo extrapolation in the absence of any protein standard.
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Affiliation(s)
- Buyun Chen
- Genentech Inc, 1 DNA Way, South San Francisco, California, 94080, USA.
| | - Liling Liu
- Genentech Inc, 1 DNA Way, South San Francisco, California, 94080, USA
| | - Hoangdung Ho
- Genentech Inc, 1 DNA Way, South San Francisco, California, 94080, USA
| | - Yuan Chen
- Genentech Inc, 1 DNA Way, South San Francisco, California, 94080, USA
| | - Ze Yang
- Stanford University, 450 Serra Mall, Stanford, California, 94305, USA
| | - Xiaorong Liang
- Genentech Inc, 1 DNA Way, South San Francisco, California, 94080, USA
| | - Jian Payandeh
- Genentech Inc, 1 DNA Way, South San Francisco, California, 94080, USA
| | - Brian Dean
- Genentech Inc, 1 DNA Way, South San Francisco, California, 94080, USA
| | | | - Yuzhong Deng
- Genentech Inc, 1 DNA Way, South San Francisco, California, 94080, USA
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15
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Li J, Tian W, Song J. Proteomics Applications in Dental Derived Stem Cells. J Cell Physiol 2017; 232:1602-1610. [PMID: 27791269 DOI: 10.1002/jcp.25667] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 10/26/2016] [Indexed: 02/05/2023]
Affiliation(s)
- Jie Li
- College of Stomatology; Chongqing Medical University; Chongqing China
- Chongqing Key Laboratory for Oral Diseases and Biomedical Sciences; Chongqing China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education; Chongqing China
| | - Weidong Tian
- National Engineering Laboratory for Oral Regenerative Medicine; West China Hospital of Stomatology; Sichuan University; Chengdu China
| | - Jinlin Song
- College of Stomatology; Chongqing Medical University; Chongqing China
- Chongqing Key Laboratory for Oral Diseases and Biomedical Sciences; Chongqing China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education; Chongqing China
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16
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Lehmann WD. A timeline of stable isotopes and mass spectrometry in the life sciences. MASS SPECTROMETRY REVIEWS 2017; 36:58-85. [PMID: 26919394 DOI: 10.1002/mas.21497] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 01/21/2016] [Indexed: 06/05/2023]
Abstract
This review retraces the role of stable isotopes and mass spectrometry in the life sciences. The timeline is divided into four segments covering the years 1920-1950, 1950-1980, 1980-2000, and 2000 until today. For each period methodic progress and typical applications are discussed. Application of stable isotopes is driven by improvements of mass spectrometry, chromatography, and related fields in sensitivity, mass accuracy, structural specificity, complex sample handling ability, data output, and data evaluation. We currently experience the vision of omics-type analyses, that is, the comprehensive identification and quantification of a complete compound class within one or a few analytical runs. This development is driven by stable isotopes without competition by radioisotopes. In metabolic studies as classic field of isotopic tracer experiments, stable isotopes and radioisotopes were competing solutions, with stable isotopes as the long-term junior partner. Since the 1990s the number of metabolic studies with radioisotopes decreases, whereas stable isotope studies retain their slow but stable upward tendency. Unique fields of stable isotopes are metabolic tests in newborns, metabolic experiments in healthy controls, newborn screening for inborn errors, quantification of drugs and drug metabolites in doping control, natural isotope fractionation in geology, ecology, food authentication, or doping control, and more recently the field of quantitative omics-type analyses. There, cells or whole organisms are systematically labeled with stable isotopes to study proteomic differences or specific responses to stimuli or genetic manipulation. The duo of stable isotopes and mass spectrometry will probably continue to grow in the life sciences, since it delivers reference-quality quantitative data with molecular specificity, often combined with informative isotope effects. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:58-85, 2017.
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Affiliation(s)
- Wolf D Lehmann
- German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany
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17
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Psatha K, Kollipara L, Voutyraki C, Divanach P, Sickmann A, Rassidakis GZ, Drakos E, Aivaliotis M. Deciphering lymphoma pathogenesis via state-of-the-art mass spectrometry-based quantitative proteomics. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1047:2-14. [PMID: 27979587 DOI: 10.1016/j.jchromb.2016.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 10/18/2016] [Accepted: 11/04/2016] [Indexed: 12/13/2022]
Abstract
Mass spectrometry-based quantitative proteomics specifically applied to comprehend the pathogenesis of lymphoma has incremental value in deciphering the heterogeneity in complex deregulated molecular mechanisms/pathways of the lymphoma entities, implementing the current diagnostic and therapeutic strategies. Essential global, targeted and functional differential proteomics analyses although still evolving, have been successfully implemented to shed light on lymphoma pathogenesis to discover and explore the role of potential lymphoma biomarkers and drug targets. This review aims to outline and appraise the present status of MS-based quantitative proteomic approaches in lymphoma research, introducing the current state-of-the-art MS-based proteomic technologies, the opportunities they offer in biological discovery in human lymphomas and the related limitation issues arising from sample preparation to data evaluation. It is a synopsis containing information obtained from recent research articles, reviews and public proteomics repositories (PRIDE). We hope that this review article will aid, assimilate and assess all the information aiming to accelerate the development and validation of diagnostic, prognostic or therapeutic targets for an improved and empowered clinical proteomics application in lymphomas in the nearby future.
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Affiliation(s)
- Konstantina Psatha
- Institute of Molecular Biology and Biotechnology, FORTH, Heraklion, Greece; School of Medicine, National and Kapodistrian University of Athens, Athens, Greece; Department of Pathology, School of Medicine, University of Crete, Heraklion, Greece
| | - Laxmikanth Kollipara
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany
| | | | - Peter Divanach
- Institute of Molecular Biology and Biotechnology, FORTH, Heraklion, Greece
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany; Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom; Medizinische Fakultät, Medizinische Proteom-Center (MPC), Ruhr-Universität Bochum, Bochum, Germany
| | - George Z Rassidakis
- School of Medicine, National and Kapodistrian University of Athens, Athens, Greece; Department of Pathology and Cytology, Karolinska University Hospital and Karolinska Institute, Radiumhemmet, Stockholm, SE-17176, Sweden
| | - Elias Drakos
- Department of Pathology, School of Medicine, University of Crete, Heraklion, Greece
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18
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Duhamel N, Martin D, Larcher R, Fedrizzi B, Barker D. Convenient synthesis of deuterium labelled sesquiterpenes. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.08.079] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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Zühlke D, Dörries K, Bernhardt J, Maaß S, Muntel J, Liebscher V, Pané-Farré J, Riedel K, Lalk M, Völker U, Engelmann S, Becher D, Fuchs S, Hecker M. Costs of life - Dynamics of the protein inventory of Staphylococcus aureus during anaerobiosis. Sci Rep 2016; 6:28172. [PMID: 27344979 PMCID: PMC4921807 DOI: 10.1038/srep28172] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 05/31/2016] [Indexed: 01/19/2023] Open
Abstract
Absolute protein quantification was applied to follow the dynamics of the cytoplasmic proteome of Staphylococcus aureus in response to long-term oxygen starvation. For 1,168 proteins, the majority of all expressed proteins, molecule numbers per cell have been determined to monitor the cellular investments in single branches of bacterial life for the first time. In the presence of glucose the anaerobic protein pattern is characterized by increased amounts of glycolytic and fermentative enzymes such as Eno, GapA1, Ldh1, and PflB. Interestingly, the ferritin-like protein FtnA belongs to the most abundant proteins during anaerobic growth. Depletion of glucose finally leads to an accumulation of different enzymes such as ArcB1, ArcB2, and ArcC2 involved in arginine deiminase pathway. Concentrations of 29 exo- and 78 endometabolites were comparatively assessed and have been integrated to the metabolic networks. Here we provide an almost complete picture on the response to oxygen starvation, from signal transduction pathways to gene expression pattern, from metabolic reorganization after oxygen depletion to beginning cell death and lysis after glucose exhaustion. This experimental approach can be considered as a proof of principle how to combine cell physiology with quantitative proteomics for a new dimension in understanding simple life processes as an entity.
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Affiliation(s)
- Daniela Zühlke
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany
| | - Kirsten Dörries
- Institute of Biochemistry, Ernst-Moritz-Arndt-University Greifswald, Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany
| | - Jörg Bernhardt
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany
| | - Sandra Maaß
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany
| | - Jan Muntel
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany
| | - Volkmar Liebscher
- Department of Mathematics and Informatics, Ernst-Moritz-Arndt-University Greifswald, Walther-Rathenau-Strasse 47, D-17487 Greifswald, Germany
| | - Jan Pané-Farré
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany
| | - Katharina Riedel
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany
| | - Michael Lalk
- Institute of Biochemistry, Ernst-Moritz-Arndt-University Greifswald, Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15 a, D-17487 Greifswald, Germany
| | - Susanne Engelmann
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany.,Institute of Microbiology, Technical University Braunschweig, Inhoffenstrasse 7, D-38124 Braunschweig, Germany.,Helmholtz Institute for Infection Research, Microbial Proteomics, Inhoffenstrasse 7, D-38124 Braunschweig, Germany
| | - Dörte Becher
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany
| | - Stephan Fuchs
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany.,Robert Koch Institute, FG13 Nosocomial Pathogens and Antibiotic Resistance, Burgstrasse 37, D-38855 Wernigerode, Germany
| | - Michael Hecker
- Institute of Microbiology, Ernst-Moritz-Arndt-University Greifswald, F.-L.-Jahn-Strasse 15, D-17487 Greifswald, Germany
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20
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Bakalarski CE, Kirkpatrick DS. A Biologist's Field Guide to Multiplexed Quantitative Proteomics. Mol Cell Proteomics 2016; 15:1489-97. [PMID: 26873251 DOI: 10.1074/mcp.o115.056986] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Indexed: 12/22/2022] Open
Abstract
High-throughput genomic and proteomic studies have generated near-comprehensive catalogs of biological constituents within many model systems. Nevertheless, static catalogs are often insufficient to fully describe the dynamic processes that drive biology. Quantitative proteomic techniques address this need by providing insight into closely related biological states such as the stages of a therapeutic response or cellular differentiation. The maturation of quantitative proteomics in recent years has brought about a variety of technologies, each with their own strengths and weaknesses. It can be difficult for those unfamiliar with this evolving landscape to match the experiment at hand with the best tool for the job. Here, we outline quantitative methods for proteomic mass spectrometry and discuss their benefits and weaknesses from the perspective of the biologist aiming to generate meaningful data and address mechanistic questions.
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Affiliation(s)
- Corey E Bakalarski
- From the Departments of ‡Protein Chemistry and §Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, California 94080
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21
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Yugi K, Kubota H, Hatano A, Kuroda S. Trans-Omics: How To Reconstruct Biochemical Networks Across Multiple 'Omic' Layers. Trends Biotechnol 2016; 34:276-290. [PMID: 26806111 DOI: 10.1016/j.tibtech.2015.12.013] [Citation(s) in RCA: 159] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 12/14/2015] [Accepted: 12/16/2015] [Indexed: 12/17/2022]
Abstract
We propose 'trans-omic' analysis for reconstructing global biochemical networks across multiple omic layers by use of both multi-omic measurements and computational data integration. We introduce technologies for connecting multi-omic data based on prior knowledge of biochemical interactions and characterize a biochemical trans-omic network by concepts of a static and dynamic nature. We introduce case studies of metabolism-centric trans-omic studies to show how to reconstruct a biochemical trans-omic network by connecting multi-omic data and how to analyze it in terms of the static and dynamic nature. We propose a trans-ome-wide association study (trans-OWAS) connecting phenotypes with trans-omic networks that reflect both genetic and environmental factors, which can characterize several complex lifestyle diseases as breakdowns in the trans-omic system.
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Affiliation(s)
- Katsuyuki Yugi
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan; PRESTO, Japan Science and Technology Agency, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Hiroyuki Kubota
- Division of Integrated Omics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan; PRESTO, Japan Science and Technology Agency, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Atsushi Hatano
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shinya Kuroda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan; CREST, Japan Science and Technology Agency, Bunkyo-ku, Tokyo 113-0033, Japan.
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22
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Deng W, Babu IR, Su D, Yin S, Begley TJ, Dedon PC. Trm9-Catalyzed tRNA Modifications Regulate Global Protein Expression by Codon-Biased Translation. PLoS Genet 2015; 11:e1005706. [PMID: 26670883 PMCID: PMC4689569 DOI: 10.1371/journal.pgen.1005706] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 11/06/2015] [Indexed: 12/30/2022] Open
Abstract
Post-transcriptional modifications of transfer RNAs (tRNAs) have long been recognized to play crucial roles in regulating the rate and fidelity of translation. However, the extent to which they determine global protein production remains poorly understood. Here we use quantitative proteomics to show a direct link between wobble uridine 5-methoxycarbonylmethyl (mcm5) and 5-methoxy-carbonyl-methyl-2-thio (mcm5s2) modifications catalyzed by tRNA methyltransferase 9 (Trm9) in tRNAArg(UCU) and tRNAGlu(UUC) and selective translation of proteins from genes enriched with their cognate codons. Controlling for bias in protein expression and alternations in mRNA expression, we find that loss of Trm9 selectively impairs expression of proteins from genes enriched with AGA and GAA codons under both normal and stress conditions. Moreover, we show that AGA and GAA codons occur with high frequency in clusters along the transcripts, which may play a role in modulating translation. Consistent with these results, proteins subject to enhanced ribosome pausing in yeast lacking mcm5U and mcm5s2U are more likely to be down-regulated and contain a larger number of AGA/GAA clusters. Together, these results suggest that Trm9-catalyzed tRNA modifications play a significant role in regulating protein expression within the cell. Here we present evidence for a more complicated role for transfer RNAs (tRNAs) than as mere adapters that link the genetic code in messenger RNA (mRNA) to the amino acid sequence of a protein during translation. tRNAs have long been known to be modified with dozens of different chemical structures other than the 4 canonical ribonucleosides, though the role of these modifications in controlling translation is poorly understood. By quantifying the expression of thousands of proteins in the yeast S. cerevisiae, we identified a mechanistic link between modified ribonucleosides located at the wobble position of two tRNAs, tRNAArg(UCU) and tRNAGlu(UUC), and the translation of proteins derived from genes enriched with codons read by these tRNAs: AGA and GAA. In cells lacking the enzyme that inserts these modifications, tRNA methyltransferase 9 (Trm9), we found a significant reduction in proteins from genes enriched with AGA and GAA codons and with runs of these codons. Also, mRNAs enriched with runs of AGA and GAA codons are subject to stalled translation on ribosomes in yeast lacking mcm5U and mcm5s2U. Together, these results reveal a distinct role for Trm9-catalyzed tRNA modifications in selectively regulating the expression of proteins enriched with AGA and GAA codons.
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Affiliation(s)
- Wenjun Deng
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - I. Ramesh Babu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Dan Su
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Shanye Yin
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Thomas J. Begley
- SUNY College of Nanoscale Science and Engineering, Albany, New York, United States of America
- RNA Institute and Cancer Research Center, University at Albany, State University of New York, Albany, New York, United States of America
| | - Peter C. Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Singapore-MIT Alliance for Research and Technology, Singapore
- * E-mail:
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23
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Domingo-Sananes MR, Szöőr B, Ferguson MAJ, Urbaniak MD, Matthews KR. Molecular control of irreversible bistability during trypanosome developmental commitment. J Cell Biol 2015; 211:455-68. [PMID: 26483558 PMCID: PMC4621835 DOI: 10.1083/jcb.201506114] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/02/2015] [Indexed: 12/15/2022] Open
Abstract
Phosphoproteomic and functional analysis of the developmental progression of Trypanosomes demonstrates that this transition shows bistability, with commitment to differentiation requiring new protein synthesis, and that the protein kinase NRK is a key regulator. The life cycle of Trypanosoma brucei involves developmental transitions that allow survival, proliferation, and transmission of these parasites. One of these, the differentiation of growth-arrested stumpy forms in the mammalian blood into insect-stage procyclic forms, can be induced synchronously in vitro with cis-aconitate. Here, we show that this transition is an irreversible bistable switch, and we map the point of commitment to differentiation after exposure to cis-aconitate. This irreversibility implies that positive feedback mechanisms operate to allow commitment (i.e., the establishment of “memory” of exposure to the differentiation signal). Using the reversible translational inhibitor cycloheximide, we show that this signal memory requires new protein synthesis. We further performed stable isotope labeling by amino acids in cell culture to analyze synchronized parasite populations, establishing the protein and phosphorylation profile of parasites pre- and postcommitment, thereby defining the “commitment proteome.” Functional interrogation of this data set identified Nek-related kinase as the first-discovered protein kinase controlling the initiation of differentiation to procyclic forms.
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Affiliation(s)
- Maria Rosa Domingo-Sananes
- Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, Scotland, UK
| | - Balazs Szöőr
- Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, Scotland, UK
| | - Michael A J Ferguson
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Michael D Urbaniak
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster LA1 4YG, England, UK
| | - Keith R Matthews
- Centre for Immunity, Infection and Evolution, Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, Scotland, UK
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24
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Serum apolipoprotein A-1 quantification by LC-MS with a SILAC internal standard reveals reduced levels in smokers. Bioanalysis 2015; 7:2895-911. [PMID: 26394123 PMCID: PMC4737526 DOI: 10.4155/bio.15.195] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Background: Absolute quantification of protein biomarkers such as serum apolipoprotein A1 by both immunoassays and LC–MS can provide misleading results. Results: Recombinant ApoA-1 internal standard was prepared using stable isotope labeling by amino acids in cell culture with [13C615N2]-lysine and [13C915N1]-tyrosine in human cells. A stable isotope dilution LC–MS method for serum ApoA-1 was validated and levels analyzed for 50 nonsmokers and 50 smokers. Conclusion: The concentration of ApoA-1 in nonsmokers was 169.4 mg/dl with an 18.4% reduction to 138.2 mg/dl in smokers. The validated assay will have clinical utility for assessing effects of smoking cessation and therapeutic or dietary interventions in high-risk populations.
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25
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Chen X, Wei S, Ji Y, Guo X, Yang F. Quantitative proteomics using SILAC: Principles, applications, and developments. Proteomics 2015; 15:3175-92. [DOI: 10.1002/pmic.201500108] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 04/24/2015] [Accepted: 06/08/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Xiulan Chen
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
| | - Shasha Wei
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
| | - Yanlong Ji
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
- University of Chinese Academy of Sciences; Beijing P. R. China
| | - Xiaojing Guo
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
| | - Fuquan Yang
- Key Laboratory of Protein and Peptide Pharmaceuticals and Laboratory of Proteomics; Institute of Biophysics; Chinese Academy of Sciences; Beijing P. R. China
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26
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Chan CTY, Deng W, Li F, DeMott MS, Babu IR, Begley TJ, Dedon PC. Highly Predictive Reprogramming of tRNA Modifications Is Linked to Selective Expression of Codon-Biased Genes. Chem Res Toxicol 2015; 28:978-88. [PMID: 25772370 PMCID: PMC4438938 DOI: 10.1021/acs.chemrestox.5b00004] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Cells respond to stress by controlling
gene expression at several
levels, with little known about the role of translation. Here, we
demonstrate a coordinated translational stress response system involving
stress-specific reprogramming of tRNA wobble modifications that leads
to selective translation of codon-biased mRNAs representing different
classes of critical response proteins. In budding yeast exposed to
four oxidants and five alkylating agents, tRNA modification patterns
accurately distinguished among chemically similar stressors, with
14 modified ribonucleosides forming the basis for a data-driven model
that predicts toxicant chemistry with >80% sensitivity and specificity.
tRNA modification subpatterns also distinguish SN1 from
SN2 alkylating agents, with SN2-induced increases
in m3C in tRNA mechanistically linked to selective translation
of threonine-rich membrane proteins from genes enriched with ACC and
ACT degenerate codons for threonine. These results establish tRNA
modifications as predictive biomarkers of exposure and illustrate
a novel regulatory mechanism for translational control of cell stress
response.
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Affiliation(s)
| | | | | | | | | | - Thomas J Begley
- ∥College of Nanoscale Science, State University of New York, Albany, New York 12203, United States
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27
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Mangrum JB, Martin EJ, Brophy DF, Hawkridge AM. Intact stable isotope labeled plasma proteins from the SILAC-labeled HepG2 secretome. Proteomics 2015; 15:3104-15. [DOI: 10.1002/pmic.201400369] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 11/05/2014] [Accepted: 12/05/2014] [Indexed: 01/26/2023]
Affiliation(s)
- John B. Mangrum
- Department of Pharmaceutics; Virginia Commonwealth University; Richmond VA USA
| | - Erika J. Martin
- Department of Pharmacotherapy & Outcomes Science; Virginia Commonwealth University; Richmond VA USA
| | - Donald F. Brophy
- Department of Pharmacotherapy & Outcomes Science; Virginia Commonwealth University; Richmond VA USA
| | - Adam M. Hawkridge
- Department of Pharmaceutics; Virginia Commonwealth University; Richmond VA USA
- Department of Pharmacotherapy & Outcomes Science; Virginia Commonwealth University; Richmond VA USA
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28
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Liu Y, Zhou Q, Tang M, Fu N, Shao W, Zhang S, Yin Y, Zeng R, Wang X, Hu G, Zhou J. Upregulation of alphaB-crystallin expression in the substantia nigra of patients with Parkinson's disease. Neurobiol Aging 2015; 36:1686-1691. [PMID: 25683516 DOI: 10.1016/j.neurobiolaging.2015.01.015] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Revised: 11/18/2014] [Accepted: 01/16/2015] [Indexed: 02/03/2023]
Abstract
Parkinson's disease (PD) is one of the most devastating neurodegenerative disorders. The underlying mechanisms of the characteristic neurodegeneration in the substantia nigra (SN) are still not fully understood. To better understand the molecular events occurring in the SN of PD brain, we used the culture-derived isotope tag-based quantitative proteomics to compare the protein expression profiles in the nigral tissue of PD patients and control subjects. We identified a total of 11 differentially expressed proteins, including alphaB-crystallin (Cryab). Both the levels and pattern of Cryab expression in the SN were validated. It was revealed that Cryab was markedly upregulated in the SN of PD brain. Cryab expression was also upregulated in reactive astrocytes and microglia in a neurotoxin-induced mouse PD model. Moreover, we showed increased expression of Cryab in cytoplasmic inclusions in a subset of glial cells in Parkinsonian brain. Thus, we identified Cryab that is highly expressed in the SN of PD brain and may be involved in the glial pathology during dopaminergic neuron degeneration in PD.
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Affiliation(s)
- Yingjun Liu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qinbo Zhou
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Mi Tang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China; Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Ning Fu
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wei Shao
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Shuzhen Zhang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yanqing Yin
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Rong Zeng
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xiaomin Wang
- Center of Parkinson's Disease, Beijing Institute for Brain Disorders, Beijing, China
| | - Gang Hu
- Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jiawei Zhou
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
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29
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Abstract
Stable isotope labeling with amino acids in cell culture (SILAC) has risen as a powerful quantification technique in mass spectrometry (MS)-based proteomics in classical and modified forms. Previously, SILAC was limited to cultured cells because of the requirement of active protein synthesis; however, in recent years, it was expanded to model organisms and tissue samples. Specifically, the super-SILAC technique uses a mixture of SILAC-labeled cells as a spike-in standard for accurate quantification of unlabeled samples, thereby enabling quantification of human tissue samples. Here, we highlight the recent developments in super-SILAC and its application to the study of clinical samples, secretomes, post-translational modifications and organelle proteomes. Finally, we propose super-SILAC as a robust and accurate method that can be commercialized and applied to basic and clinical research.
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Affiliation(s)
- Anjana Shenoy
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
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30
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The proteomic landscape of the suprachiasmatic nucleus clock reveals large-scale coordination of key biological processes. PLoS Genet 2014; 10:e1004695. [PMID: 25330117 PMCID: PMC4199512 DOI: 10.1371/journal.pgen.1004695] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 08/21/2014] [Indexed: 11/19/2022] Open
Abstract
The suprachiasmatic nucleus (SCN) acts as the central clock to coordinate circadian oscillations in mammalian behavior, physiology and gene expression. Despite our knowledge of the circadian transcriptome of the SCN, how it impacts genome-wide protein expression is not well understood. Here, we interrogated the murine SCN proteome across the circadian cycle using SILAC-based quantitative mass spectrometry. Of the 2112 proteins that were accurately quantified, 20% (421 proteins) displayed a time-of-day-dependent expression profile. Within this time-of-day proteome, 11% (48 proteins) were further defined as circadian based on a sinusoidal expression pattern with a ∼24 h period. Nine circadianly expressed proteins exhibited 24 h rhythms at the transcript level, with an average time lag that exceeded 8 h. A substantial proportion of the time-of-day proteome exhibited abrupt fluctuations at the anticipated light-to-dark and dark-to-light transitions, and was enriched for proteins involved in several key biological pathways, most notably, mitochondrial oxidative phosphorylation. Additionally, predicted targets of miR-133ab were enriched in specific hierarchical clusters and were inversely correlated with miR133ab expression in the SCN. These insights into the proteomic landscape of the SCN will facilitate a more integrative understanding of cellular control within the SCN clock. The suprachiasmatic nucleus (SCN) serves as the master circadian pacemaker in mammals, coordinating the physiological responses of a myriad of peripheral clocks throughout the body and linking their rhythms to the environmental light-dark cycle. In this study, we interrogated the murine SCN proteome across the circadian cycle using stable isotope labeling by amino acids in cell culture (SILAC)-based quantitative mass spectrometry. Among 3275 identified proteins in the SCN, 421 displayed a time-of-day-dependent expression profile, 48 fit a circadian expression profile with a ∼24 h period, and a surprising number of proteins were ultradianly expressed. Nine circadianly expressed proteins were accompanied by transcripts that were also 24 h rhythmic, but with a significant time lag (>8 h) between the phases of peak mRNA vs. protein expression. A substantial proportion of the time-of-day proteome exhibited abrupt fluctuations at the anticipated dawn and dusk, and was involved in mitochondrial oxidative phosphorylation. Additionally, predicted targets of miR-133ab were enriched in specific hierarchical clusters and were inversely correlated with miR133ab expression in the SCN. Our study underscores the significance of post-transcriptional regulation, the surprising prevalence of ultradian protein expression, and the functional implications on mitochondrial energy metabolism.
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31
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Zhang G, Annan RS, Carr SA, Neubert TA. Overview of peptide and protein analysis by mass spectrometry. ACTA ACUST UNITED AC 2014; 108:10.21.1-10.21.30. [PMID: 25271712 DOI: 10.1002/0471142727.mb1021s108] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Mass spectrometry is an indispensable tool for peptide and protein analysis owing to its speed, sensitivity, and versatility. It can be used to determine amino acid sequences of peptides, and to characterize a wide variety of post-translational modifications such as phosphorylation and glycosylation. Mass spectrometry can also be used to determine absolute and relative protein quantities, and can identify and quantify thousands of proteins from complex samples, which makes it an extremely powerful tool for systems biology studies. The main goals of this unit are to familiarize peptide and protein chemists and biologists with the types of mass spectrometers that are appropriate for the majority of their analytical needs, to describe the kinds of experiments that can be performed with these instruments on a routine basis, and to discuss the kinds of information that these experiments provide.
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Affiliation(s)
- Guoan Zhang
- Kimmel Center for Biology and Medicine, Skirball Institute and Department of Pharmacology, New York University School of Medicine, New York, New York
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32
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Abstract
During interphase, chromatin hosts fundamental cellular processes, such as gene expression, DNA replication and DNA damage repair. To analyze chromatin on a proteomic scale, we have developed chromatin enrichment for proteomics (ChEP), which is a simple biochemical procedure that enriches interphase chromatin in all its complexity. It enables researchers to take a 'snapshot' of chromatin and to isolate and identify even transiently bound factors. In ChEP, cells are fixed with formaldehyde; subsequently, DNA together with all cross-linked proteins is isolated by centrifugation under denaturing conditions. This approach enables the analysis of global chromatin composition and its changes, which is in contrast with existing chromatin enrichment procedures, which either focus on specific chromatin loci (e.g., affinity purification) or are limited in specificity, such as the analysis of the chromatin pellet (i.e., analysis of all insoluble nuclear material). ChEP takes half a day to complete and requires no specialized laboratory skills or equipment. ChEP enables the characterization of chromatin response to drug treatment or physiological processes. Beyond proteomics, ChEP may preclear chromatin for chromatin immunoprecipitation (ChIP) analyses.
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Affiliation(s)
- Georg Kustatscher
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Karen L H Wills
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Cristina Furlan
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Juri Rappsilber
- 1] Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, UK. [2] Department of Biotechnology, Institute of Bioanalytics, Technische Universität Berlin, Berlin, Germany
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33
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Zhang Z, Xin W, Wang S, Zhang X, Dai H, Sun R, Frazier T, Zhang B, Wang Q. Xylem sap in cotton contains proteins that contribute to environmental stress response and cell wall development. Funct Integr Genomics 2014; 15:17-26. [PMID: 25163431 DOI: 10.1007/s10142-014-0395-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 08/18/2014] [Accepted: 08/19/2014] [Indexed: 12/24/2022]
Abstract
The xylem sap of a plant is primarily responsible for transporting molecules from the underground root system to the aboveground parts of the plant body. In order to understand the role that roots play in cotton growth and development, the components present in xylem sap must be elucidated. In this study, we used a shotgun HPLC-ESI-MS/MS proteomics approach to identify 455 peptides from the xylem sap of field-grown cotton plants at peak blooming stage. Of these peptides, 384 (84.4%) were found to be secreted proteins and 320 (70.3%) had special molecular functions. Based on Gene Ontology (GO) analysis, 348 peptides were annotated in terms of molecular function, biological process, and cellular localization, with 46.9 and 45.1% being related to catalytic activity and binding activity, respectively. Many xylem sap-containing proteins were predicted to be involved in different phases of xylem differentiation including cell wall metabolism, secondary cell wall development and patterning, and programmed cell death. The identification of starch and sucrose hydrolyzing enzymes implicated the interaction between roots and aboveground parts on the aspect of carbohydrate metabolism. Many of the proteins identified in this study are involved in defense mechanisms including pathogen-related proteins, such as peroxidases, chitinases, and germin-like proteins, proteases involved in disease resistance, and phytoalexin phenylpropanoid synthesis-related proteins. The majority of identified signaling proteins were fasciclin-like arabinogalactan proteins and kinases. The results of this study provide useful insight into the communication mechanisms between cotton roots and the rest of the cotton plant.
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Affiliation(s)
- Zhiyong Zhang
- School of Life Science and Technology, Henan Institute of Science and Technology, Hualan Road, 453003, Xinxiang, China
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34
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Yugi K, Kubota H, Toyoshima Y, Noguchi R, Kawata K, Komori Y, Uda S, Kunida K, Tomizawa Y, Funato Y, Miki H, Matsumoto M, Nakayama KI, Kashikura K, Endo K, Ikeda K, Soga T, Kuroda S. Reconstruction of insulin signal flow from phosphoproteome and metabolome data. Cell Rep 2014; 8:1171-83. [PMID: 25131207 DOI: 10.1016/j.celrep.2014.07.021] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 06/13/2014] [Accepted: 07/15/2014] [Indexed: 12/20/2022] Open
Abstract
Cellular homeostasis is regulated by signals through multiple molecular networks that include protein phosphorylation and metabolites. However, where and when the signal flows through a network and regulates homeostasis has not been explored. We have developed a reconstruction method for the signal flow based on time-course phosphoproteome and metabolome data, using multiple databases, and have applied it to acute action of insulin, an important hormone for metabolic homeostasis. An insulin signal flows through a network, through signaling pathways that involve 13 protein kinases, 26 phosphorylated metabolic enzymes, and 35 allosteric effectors, resulting in quantitative changes in 44 metabolites. Analysis of the network reveals that insulin induces phosphorylation and activation of liver-type phosphofructokinase 1, thereby controlling a key reaction in glycolysis. We thus provide a versatile method of reconstruction of signal flow through the network using phosphoproteome and metabolome data.
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Affiliation(s)
- Katsuyuki Yugi
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroyuki Kubota
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan; Division of integrated Omics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan; PRESTO, Japan Science and Technology Corporation, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Yu Toyoshima
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Rei Noguchi
- Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kentaro Kawata
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yasunori Komori
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shinsuke Uda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan; Division of integrated Omics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Katsuyuki Kunida
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yoko Tomizawa
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yosuke Funato
- Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Hiroaki Miki
- Department of Cellular Regulation, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Masaki Matsumoto
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Keiichi I Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan
| | - Kasumi Kashikura
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Keiko Endo
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Kazutaka Ikeda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Shinya Kuroda
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan; Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan; CREST, Japan Science and Technology Corporation, Bunkyo-ku, Tokyo 113-0033, Japan.
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35
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Ling HH, Beaulé C, Chiang CK, Tian R, Figeys D, Cheng HYM. Time-of-day- and light-dependent expression of ubiquitin protein ligase E3 component N-recognin 4 (UBR4) in the suprachiasmatic nucleus circadian clock. PLoS One 2014; 9:e103103. [PMID: 25084275 PMCID: PMC4118842 DOI: 10.1371/journal.pone.0103103] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Accepted: 06/25/2014] [Indexed: 12/20/2022] Open
Abstract
Circadian rhythms of behavior and physiology are driven by the biological clock that operates endogenously but can also be entrained to the light-dark cycle of the environment. In mammals, the master circadian pacemaker is located in the suprachiasmatic nucleus (SCN), which is composed of individual cellular oscillators that are driven by a set of core clock genes interacting in transcriptional/translational feedback loops. Light signals can trigger molecular events in the SCN that ultimately impact on the phase of expression of core clock genes to reset the master pacemaker. While transcriptional regulation has received much attention in the field of circadian biology in the past, other mechanisms including targeted protein degradation likely contribute to the clock timing and entrainment process. In the present study, proteome-wide screens of the murine SCN led to the identification of ubiquitin protein ligase E3 component N-recognin 4 (UBR4), a novel E3 ubiquitin ligase component of the N-end rule pathway, as a time-of-day-dependent and light-inducible protein. The spatial and temporal expression pattern of UBR4 in the SCN was subsequently characterized by immunofluorescence microscopy. UBR4 is expressed across the entire rostrocaudal extent of the SCN in a time-of-day-dependent fashion. UBR4 is localized exclusively to arginine vasopressin (AVP)-expressing neurons of the SCN shell. Upon photic stimulation in the early subjective night, the number of UBR4-expressing cells within the SCN increases. This study is the first to identify a novel E3 ubiquitin ligase component, UBR4, in the murine SCN and to implicate the N-end rule degradation pathway as a potential player in regulating core clock mechanisms and photic entrainment.
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Affiliation(s)
- Harrod H. Ling
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Christian Beaulé
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Cheng-Kang Chiang
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Ruijun Tian
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Hai-Ying M. Cheng
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
- * E-mail:
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36
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Taga Y, Kusubata M, Ogawa-Goto K, Hattori S. Stable Isotope-Labeled Collagen: A Novel and Versatile Tool for Quantitative Collagen Analyses Using Mass Spectrometry. J Proteome Res 2014; 13:3671-8. [DOI: 10.1021/pr500213a] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Yuki Taga
- Nippi Research Institute of Biomatrix, 520-11
Kuwabara, Toride, Ibaraki 302-0017, Japan
| | - Masashi Kusubata
- Nippi Research Institute of Biomatrix, 520-11
Kuwabara, Toride, Ibaraki 302-0017, Japan
| | - Kiyoko Ogawa-Goto
- Nippi Research Institute of Biomatrix, 520-11
Kuwabara, Toride, Ibaraki 302-0017, Japan
| | - Shunji Hattori
- Nippi Research Institute of Biomatrix, 520-11
Kuwabara, Toride, Ibaraki 302-0017, Japan
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37
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Qiu X, Zhang H, Lai Y. Quantitative targeted proteomics for membrane transporter proteins: method and application. AAPS JOURNAL 2014; 16:714-26. [PMID: 24830943 DOI: 10.1208/s12248-014-9607-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 04/05/2014] [Indexed: 01/04/2023]
Abstract
Although global proteomics has shown promise for discovery of many new proteins, biomarkers, protein modifications, and polymorphisms, targeted proteomics is emerging in the proteomics research field as a complement to untargeted shotgun proteomics, particularly when a determined set of low-abundance functional proteins need to be measured. The function and expression of proteins related to drug absorption, distribution, metabolism, and excretion (ADME) such as cytochrome P450 enzymes and membrane transporters are of great interest in biopharmaceutical research. Since the variation in ADME-related protein expression is known to be a major complicating factor encountered during in vitro-in vivo and in vivo-in vivo extrapolations (IVIVE), the accurate quantification of the ADME proteins in complex biological systems becomes a fundamental element in establishing IVIVE for pharmacokinetic predictions. In this review, we provide an overview of relevant methodologies followed by a summary of recent applications encompassing mass spectrometry-based targeted quantifications of membrane transporters.
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Affiliation(s)
- Xi Qiu
- Pharmaceutical Candidate Optimization, Bristol-Myers Squibb, Princeton, New Jersey, 08543, USA
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38
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Miller RA, Winrow CJ, Spellman DS, Song Q, Reiss DR, Conway JP, Taylor RR, Coleman PJ, Hendrickson RC, Renger JJ. Quantitative proteomics in laser capture microdissected sleep nuclei from rat brain. J Neurogenet 2014; 28:136-45. [PMID: 24579665 PMCID: PMC4075250 DOI: 10.3109/01677063.2014.883389] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The combination of stable isotope labeling of amino acids in mammals (SILAM) and laser capture microdissection (LCM) for selective proteomic analysis of the targeted tissues holds tremendous potential for refined characterization of proteome changes within complex tissues such as the brain. The authors have applied this approach to measure changes in relative protein abundance in ventral tegmental area (VTA) of the rat brain that correlate to pharmacological perturbations. Enriched 13C615N2-lysine was introduced in vivo via diet. These animals were sacrificed during the middle of the 12-hour light period to extract isotopically “heavy” proteins, which were then used as a reference for extracts from dosed, unlabeled rats. Animals were administered an orexin peptide (Ox-B), an orexin receptor antagonist (ORA), or a mixture of both (Ox-B + ORA). All samples were obtained at same phase of the sleep cycle. Labeled-pair identification and differential quantitation provided protein identification and expression ratio data. Five proteins were found to exhibit decreased relative abundance after administration of an ORA, including α-synuclein and rat myelin basic protein. Conversely, six proteins showed increased relative abundance upon antagonist treatment, including 2’,3’-cyclic nucleotide 3’-phosphodiesterase.
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Affiliation(s)
- Ronald A Miller
- Department of Proteomics, Molecular Profiling and Research Informatics, Merck Research Laboratories , West Point, Pennsylvania , USA
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39
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Skandarajah AR, Moritz RL, Tjandra JJ, Simpson RJ. Proteomic analysis of colorectal cancer: discovering novel biomarkers. Expert Rev Proteomics 2014; 2:681-92. [PMID: 16209648 DOI: 10.1586/14789450.2.5.681] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Colorectal cancer is one of the most common cancers in the Western world. When detected at an early stage, the majority of cancers can be cured with current treatment modalities. However, most cancers present at an intermediate stage. The discovery of sensitive and specific biomarkers has the potential to improve preclinical diagnosis of primary and recurrent colorectal cancer, and holds the promise of prognostic and therapeutic application. Current biomarkers such as carcinoembryonic antigen lack sensitivity and specificity for general population screening. This review aims to highlight the role of current proteomic technologies in the discovery and validation of potential biomarkers with a view to translation to the clinic.
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Affiliation(s)
- Anita R Skandarajah
- Department of Surgery, Royal Melbourne Hospital, University of Melbourne, Grattan Street, Parkville 3050, Victoria, Australia.
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40
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Li KW, Jimenez CR. Synapse proteomics: current status and quantitative applications. Expert Rev Proteomics 2014; 5:353-60. [DOI: 10.1586/14789450.5.2.353] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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41
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van Gool AJ, Hendrickson RC. The proteomic toolbox for studying cerebrospinal fluid. Expert Rev Proteomics 2014; 9:165-79. [DOI: 10.1586/epr.12.6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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42
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Campanella B, Bramanti E. Detection of proteins by hyphenated techniques with endogenous metal tags and metal chemical labelling. Analyst 2014; 139:4124-53. [DOI: 10.1039/c4an00722k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The absolute and relative quantitation of proteins plays a fundamental role in modern proteomics, as it is the key to understand still unresolved biological questions in medical and pharmaceutical applications.
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Affiliation(s)
- Beatrice Campanella
- National Research Council of Italy
- C.N.R
- Istituto di Chimica dei Composti Organo Metallici-ICCOM-UOS Pisa
- 56124 Pisa, Italy
| | - Emilia Bramanti
- National Research Council of Italy
- C.N.R
- Istituto di Chimica dei Composti Organo Metallici-ICCOM-UOS Pisa
- 56124 Pisa, Italy
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43
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Hoedt E, Zhang G, Neubert TA. Stable isotope labeling by amino acids in cell culture (SILAC) for quantitative proteomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 806:93-106. [PMID: 24952180 DOI: 10.1007/978-3-319-06068-2_5] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Stable isotope labeling by amino acids in cell culture (SILAC) is a powerful approach for high-throughput quantitative proteomics. SILAC allows highly accurate protein quantitation through metabolic encoding of whole cell proteomes using stable isotope labeled amino acids. Since its introduction in 2002, SILAC has become increasingly popular. In this chapter we review the methodology and application of SILAC, with an emphasis on three research areas: dynamics of posttranslational modifications, protein-protein interactions, and protein turnover.
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Affiliation(s)
- Esthelle Hoedt
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 540 First Avenue, New York, NY, 10016, USA
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44
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Pozniak Y, Geiger T. Design and application of super-SILAC for proteome quantification. Methods Mol Biol 2014; 1188:281-91. [PMID: 25059619 DOI: 10.1007/978-1-4939-1142-4_20] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Stable isotope labeling with amino acids in cell culture (SILAC) is considered the most accurate method for proteome quantification by mass spectrometry. As it relies on active protein translation, it was traditionally limited to cells in culture and was not applicable to tissues. We have previously developed the super-SILAC mix, which is a mixture of several cell lines that serves as an internal spike-in standard for the study of human tumor tissue. The super-SILAC mix greatly improves the quantification accuracy while lowering error rates, and it is a simple, economic, and robust technique. Here we describe the design and application of super-SILAC to a broad range of biological systems, for basic biological research as well as clinical one.
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Affiliation(s)
- Yair Pozniak
- The Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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45
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Mayne J, Starr AE, Ning Z, Chen R, Chiang CK, Figeys D. Fine Tuning of Proteomic Technologies to Improve Biological Findings: Advancements in 2011–2013. Anal Chem 2013; 86:176-95. [DOI: 10.1021/ac403551f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Janice Mayne
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
| | - Amanda E. Starr
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
| | - Zhibin Ning
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
| | - Rui Chen
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
| | - Cheng-Kang Chiang
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
| | - Daniel Figeys
- Ottawa Institute of
Systems Biology, Department of Biochemistry, Microbiology
and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON, Canada K1H8M5
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46
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Deracinois B, Flahaut C, Duban-Deweer S, Karamanos Y. Comparative and Quantitative Global Proteomics Approaches: An Overview. Proteomes 2013; 1:180-218. [PMID: 28250403 PMCID: PMC5302699 DOI: 10.3390/proteomes1030180] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 10/08/2013] [Accepted: 10/08/2013] [Indexed: 01/14/2023] Open
Abstract
Proteomics became a key tool for the study of biological systems. The comparison between two different physiological states allows unravelling the cellular and molecular mechanisms involved in a biological process. Proteomics can confirm the presence of proteins suggested by their mRNA content and provides a direct measure of the quantity present in a cell. Global and targeted proteomics strategies can be applied. Targeted proteomics strategies limit the number of features that will be monitored and then optimise the methods to obtain the highest sensitivity and throughput for a huge amount of samples. The advantage of global proteomics strategies is that no hypothesis is required, other than a measurable difference in one or more protein species between the samples. Global proteomics methods attempt to separate quantify and identify all the proteins from a given sample. This review highlights only the different techniques of separation and quantification of proteins and peptides, in view of a comparative and quantitative global proteomics analysis. The in-gel and off-gel quantification of proteins will be discussed as well as the corresponding mass spectrometry technology. The overview is focused on the widespread techniques while keeping in mind that each approach is modular and often recovers the other.
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Affiliation(s)
- Barbara Deracinois
- Université Lille Nord de France, Lille F-59000, France.
- Université d'Artois, LBHE, Lens F-62307, France.
- IMPRT-IFR114, Lille F-59000, France.
| | - Christophe Flahaut
- Université Lille Nord de France, Lille F-59000, France.
- Université d'Artois, LBHE, Lens F-62307, France.
- IMPRT-IFR114, Lille F-59000, France.
| | - Sophie Duban-Deweer
- Université Lille Nord de France, Lille F-59000, France.
- Université d'Artois, LBHE, Lens F-62307, France.
- IMPRT-IFR114, Lille F-59000, France.
| | - Yannis Karamanos
- Université Lille Nord de France, Lille F-59000, France.
- Université d'Artois, LBHE, Lens F-62307, France.
- IMPRT-IFR114, Lille F-59000, France.
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Schweppe DK, Rigas JR, Gerber SA. Quantitative phosphoproteomic profiling of human non-small cell lung cancer tumors. J Proteomics 2013; 91:286-96. [PMID: 23911959 DOI: 10.1016/j.jprot.2013.07.023] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 07/05/2013] [Accepted: 07/22/2013] [Indexed: 12/27/2022]
Abstract
UNLABELLED Non-small cell lung cancer (NSCLC) is the leading cause of cancer-related deaths worldwide. Within the molecular scope of NCSLC, a complex landscape of dysregulated cellular signaling has emerged, defined largely by mutations in select mediators of signal transduction, including the epidermal growth factor receptor (EGFR) and anaplastic lymphoma (ALK) kinases. Consequently, these mutant kinases become constitutively activated and targets for chemotherapeutic intervention. Encouragingly, small molecule inhibitors of these pathways have shown promise in clinical trials or are approved for clinical use. However, many protein kinases are dysregulated in NSCLC without genetic mutations. To quantify differences in tumor cell signaling that are transparent to genomic methods, we established a super-SILAC internal standard derived from NSCLC cell lines grown in vitro and labeled with heavy lysine and arginine, and deployed them in a phosphoproteomic workflow. We identified 9019 and 8753 phosphorylation sites in two separate tumors. Relative quantification of phosphopeptide abundance between tumor samples allowed for the determination of specific hubs and pathways differing between each tumor. Sites downstream of Ras showed decreased inhibitory phosphorylation (Raf/Mek) and increased activating phosphorylation (Erk1/2) in one tumor versus another. In this way, we were able to quantitatively access oncogenic kinase signaling in primary human tumors. BIOLOGICAL SIGNIFICANCE Through the use of quantitative proteomics, we demonstrated the feasibility and coverage that large scale mass spectrometry can leverage for understanding kinase networks in cancer. By incorporating Super-SILAC based quantitation into a typical pathology workflow, we were able to access and compare tumors from multiple patients in this analysis with high accuracy and dynamic range. We analyzed tumors from patients diagnosed with non-small cell lung cancer and were able to detect comprehensive phosphorylation networks relaying through known hubs of oncogenesis in lung cancer. We hereby show that it is possible to track changes to phosphorylation networks across multiple tumors, opening up the possibility that drug susceptibility and patient-specific stratification can be implemented downstream of classical pathology.
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Affiliation(s)
- Devin K Schweppe
- Department of Genetics, Geisel School of Medicine, Lebanon, NH 03756, United States
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Liberski AR, Al-Noubi MN, Rahman ZH, Halabi NM, Dib SS, Al-Mismar R, Billing AM, Krishnankutty R, Ahmad FS, Raynaud CM, Rafii A, Engholm-Keller K, Graumann J. Adaptation of a commonly used, chemically defined medium for human embryonic stem cells to stable isotope labeling with amino acids in cell culture. J Proteome Res 2013; 12:3233-45. [PMID: 23734825 DOI: 10.1021/pr400099j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Metabolic labeling with stable isotopes is a prominent technique for comparative quantitative proteomics, and stable isotope labeling with amino acids in cell culture (SILAC) is the most commonly used approach. SILAC is, however, traditionally limited to simple tissue culture regimens and only rarely employed in the context of complex culturing conditions as those required for human embryonic stem cells (hESCs). Classic hESC culture is based on the use of mouse embryonic fibroblasts (MEFs) as a feeder layer, and as a result, possible xenogeneic contamination, contribution of unlabeled amino acids by the feeders, interlaboratory variability of MEF preparation, and the overall complexity of the culture system are all of concern in conjunction with SILAC. We demonstrate a feeder-free SILAC culture system based on a customized version of a commonly used, chemically defined hESC medium developed by Ludwig et al. and commercially available as mTeSR1 [mTeSR1 is a trade mark of WiCell (Madison, WI) licensed to STEMCELL Technologies (Vancouver, Canada)]. This medium, together with adjustments to the culturing protocol, facilitates reproducible labeling that is easily scalable to the protein amounts required by proteomic work flows. It greatly enhances the usability of quantitative proteomics as a tool for the study of mechanisms underlying hESCs differentiation and self-renewal. Associated data have been deposited to the ProteomeXchange with the identifier PXD000151.
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Nakazawa CM, Shikata K, Uesugi M, Katayama H, Aoshima K, Tahara K, Takahashi E, Hida T, Shibata H, Ogura H, Seiki T, Oda Y, Kuromitsu J, Miyamoto N. Prediction of relaxin-3-induced downstream pathway resulting in anxiolytic-like behaviors in rats based on a microarray and peptidome analysis. J Recept Signal Transduct Res 2013; 33:224-33. [PMID: 23697547 DOI: 10.3109/10799893.2012.756895] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The effect of the intracerebroventricular (i.c.v.) injection of relaxin-3 (RLX3) was evaluated using anxiety-related behavioral tests in rats. RLX3-injected animals showed normal locomotion activity in a habituated environment and declined anxiety cognition in the elevated plus maze test and the shock probe-burying test. The measurement of spontaneous locomotor activity in a novel environment also suggested that RLX3 reduced the stress response. To elucidate the regulatory mechanisms of the downstream signaling pathways underlying RLX3 activity and its relation to anxiolytic and hyperphagic behavior phenotypes, RLX3-i.c.v.-injected rat hypothalamic responses were examined using a microarray analysis. Ingenuity Pathway Analysis software listed the phenotype-relating genes and they showed characteristic expression patterns in the rat hypothalamus. When peptidome data sets for the same listed genes was analyzed using a semi-quantitative approach, the expressions of two neuropeptides were found to have increased. One of these neuropeptides, oxytocin (Oxt), exhibited increased expression in both the microarray and the peptidomic analysis, and a Western blot analysis validated the mass spectrometry results. A cross-omics data analysis is useful for predicting downstream signaling pathways, and the anxiolytic-like behavior of RLX3 may be mediated by an oxytocin signaling pathway in rats. These results suggest that RLX3 acts as an anxiolytic peptide and that the downstream pathways mediated by its receptors may be potential candidates for the treatment of anxieties in the future.
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Affiliation(s)
- Chihiro Miyamoto Nakazawa
- KAN Product Creation Unit, Eisai Product Creation Systems, Eisai Co., Ltd., Tsukuba, Ibaraki, Japan.
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50
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The Application of SILAC Mouse in Human Body Fluid Proteomics Analysis Reveals Protein Patterns Associated with IgA Nephropathy. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2013; 2013:275390. [PMID: 23762118 PMCID: PMC3671237 DOI: 10.1155/2013/275390] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Accepted: 04/18/2013] [Indexed: 01/07/2023]
Abstract
Body fluid proteome is the most informative proteome from a medical viewpoint. But the lack of accurate quantitation method for complicated body fluid limited its application in disease research and biomarker discovery. To address this problem, we introduced a novel strategy, in which SILAC-labeled mouse serum was used as internal standard for human serum and urine proteome analysis. The SILAC-labeled mouse serum was mixed with human serum and urine, and multidimensional separation coupled with tandem mass spectrometry (IEF-LC-MS/MS) analysis was performed. The shared peptides between two species were quantified by their SILAC pairs, and the human-only peptides were quantified by mouse peptides with coelution. The comparison for the results from two replicate experiments indicated the high repeatability of our strategy. Then the urine from Immunoglobulin A nephropathy patients treated and untreated was compared by this quantitation strategy. Fifty-three peptides were found to be significantly changed between two groups, including both known diagnostic markers for IgAN and novel candidates, such as Complement C3, Albumin, VDBP, ApoA,1 and IGFBP7. In conclusion, we have developed a practical and accurate quantitation strategy for comparison of complicated human body fluid proteome. The results from such strategy could provide potential disease-related biomarkers for evaluation of treatment.
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