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Wang W, Li X, Li Y, Li S, Fan K, Yang K. A genetic biosensor for identification of transcriptional repressors of target promoters. Sci Rep 2015; 5:15887. [PMID: 26510468 PMCID: PMC4625125 DOI: 10.1038/srep15887] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 10/05/2015] [Indexed: 02/06/2023] Open
Abstract
Transcriptional repressors provide widespread biological significance in the regulation of gene expression. However, in prokaryotes, it is particularly difficult to find transcriptional repressors that recognize specific target promoters on genome-scale. To address this need, a genetic biosensor for identifying repressors of target promoters was developed in Escherichia coli from a de novo designed genetic circuit. This circuit can convert the negative input of repressors into positive output of reporters, thereby facilitating the selection and identification of repressors. After evaluating the sensitivity and bias, the biosensor was used to identify the repressors of scbA and aco promoters (PscbA and Paco), which control the transcription of signalling molecule synthase genes in Streptomyces coelicolor and Streptomyces avermitilis, respectively. Two previously unknown repressors of PscbA were identified from a library of TetR family regulators in S. coelicolor, and three novel repressors of Paco were identified from a genomic library of S. avermitilis. Further in vivo and in vitro experiments confirmed that these newly identified repressors attenuated the transcription of their target promoters by direct binding. Overall, the genetic biosensor developed here presents an innovative and powerful strategy that could be applied for identifying genome-wide unknown repressors of promoters in bacteria.
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Affiliation(s)
- Weishan Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Xiao Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Yue Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Shanshan Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Keqiang Fan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Keqian Yang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
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Zürbig P, Jahn H. Use of proteomic methods in the analysis of human body fluids in Alzheimer research. Electrophoresis 2013; 33:3617-30. [PMID: 23160951 DOI: 10.1002/elps.201200360] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 09/27/2012] [Accepted: 09/27/2012] [Indexed: 01/23/2023]
Abstract
Proteomics is the study of the entire population of proteins and peptides in an organism or a part of it, such as a cell, tissue, or fluids like cerebrospinal fluid, plasma, serum, urine, or saliva. It is widely assumed that changes in the composition of the proteome may reflect disease states and provide clues to its origin, eventually leading to targets for new treatments. The ability to perform large-scale proteomic studies now is based jointly on recent advances in our analytical methods. Separation techniques like CE and 2DE have developed and matured. Detection methods like MS have also improved greatly in the last 5 years. These developments have also driven the fields of bioinformatics, needed to deal with the increased data production and systems biology. All these developing methods offer specific advantages but also come with certain limitations. This review describes the different proteomic methods used in the field, their limitations, and their possible pitfalls. Based on a literature search in PubMed, we identified 112 studies that applied proteomic techniques to identify biomarkers for Alzheimer disease. This review describes the results of these studies on proteome changes in human body fluids of Alzheimer patients reviewing the most important studies. We extracted a list of 366 proteins and peptides that were identified by these studies as potential targets in Alzheimer research.
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L.S. Tang N, Poon T, Poon TCW. Advances in MALDI mass spectrometry in clinical diagnostic applications. Top Curr Chem (Cham) 2013; 336:139-75. [PMID: 23563502 PMCID: PMC7121589 DOI: 10.1007/128_2012_413] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The concept of matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) was first reported in 1985. Since then, MALDI MS technologies have been evolving, and successfully used in genome, proteome, metabolome, and clinical diagnostic research. These technologies are high-throughput and sensitive. Emerging evidence has shown that they are not only useful in qualitative and quantitative analyses of proteins, but also of other types of biomolecules, such as DNA, glycans, and metabolites. Recently, parallel fragmentation monitoring (PFM), which is a method comparable to selected reaction monitoring, has been reported. This highlights the potentials of MALDI-TOF/TOF tandem MS in quantification of metabolites. Here we critically review the applications of the major MALDI MS technologies, including MALDI-TOF MS, MALDI-TOF/TOF MS, SALDI-TOF MS, MALDI-QqQ MS, and SELDI-TOF MS, to the discovery and quantification of disease biomarkers in biological specimens, especially those in plasma/serum specimens. Using SELDI-TOF MS as an example, the presence of systemic bias in biomarker discovery studies employing MALDI-TOF MS and its possible solutions are also discussed in this chapter. The concepts of MALDI, SALDI, SELDI, and PFM are complementary to each other. Theoretically, all these technologies can be combined, leading to the next generation of the MALDI MS technologies. Real applications of MALDI MS technologies in clinical diagnostics should be forthcoming.
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Affiliation(s)
- Nelson L.S. Tang
- grid.10784.3a0000000419370482Dept. of Chemical Pathology and Lab. of Genetics of Disease Suscept., The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Terence Poon
- grid.10784.3a0000000419370482Department of Paediatrics and Proteomics Laboratory, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
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Zhang S, Xu M, Li S, Su Z. Genome-wide de novo prediction of cis-regulatory binding sites in prokaryotes. Nucleic Acids Res 2009; 37:e72. [PMID: 19383880 PMCID: PMC2691844 DOI: 10.1093/nar/gkp248] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Although cis-regulatory binding sites (CRBSs) are at least as important as the coding sequences in a genome, our general understanding of them in most sequenced genomes is very limited due to the lack of efficient and accurate experimental and computational methods for their characterization, which has largely hindered our understanding of many important biological processes. In this article, we describe a novel algorithm for genome-wide de novo prediction of CRBSs with high accuracy. We designed our algorithm to circumvent three identified difficulties for CRBS prediction using comparative genomics principles based on a new method for the selection of reference genomes, a new metric for measuring the similarity of CRBSs, and a new graph clustering procedure. When operon structures are correctly predicted, our algorithm can predict 81% of known individual binding sites belonging to 94% of known cis-regulatory motifs in the Escherichia coli K12 genome, while achieving high prediction specificity. Our algorithm has also achieved similar prediction accuracy in the Bacillus subtilis genome, suggesting that it is very robust, and thus can be applied to any other sequenced prokaryotic genome. When compared with the prior state-of-the-art algorithms, our algorithm outperforms them in both prediction sensitivity and specificity.
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Affiliation(s)
- Shaoqiang Zhang
- Department of Bioinformatics and Genomics, Bioinformatics Research Center, the University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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Abstract
Complex biological samples hold significant information on the health status and on development of disease. Approximately 35,000 human genes give rise to more than 1,000,000 functional entities at the protein level. Thus, the proteome provides a much richer source of information than the genome for describing the state of health or disease of humans. The composition body fluids comprise a rich source of information on changes of protein and peptide expression. Here we describe the application of capillary electrophoresis (CE) coupled online to an electrospray-ionization time-of-flight mass spectrometer (ESI-TOF-MS) to analyze human urine for the identification of biomarkers specific for complications after allogeneic hematopoietic stem cell transplantation (HSCT). Sequencing of native proteins/peptides is necessary for the identification of possible new therapeutic targets.
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Hégarat N, François JC, Praseuth D. Modern tools for identification of nucleic acid-binding proteins. Biochimie 2008; 90:1265-72. [PMID: 18452716 DOI: 10.1016/j.biochi.2008.03.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2008] [Accepted: 03/21/2008] [Indexed: 11/25/2022]
Abstract
Numerous biological mechanisms depend on nucleic acid--protein interactions. The first step to the understanding of these mechanisms is to identify interacting molecules. Knowing one partner, the identification of other associated molecular species can be carried out using affinity-based purification procedures. When the nucleic acid-binding protein is known, the nucleic acid can be isolated and identified by sensitive techniques such as polymerase chain reaction followed by DNA sequencing or hybridization on chips. The reverse identification procedure is less straightforward in part because interesting nucleic acid-binding proteins are generally of low abundance and there are no methods to amplify amino acid sequences. In this article, we will review the strategies that have been developed to identify nucleic acid-binding proteins. We will focus on methods permitting the identification of these proteins without a priori knowledge of protein candidates.
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Affiliation(s)
- Nadia Hégarat
- INSERM, U565 Case Postale 26, 57 rue Cuvier, 75231 Paris Cedex 05, France
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7
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Schiffer E, Mischak H, Vanholder RC. Biomarkers for Renal Disease and Uremic Toxins. Clin Proteomics 2008. [DOI: 10.1002/9783527622153.ch25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Kiehntopf M, Siegmund R, Deufel T. Use of SELDI-TOF mass spectrometry for identification of new biomarkers: potential and limitations. Clin Chem Lab Med 2008; 45:1435-49. [PMID: 17970700 DOI: 10.1515/cclm.2007.351] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Surface-enhanced laser desorption time of flight mass spectrometry (SELDI-TOF-MS) is an important proteomic technology that is immediately available for the high throughput analysis of complex protein samples. Over the last few years, several studies have demonstrated that comparative protein profiling using SELDI-TOF-MS breaks new ground in diagnostic protein analysis particularly with regard to the identification of novel biomarkers. Importantly, researchers have acquired a better understanding also of the limitations of this technology and various pitfalls in biomarker discovery. Bearing these in mind, great emphasis must be placed on the development of rigorous standards and quality control procedures for the pre-analytical as well as the analytical phase and subsequent bioinformatics applied to analysis of the data. To avoid the risk of false-significant results studies must be designed carefully and control groups accurately selected. In addition, appropriate tools, already established for analysis of highly complex microarray data, need to be applied to protein profiling data. To validate the significance of any candidate biomarker derived from pilot studies in appropriately designed prospective multi-center studies is mandatory; reproducibility of the clinical results must be shown over time and in different diagnostic settings. SELDI-TOF-MS-based studies that are in compliance with these requirements are now required; only a few have been published so far. In the meantime, further evaluation and optimization of both technique and marker validation strategies are called for before MS-based proteomic algorithms can be translated into routine laboratory testing.
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Affiliation(s)
- Michael Kiehntopf
- Institut für Klinische Chemie und Laboratoriumsdiagnostik, Universitätsklinikum Jena, Jena, Germany.
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Schiffer E, Mischak H, Theodorescu D, Vlahou A. Challenges of using mass spectrometry as a bladder cancer biomarker discovery platform. World J Urol 2008; 26:67-74. [PMID: 18175124 DOI: 10.1007/s00345-007-0234-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Accepted: 12/11/2007] [Indexed: 12/28/2022] Open
Abstract
INTRODUCTION Bladder cancer (BCa) is one of the most prevalent malignancies worldwide, mostly due to its high recurrence rates. In consequence, the necessity of repeated screening for reappearance demonstrates the urgent need for novel biomarkers as alternatives to invasive standard procedures. METHODS Proteomic technologies have emerged as powerful platforms for unbiased biomarker discovery and revolutionized the classical "target-driven" analysis of single marker candidates. Although proteome profiling is still far from demonstrating its full potential in clinical diagnosis, first studies clearly denote its significant potential. CONCLUSIONS This review provides a discussion of the challenges related to clinical proteomics using mass spectrometry, emphasizing bladder cancer biomarker discovery. An outline of the technological prerequisites for reliable proteome profiling, data mining and interpretation, as well as, reflections on future trends in the field are provided.
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Affiliation(s)
- Eric Schiffer
- Mosaiques Diagnostics and Therapeutics AG, Hannover, Germany
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Theodorescu D, Mischak H. Mass spectrometry based proteomics in urine biomarker discovery. World J Urol 2007; 25:435-43. [PMID: 17703310 DOI: 10.1007/s00345-007-0206-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2007] [Accepted: 07/13/2007] [Indexed: 11/28/2022] Open
Abstract
All organisms contain 1,000s of proteins and peptides in their body fluids, which undergo disease-specific changes. Advances in the understanding of the functional relevance of these polypeptides under different (patho)physiological conditions and the identification of indicative changes with disease would greatly enhance diagnosis and therapy. The low-molecular-weight proteome, also termed peptidome, provides a rich source of information. Due to its lower molecular weight, the peptidome can be assessed without the need for sample manipulation like tryptic digests. This advantage facilitates comparative analysis but it also raises technical challenges differing from those in proteomics. The first part of this manuscript, is focused on the low-molecular-weight urinary proteome and reviews methodological aspects of sample collection, preparation, analysis, and data evaluation. The second part summarizes the recent progress in the definition and identification of clinically relevant polypeptide markers.
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Affiliation(s)
- Dan Theodorescu
- Department of Molecular Physiology, University of Virginia, Charlottesville, USA
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Mischak H, Julian BA, Novak J. High-resolution proteome/peptidome analysis of peptides and low-molecular-weight proteins in urine. Proteomics Clin Appl 2007; 1:792. [PMID: 20107618 PMCID: PMC2811330 DOI: 10.1002/prca.200700043] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2007] [Indexed: 11/09/2022]
Abstract
All organisms contain thousands of proteins and peptides in their body fluids. A deeper insight into the functional relevance of these polypeptides under different physiological and pathophysiological conditions and the discovery of specific peptide biomarkers would greatly enhance diagnosis and therapy of specific diseases. The low-molecular-weight proteome, also termed peptidome, provides a rich source of information. Due to its unique features, the technical challenges differ somewhat from those in "common" proteomics. In this manuscript, we focus on the low-molecular-weight urinary proteome. We review the methodological aspects of sample collection, preparation, analysis, and subsequent data evaluation. In the second part of this review, we summarize the recent progress in the definition and identification of clinically relevant polypeptide markers.
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Affiliation(s)
| | | | - Jan Novak
- University of Alabama at Birmingham, Birmingham, AL, USA
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12
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Abstract
With the growth of the "-omics" such as functional genomics and proteomics, one of the foremost challenges in biotechnologies has become the development of novel methods to monitor biological process and acquire the information of biomolecular interactions in a systematic manner. To fully understand the roles of newly discovered genes or proteins, it is necessary to elucidate the functions of these molecules in their interaction network. Microarray technology is becoming the method of choice for such a task. Although protein microarray can provide a high throughput analytical platform for protein profiling and protein-protein interaction, most of the current reports are limited to labeled detection using fluorescence or radioisotope techniques. These limitations deflate the potential of the method and prevent the technology from being adapted in a broader range of proteomics applications. In recent years, label-free analytical approaches have gone through intensified development and have been coupled successfully with protein microarray. In many examples of label-free study, the microarray has not only offered the high throughput detection in real time, but also provided kinetics information as well as in situ identification. This article reviews the most significant label-free detection methods for microarray technology, including surface plasmon resonance imaging, atomic force microscope, electrochemical impedance spectroscopy and MS and their applications in proteomics research.
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Affiliation(s)
- Xiaobo Yu
- Department of Biochemistry, Beijing Institute of Radiation Medicine, Beijing Proteome Research Center, Beijing, PR China
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13
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Nordhoff E, Lehrach H. Identification and characterization of DNA-binding proteins by mass spectrometry. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2006; 104:111-95. [PMID: 17290821 DOI: 10.1007/10_2006_037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Mass spectrometry is the most sensitive and specific analytical technique available for protein identification and quantification. Over the past 10 years, by the use of mass spectrometric techniques hundreds of previously unknown proteins have been identified as DNA-binding proteins that are involved in the regulation of gene expression, replication, or DNA repair. Beyond this task, the applications of mass spectrometry cover all aspects from sequence and modification analysis to protein structure, dynamics, and interactions. In particular, two new, complementary ionization techniques have made this possible: matrix-assisted laser desorption/ionization and electrospray ionization. Their combination with different mass-over-charge analyzers and ion fragmentation techniques, as well as specific enzymatic or chemical reactions and other analytical techniques, has led to the development of a broad repertoire of mass spectrometric methods that are now available for the identification and detailed characterization of DNA-binding proteins. These techniques, how they work, what their requirements and limitations are, and selected examples that document their performance are described and discussed in this chapter.
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Affiliation(s)
- Eckhard Nordhoff
- Department Lehrach, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany.
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Schiffer E, Mischak H, Novak J. High resolution proteome/peptidome analysis of body fluids by capillary electrophoresis coupled with MS. Proteomics 2006; 6:5615-27. [PMID: 16991199 DOI: 10.1002/pmic.200600230] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
All organisms contain thousands of proteins and peptides in their body fluids. A deeper insight into the functional relevance of these polypeptides under different physiological and pathophysiological conditions and the discovery of specific peptide biomarkers would greatly enhance both diagnosis and therapy of specific diseases. Proteomic methods can provide means to accomplish this grand medical vision. In this review, we will focus on the potential use of proteome analysis for clinical applications, such as disease diagnosis and assessment of response to therapy. We focus on CE coupled with MS (CE-MS) and review in detail different aspects of CE-MS coupling and the results obtained using CE-MS analysis of clinically relevant samples. We also discuss clinical applications of the technology for the diagnosis of renal diseases, urogenital cancer, and arteriosclerosis as well as monitoring the responses to therapeutic interventions.
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Affiliation(s)
- Eric Schiffer
- Mosaiques Diagnostics & Therapeutics AG, Hanover, Germany
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15
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Zhu Y, Valdes R, Simmons CQ, Linder MW, Pugia MJ, Jortani SA. Analysis of ligand binding by bioaffinity mass spectrometry. Clin Chim Acta 2006; 371:71-8. [PMID: 16624266 DOI: 10.1016/j.cca.2006.02.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2006] [Accepted: 02/16/2006] [Indexed: 11/19/2022]
Abstract
BACKGROUND Ligand binding is commonly analyzed using various immunoassays that are generally time-consuming and some may require secondary antibodies or gel electrophoresis which are also time-consuming and sometimes subjective. We introduced various examples for a more rapid approach using pre-activated surface chips which are analyzed by surface enhanced laser desorption/ionization-time of flight mass spectrometry (SELDI-TOF MS). Specific applications presented in this study include immobilization of antigen, antibody or oligo DNA on pre-activated chips with subsequent identification of the binding antibodies, antigens or DNA binding proteins to demonstrate the universal utility of this novel approach. METHODS BSA-digoxin conjugate (BSA-Dig), anti-digoxin antibody, anti-urinary trypsin inhibitor (uTi) antibody, or a double stranded oligo nucleotide based on the nucleotide sequence between -91 and -10 of the human CYP 450 2E1 promoter were immobilized on the Ciphergen pre-activated surface chips. Anti-digoxin antibody, BSA-digoxin conjugate, uTi, and CYP450 2E1 promoter binding protein were captured on the chip and identified by SELDI-TOF MS. RESULTS A protein with 141kDa was identified from anti-digoxin serum using BSA-Dig chips. This binding was competitively inhibited by addition of digoxin. Using anti-digoxin antibody, a peak at approximately 66kDa was detected in the preparation of BSA-Dig. This peak was also inhibited by free digoxin, suggesting BSA-Dig is detected. uTi fragments with approximately 3kDa to approximately 30kDa in the standard and urine samples were captured on the chip by anti-uTi antibody. Finally, we identified a 95-kDa CYP 450 2E1 promoter binding protein in HeLa cells nuclear extracts. CONCLUSIONS Bioaffinity SELDI-TOF MS is a powerful and versatile approach for analysis of ligands. It eliminates tracer-labeled secondary antibodies and allows for determination of molecular weights of binding proteins and their ligands directly. This approach may also be considered for the detection of enzymes, receptors, or any other specific ligands.
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Affiliation(s)
- Yusheng Zhu
- Department of Pathology and Laboratory Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
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Zhu Y, Valdes R, Jortani SA. Application of bioaffinity mass spectrometry for analysis of ligands. Ther Drug Monit 2006; 27:694-9. [PMID: 16404796 DOI: 10.1097/01.ftd.0000179851.32093.dc] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Bioaffinity mass spectrometry is a novel technology for analysis of binding proteins and their ligands. In this review, we introduce the concepts and principles of bioaffinity surface-enhanced laser desorption/ionization-time of flight mass spectrometry (SELDI-TOF MS). Various preactivated chip types and several approaches for binding of ligands or their binders to the chips are discussed. We also provide specific examples for the use of this technology for screening antibodies, analyzing ligands, glycoconjugates, protein-protein inter-actions, and DNA (RNA) binding proteins. In pursuit of developing new tests or studies of mechanism of drug action in therapeutic drug monitoring practice, this technology may provide a more rapid approach for ligand-binder studies.
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Affiliation(s)
- Yusheng Zhu
- Department of Pathology and Laboratory Medicine, University of Louisville School of Medicine, KY 40202, USA
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17
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Park SS, Ko BJ, Kim BG. Mass spectrometric screening of transcriptional regulators using DNA affinity capture assay. Anal Biochem 2005; 344:152-4. [PMID: 16005423 DOI: 10.1016/j.ab.2005.05.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2005] [Revised: 05/09/2005] [Accepted: 05/16/2005] [Indexed: 01/08/2023]
Affiliation(s)
- Sung-Soo Park
- School of Chemical and Biological Engineering, Institute of Molecular Biology and Genetics, Seoul National University, Kwanak-gu, Seoul 151-742, Republic of Korea
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18
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Alessandro R, Belluco C, Kohn EC. Proteomic approaches in colon cancer: promising tools for new cancer markers and drug target discovery. Clin Colorectal Cancer 2005; 4:396-402. [PMID: 15807933 DOI: 10.3816/ccc.2005.n.012] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Novel technologies are needed from which to identify new and more efficient biomarkers and improved molecular targets for the expedient and accurate diagnosis and treatment of colorectal cancer. Many advances have been made in direct and virtual imaging for detection of polyps and malignant-type lesions. These require tissue verification before definitive intervention. Inclusion of a simple serum test, more accurate than CEA, especially for early cancer detection, would make virtual imaging much more successful. Proteomics, the study of the proteins and protein pathways involved in disease, is a new dimension in preclinical and clinical development. Mass spectrometric analysis of serum proteins has been shown to be a fast and simple approach yielding a large datastream of information to mine for biomarker patterns. Preliminary studies in a variety of cancers has shown this to be a promising direction. Protein arrays of tumor lysates allows assessment of expression and activation of proteins that may be specific colorectal cancer targets or targets that are shown to be universally important in cancer, such as those proteins involved in angiogenesis. Small quantities of tumor are needed for this technique and allow direct analysis of the biochemical events ongoing in the tumor and/or the stroma. This provides insight into the biology of the disease and can be used to identify targets for therapeutic intervention as well as to monitor the ability to successfully attack those targets. Together, these 2 technologies have been shown to advance the field and may be important new steps in diagnosis, prognosis, and treatment of colorectal cancer.
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Affiliation(s)
- Riccardo Alessandro
- Department of Biopathology and Biomedical Methodology, Universita di Palermo, Palermo, Italy
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Banoub JH, Newton RP, Esmans E, Ewing DF, Mackenzie G. Recent developments in mass spectrometry for the characterization of nucleosides, nucleotides, oligonucleotides, and nucleic acids. Chem Rev 2005; 105:1869-915. [PMID: 15884792 DOI: 10.1021/cr030040w] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joseph H Banoub
- Fisheries and Oceans Canada, Science Branch, Special Projects, P.O. Box 5667, St. John's NL A1C 5X1, Canada.
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20
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Xiao Z, Prieto D, Conrads TP, Veenstra TD, Issaq HJ. Proteomic patterns: their potential for disease diagnosis. Mol Cell Endocrinol 2005; 230:95-106. [PMID: 15664456 DOI: 10.1016/j.mce.2004.10.010] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2004] [Revised: 10/06/2004] [Accepted: 10/14/2004] [Indexed: 10/26/2022]
Abstract
Alterations in proteins abundance, structure, or function, act as useful indicators of pathological abnormalities prior to development of clinical symptoms and as such are often useful diagnostic and prognostic biomarkers. The underlying mechanism of diseases such as cancer are, however, quite complicated in that often multiple dysregulated proteins are involved. It is for this reason that recent hypotheses suggest that detection of panels of biomarkers may provide higher sensitivities and specificities for disease diagnosis than is afforded with single markers. Recently, a novel approach based on the analysis of protein patterns has emerged that may provide a more effective means to diagnose diseases, such as ovarian and prostate cancer. The method is based on the use of surface-enhanced laser desorption/ionization (SELDI) time-of-flight mass spectrometry (TOF-MS) to detect differentially captured proteins from clinical samples, such as serum and plasma. This analysis results in the detection of "proteomic" patterns that have been shown in recent investigations to distinguish diseased and unaffected subjects to varying degrees. This review will discuss the basics of SELDI protein chip technology and highlight its recent applications in disease biomarker discovery with emphasis on cancer diagnosis.
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Affiliation(s)
- Zhen Xiao
- Laboratory of Proteomics and Analytical Technologies, SAIC-Frederick Inc., National Cancer Institute at Frederick, P.O. Box B, Frederick, MD 21702, USA
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Fetsch PA, Simone NL, Bryant-Greenwood PK, Marincola FM, Filie AC, Petricoin EF, Liotta LA, Abati A. Proteomic evaluation of archival cytologic material using SELDI affinity mass spectrometry: potential for diagnostic applications. Am J Clin Pathol 2002; 118:870-6. [PMID: 12472280 DOI: 10.1309/ejkl-7328-kfpr-56wa] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Proteomic studies of cells via surface-enhanced laser desorption/ionization spectrometry (SELDI) analysis have enabled rapid, reproducible protein profiling directly from crude samples. We applied this technique to archival cytology material to determine whether distinct, reproducible protein fingerprints could be identifiedfor potential diagnostic purposes in blinded specimens. Rapid Romanowsky-stained cytocentrifuged specimens from fine-needle aspirates of metastatic malignant melanoma (with both known cutaneous primary and unknown primary sites), clear cell sarcoma, and renal cell carcinoma and reactive effusions were examined using the SELDI technology. A unique characteristic fingerprint was identified for each disease entity. Fifteen "blinded" unknown samples then were analyzed. When the protein profilefingerprints were plotted against the known fingerprints for the aforementioned diagnoses, the appropriate match or diagnosis was obtained in 13 (87%) of 15 cases. These preliminary findings suggest a substantial potential for SELDI applications to specific pathologic diagnoses.
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Affiliation(s)
- Patricia A Fetsch
- Laboratory of Pathology, National Institutes of Health, National Cancer Institute, Bethesda, MD 20892-1500, USA
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22
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Forde CE, McCutchen-Maloney SL. Characterization of transcription factors by mass spectrometry and the role of SELDI-MS. MASS SPECTROMETRY REVIEWS 2002; 21:419-439. [PMID: 12666149 DOI: 10.1002/mas.10040] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Over the last decade, much progress has been made in the field of biological mass spectrometry, with numerous advances in technology, resolution, and affinity capture. The field of genomics has also been transformed by the sequencing and characterization of entire genomes. Some of the next challenges lie in understanding the relationship between the genome and the proteome, the protein complement of the genome, and in characterizing the regulatory processes involved in progressing from gene to functional protein. In this new age of proteomics, development of mass spectrometry methods to characterize transcription factors promises to add greatly to our understanding of regulatory networks that govern expression. However, at this time, regulatory networks of transcription factors are mostly uncharted territory. In this review, we summarize the latest advances in characterization of transcription factors by mass spectrometry including affinity capture, identification of complexes of DNA-binding proteins, structural characterization, determination of protein-DNA and protein-protein interactions, assessment of modification sites and metal binding, studies of functional activity, and the latest chip technologies that use SELDI-MS that allow the rapid capture and identification of transcription factors.
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Affiliation(s)
- Cameron E Forde
- Biodefense Division, Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, California 94550, USA
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23
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SELDI-TOF-MS Analysis of Transcriptional Activation Protein Binding to Response Elements Regulating Carcinogenesis Enzymes. Int J Mol Sci 2002. [DOI: 10.3390/i3101027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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24
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Rusconi F, Guillonneau F, Praseuth D. Contributions of mass spectrometry in the study of nucleic acid-binding proteins and of nucleic acid-protein interactions. MASS SPECTROMETRY REVIEWS 2002; 21:305-348. [PMID: 12645088 DOI: 10.1002/mas.10036] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Nucleic-acid-protein (NA-P) interactions play essential roles in a variety of biological processes-gene expression regulation, DNA repair, chromatin structure regulation, transcription regulation, RNA processing, and translation-to cite only a few. Such biological processes involve a broad spectrum of NA-P interactions as well as protein-protein (P-P) interactions. These interactions are dynamic, in terms of the chemical composition of the complexes involved and in terms of their mere existence, which may be restricted to a given cell-cycle phase. In this review, the contributions of mass spectrometry (MS) to the deciphering of these intricate networked interactions are described along with the numerous applications in which it has proven useful. Such applications include, for example, the identification of the partners involved in NA-P or P-P complexes, the identification of post-translational modifications that (may) regulate such complexes' activities, or even the precise molecular mapping of the interaction sites in the NA-P complex. From a biological standpoint, we felt that it was worth the reader's time to be as informative as possible about the functional significance of the analytical methods reviewed herein. From a technical standpoint, because mass spectrometry without proper sample preparation would serve no purpose, each application described in this review is detailed by duly emphasizing the sample preparation-whenever this step is considered innovative-that led to significant analytical achievements.
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Affiliation(s)
- Filippo Rusconi
- UMR CNRS 8646, U INSERM 565, USM MNHN 0503-43, rue Cuvier, F-75231, Paris Cedex 05, France
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25
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2002; 37:652-661. [PMID: 12112749 DOI: 10.1002/jms.253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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26
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Issaq HJ, Veenstra TD, Conrads TP, Felschow D. The SELDI-TOF MS approach to proteomics: protein profiling and biomarker identification. Biochem Biophys Res Commun 2002; 292:587-92. [PMID: 11922607 DOI: 10.1006/bbrc.2002.6678] [Citation(s) in RCA: 418] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The need for methods to identify disease biomarkers is underscored by the survival-rate of patients diagnosed at early stages of cancer progression. Surface enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) is a novel approach to biomarker discovery that combines two powerful techniques: chromatography and mass spectrometry. One of the key features of SELDI-TOF MS is its ability to provide a rapid protein expression profile from a variety of biological and clinical samples. It has been used for biomarker identification as well as the study of protein-protein, and protein-DNA interaction. The versatility of SELDI-TOF MS has allowed its use in projects ranging from the identification of potential diagnostic markers for prostate, bladder, breast, and ovarian cancers and Alzheimer's disease, to the study of biomolecular interactions and the characterization of posttranslational modifications. In this minireview we discuss the application of SELDI-TOF MS to protein biomarker discovery and profiling.
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Affiliation(s)
- Haleem J Issaq
- SAIC-Frederick, Inc., National Cancer Institute at Frederick, National Institutes of Health, Frederick, Maryland, USA.
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