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Wang J, Dong W, Yang X, Li Y, Jin B. Biosensors based on DNA-functionalized CdTe quantum dots for the enhanced electrochemical detection of human-IgG. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023. [PMID: 37424508 DOI: 10.1039/d3ay00676j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Electrochemical detection of human-IgG via biosensors is vital in clinical diagnostics, owing to their simple equipment, facile operation, high selectivity, economical, short diagnostic time, fast response, and easy miniaturization, but the need to improve sensitivity for protein detection is still a barrier limiting its wider practical applications. A hypersensitized electrochemical biosensor based on steric effects for IgG detection was developed in this work. The results indicate that IgG-modified sig-DNA attached to CdTe quantum dots (CdTe-sig-DNA) limited the ability of CdTe-sig-DNA or CdTe-sig-DNA-IgG conjugate to hybridize through the captured DNA strand (cap-DNA) immobilized on a chitosan/nitrogen-doped carbon nanocomposite (CS/N-C) modified glassy carbon electrode surface (GCE). The concentration of IgG based on CdTe concentration was detected by differential pulse anode stripping voltammetry (DPASV) on the electrode surface. The efficiency for hybridizing CdTe-sig-DNA with cap-DNA was found to be logarithmically inverse to the concentration of IgG attached. A highly sensitive and selective detection of IgG from 5 pM to 50 μM with a relatively low detection limit of 1.7 pM was achieved. Therefore, the steric hindrance effect of IgG limited the quantity of DNA that could be functionalized on CdTe QDs, significantly improving the signal, and providing a practical strategy for the clinical analysis of IgG.
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Affiliation(s)
- Jiajia Wang
- Department of Chemistry, Anhui University, Hefei 230601, China.
| | - Wenhui Dong
- Department of Chemistry, Anhui University, Hefei 230601, China.
| | - Xiaomin Yang
- Respiratory Medicine Department, The First People's Hospital of Chuzhou, Chuzhou 239001, China
| | - Yanan Li
- Department of Chemistry, Anhui University, Hefei 230601, China.
| | - Baokang Jin
- Department of Chemistry, Anhui University, Hefei 230601, China.
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2
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Han S, Ham TR, Haque S, Sparks JL, Saul JM. Alkylation of human hair keratin for tunable hydrogel erosion and drug delivery in tissue engineering applications. Acta Biomater 2015; 23:201-213. [PMID: 25997587 PMCID: PMC4522204 DOI: 10.1016/j.actbio.2015.05.013] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 05/08/2015] [Accepted: 05/12/2015] [Indexed: 12/11/2022]
Abstract
Polymeric biomaterials that provide a matrix for cell attachment and proliferation while achieving delivery of therapeutic agents are an important component of tissue engineering and regenerative medicine strategies. Keratins are a class of proteins that have received attention for numerous tissue engineering applications because, like other natural polymers, they promote favorable cell interactions and have non-toxic degradation products. Keratins can be extracted from various sources including human hair, and they are characterized by a high percentage of cysteine residues. Thiol groups on reductively extracted keratin (kerateine) form disulfide bonds, providing a more stable cross-linked hydrogel network than oxidatively extracted keratin (keratose) that cannot form disulfide crosslinks. We hypothesized that an iodoacetamide alkylation (or "capping") of cysteine thiol groups on the kerateine form of keratin could be used as a simple method to modulate the levels of disulfide crosslinking in keratin hydrogels, providing tunable rates of gel erosion and therapeutic agent release. After alkylation, the alkylated kerateines still formed hydrogels and the alkylation led to changes in the mechanical and visco-elastic properties of the materials consistent with loss of disulfide crosslinking. The alkylated kerateines did not lead to toxicity in MC3T3-E1 pre-osteoblasts. These cells adhered to keratin at levels comparable to fibronectin and greater than collagen. Alkylated kerateine gels eroded more rapidly than non-alkylated kerateine and this control over erosion led to tunable rates of delivery of rhBMP-2, rhIGF-1, and ciprofloxacin. These results demonstrate that alkylation of kerateine cysteine residues provides a cell-compatible approach to tune rates of hydrogel erosion and therapeutic agent release within the context of a naturally-derived polymeric system.
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Affiliation(s)
- Sangheon Han
- Department of Chemical, Paper and Biomedical Engineering, Miami University, 650 E. High Street, Oxford, OH 45056, USA
| | - Trevor R Ham
- Department of Chemical, Paper and Biomedical Engineering, Miami University, 650 E. High Street, Oxford, OH 45056, USA; Department of Biomedical Engineering, University of Akron, Auburn Science and Engineering Center 275, West Tower, Akron, OH 44325, USA
| | - Salma Haque
- Department of Chemical, Paper and Biomedical Engineering, Miami University, 650 E. High Street, Oxford, OH 45056, USA
| | - Jessica L Sparks
- Department of Chemical, Paper and Biomedical Engineering, Miami University, 650 E. High Street, Oxford, OH 45056, USA
| | - Justin M Saul
- Department of Chemical, Paper and Biomedical Engineering, Miami University, 650 E. High Street, Oxford, OH 45056, USA.
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Huang G, Wang Y, Wang J, Yang C, Huang T, Zhuang Z, Gu J. A morphologic and semi-quantitative technique to analyze synthesis and release of specific proteins in cells. BMC Cell Biol 2014; 15:45. [PMID: 25476158 PMCID: PMC4261763 DOI: 10.1186/s12860-014-0045-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 11/25/2014] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND With the rapid advancement of cell biology, the evaluation of a given protein's synthesis and release in cells becomes critical. However, up to now there has been no technique available to morphologically visualize and measure a newly synthesized protein in cells, nor can we measure the protein's release from the cells. RESULTS In this study, we developed a set of assays combining pulse chase amino acid substitution, non-radioactive labeling, and immunofluorescence co-localization to visualize newly synthesized proteins in individual cells and then to detect their release using modified ELISA. We demonstrated the synthesis and release of Bcl-2, MMP-9, and immunoglobulin G (IgG) in a human trophoblast cell line, of which the last finding has not been reported previously. CONCLUSIONS This new technique offers a powerful tool to evaluate the dynamics of the synthesis and release of target proteins in individual cultured cells with wide applications in genetic and protein analysis.
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Affiliation(s)
- Guowei Huang
- Department of Pathology and Pathophysiology, Guangdong Provincial Key Laboratory of Infectious Disease and Immunopathology, Shantou University Medical College, Shantou, Guangdong, 515041, China.
| | - Yun Wang
- Department of Pathology and Pathophysiology, Guangdong Provincial Key Laboratory of Infectious Disease and Immunopathology, Shantou University Medical College, Shantou, Guangdong, 515041, China.
| | - Juping Wang
- Department of Pathology and Pathophysiology, Guangdong Provincial Key Laboratory of Infectious Disease and Immunopathology, Shantou University Medical College, Shantou, Guangdong, 515041, China.
| | - Chunzhang Yang
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of health, Bethesda, Maryland, 20892, USA.
| | - Tao Huang
- Department of Pathology and Pathophysiology, Guangdong Provincial Key Laboratory of Infectious Disease and Immunopathology, Shantou University Medical College, Shantou, Guangdong, 515041, China.
| | - Zhengping Zhuang
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of health, Bethesda, Maryland, 20892, USA.
| | - Jiang Gu
- Department of Pathology and Pathophysiology, Guangdong Provincial Key Laboratory of Infectious Disease and Immunopathology, Shantou University Medical College, Shantou, Guangdong, 515041, China.
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Battle KN, Uba FI, Soper SA. Microfluidics for the analysis of membrane proteins: How do we get there? Electrophoresis 2014; 35:2253-66. [DOI: 10.1002/elps.201300625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 02/16/2014] [Accepted: 02/17/2014] [Indexed: 01/22/2023]
Affiliation(s)
- Katrina N. Battle
- Department of Chemistry; Louisiana State University; Baton Rouge LA USA
| | - Franklin I. Uba
- Department of Chemistry; University of North Carolina; Chapel Hill NC USA
| | - Steven A. Soper
- Department of Chemistry; Louisiana State University; Baton Rouge LA USA
- Department of Chemistry; University of North Carolina; Chapel Hill NC USA
- Department of Biomedical Engineering; University of North Carolina; Chapel Hill NC USA
- BioFluidica, LLC, c/o Carolina Kick-Start; Chapel Hill NC USA
- School of Nano-Bioscience and Chemical Engineering; Ulsan National Institute of Science and Technology; Ulsan Korea
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Battle KN, Jackson JM, Witek MA, Hupert ML, Hunsucker SA, Armistead PM, Soper SA. Solid-phase extraction and purification of membrane proteins using a UV-modified PMMA microfluidic bioaffinity μSPE device. Analyst 2014; 139:1355-63. [PMID: 24487280 PMCID: PMC3970079 DOI: 10.1039/c3an02400h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We present a novel microfluidic solid-phase extraction (μSPE) device for the affinity enrichment of biotinylated membrane proteins from whole cell lysates. The device offers features that address challenges currently associated with the extraction and purification of membrane proteins from whole cell lysates, including the ability to release the enriched membrane protein fraction from the extraction surface so that they are available for downstream processing. The extraction bed was fabricated in PMMA using hot embossing and was comprised of 3600 micropillars. Activation of the PMMA micropillars by UV/O3 treatment permitted generation of surface-confined carboxylic acid groups and the covalent attachment of NeutrAvidin onto the μSPE device surfaces, which was used to affinity select biotinylated MCF-7 membrane proteins directly from whole cell lysates. The inclusion of a disulfide linker within the biotin moiety permitted release of the isolated membrane proteins via DTT incubation. Very low levels (∼20 fmol) of membrane proteins could be isolated and recovered with ∼89% efficiency with a bed capacity of 1.7 pmol. Western blotting indicated no traces of cytosolic proteins in the membrane protein fraction as compared to significant contamination using a commercial detergent-based method. We highlight future avenues for enhanced extraction efficiency and increased dynamic range of the μSPE device using computational simulations of different micropillar geometries to guide future device designs.
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Affiliation(s)
- Katrina N. Battle
- Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, LA 70803-1804, USA
| | - Joshua M. Jackson
- Department of Chemistry, University of North Carolina, Campus Box 3290, Chapel Hill, NC 27599-3290, USA
| | - Małgorzata A. Witek
- Department of Biomedical Engineering, University of North Carolina,152 MacNider Hall Campus Box 7575 Chapel Hill, NC 27599-7575, USA
| | - Mateusz L. Hupert
- Department of Biomedical Engineering, University of North Carolina,152 MacNider Hall Campus Box 7575 Chapel Hill, NC 27599-7575, USA
- BioFluidica, LLC, c/o Carolina Kick-Start, 321 Bondurant Hall, Chapel Hill, NC, 27599
| | - Sally A. Hunsucker
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Paul M. Armistead
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Steven A. Soper
- Department of Chemistry, University of North Carolina, Campus Box 3290, Chapel Hill, NC 27599-3290, USA
- Department of Biomedical Engineering, University of North Carolina,152 MacNider Hall Campus Box 7575 Chapel Hill, NC 27599-7575, USA
- BioFluidica, LLC, c/o Carolina Kick-Start, 321 Bondurant Hall, Chapel Hill, NC, 27599
- School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
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Lu J, Boeren S, de Vries SC, van Valenberg HJF, Vervoort J, Hettinga K. Filter-aided sample preparation with dimethyl labeling to identify and quantify milk fat globule membrane proteins. J Proteomics 2011; 75:34-43. [PMID: 21907314 DOI: 10.1016/j.jprot.2011.07.031] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Revised: 07/19/2011] [Accepted: 07/29/2011] [Indexed: 10/17/2022]
Abstract
Bovine milk is a major nutrient source in many countries and it is produced at an industrial scale. Milk is a complex mixture of proteins, fats, carbohydrates, vitamins and minerals. The composition of the bovine milk samples can vary depending on the genetic makeup of the bovine species as well as environmental factors. It is therefore important to study the qualitative and quantitative differences of bovine milk samples. Proteins in milk can be present in casein micelles, in the serum (the water soluble fraction) or in fat globules. These fat globules have a double membrane layer with proteins being bound to or being incapsulated in the membrane layer. The identification and molecular composition of the milk proteins have gained increased interest in recent years. Proteomic techniques make it now possible to identify up to many thousands of proteins in one sample, however quantification of proteins is as yet not straightforward. We analyzed the proteins of the milk fat globule membrane using dimethyl labeling methods combined with a filter-aided sample preparation protocol. Using these methods, it is now possible to quantitatively study the detailed protein composition of many milk samples in a short period of time.
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Affiliation(s)
- Jing Lu
- Dairy Science and Technology, Product Design and Quality Management Group, Wageningen University and Research Center, Bomenweg 2, 6700 EV, Wageningen, Netherlands
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Matta A, Ralhan R, DeSouza LV, Siu KWM. Mass spectrometry-based clinical proteomics: head-and-neck cancer biomarkers and drug-targets discovery. MASS SPECTROMETRY REVIEWS 2010; 29:945-961. [PMID: 20945361 DOI: 10.1002/mas.20296] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Mass spectrometry (MS)-based proteomics is a rapidly developing technology for both qualitative and quantitative analyses of proteins, and investigations into protein posttranslational modifications, subcellular localization, and interactions. Recent advancements in MS have made tremendous impact on the throughput and comprehensiveness of cancer proteomics, paving the way to unraveling deregulated cellular pathway networks in human malignancies. In turn, this knowledge is rapidly being translated into the discovery of novel potential cancer markers (PCMs) and targets for molecular therapeutics. Head-and-neck cancer is one of the most morbid human malignancies with an overall poor prognosis and severely compromised quality of life. Early detection and novel therapeutic strategies are urgently needed for more effective disease management. The characterizations of protein profiles of head-and-neck cancers and non-malignant tissues, with unprecedented sensitivity and precision, are providing technology platforms for identification of novel PCMs and drug targets. Importantly, low-abundance proteins are being identified and characterized, not only from the tumor tissues, but also from bodily fluids (plasma, saliva, and urine) in a high-throughput and unbiased manner. This review is a critical appraisal of recent advances in MS-based proteomic technologies and platforms for facilitating the discovery of biomarkers and novel drug targets in head-and-neck cancer. A major challenge in the discovery and verification of these cancer biomarkers is the typically limited availability of well-characterized and adequately stored clinical samples in tumor and sera banks, collected using recommended procedures, and with detailed information on clinical, pathological parameters, and follow-up. Most biomarker discovery studies use limited number of clinical samples and verification of cancer markers in large number of samples is beyond the scope of a single laboratory. The validation of these potential markers in large sample cohorts in multicentric studies is needed for their translation from the bench to the bedside.
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Affiliation(s)
- Ajay Matta
- Department of Chemistry, Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3
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8
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Jagannathan J, Li J, Szerlip N, Vortmeyer AO, Lonser RR, Oldfield EH, Zhuang Z. Application and implementation of selective tissue microdissection and proteomic profiling in neurological disease. Neurosurgery 2009; 64:4-14; discussion 14. [PMID: 19145153 DOI: 10.1227/01.neu.0000335776.93176.83] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE Proteins are the primary components of cells and are vital constituents of any living organism. The proteins that make up an organism (proteome) are constantly changing and are intricately linked to neurological disease processes. The study of proteins, or proteomics, is a relatively new but rapidly expanding field with increasing relevance to neurosurgery. METHODS We present a review of the state-of-the-art proteomic technology and its applications in central nervous system diseases. RESULTS The technique of "selective microdissection" allows an investigator to selectively isolate and study a pathological tissue of interest. By evaluating protein expression in a variety of central nervous system disorders, it is clear that proteins are differentially expressed across disease states, and protein expression changes markedly during disease progression. CONCLUSION Understanding the patterns of protein expression in the nervous system has critical implications for the diagnosis and treatment of neurological disease. As gatekeepers in the diagnosis, evaluation, and treatment of central nervous system diseases, it is important for neurosurgeons to develop an appreciation for proteomic techniques and their utility.
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Affiliation(s)
- Jay Jagannathan
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD 20892-1414, USA
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9
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Electrospray ionization mass spectroscopic analysis of peptides modified with N-ethylmaleimide or iodoacetanilide. Bioorg Med Chem Lett 2008; 18:4891-5. [DOI: 10.1016/j.bmcl.2008.07.069] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2008] [Revised: 07/15/2008] [Accepted: 07/16/2008] [Indexed: 12/14/2022]
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10
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Gutstein HB, Morris JS, Annangudi SP, Sweedler JV. Microproteomics: analysis of protein diversity in small samples. MASS SPECTROMETRY REVIEWS 2008; 27:316-30. [PMID: 18271009 PMCID: PMC2743962 DOI: 10.1002/mas.20161] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Proteomics, the large-scale study of protein expression in organisms, offers the potential to evaluate global changes in protein expression and their post-translational modifications that take place in response to normal or pathological stimuli. One challenge has been the requirement for substantial amounts of tissue in order to perform comprehensive proteomic characterization. In heterogeneous tissues, such as brain, this has limited the application of proteomic methodologies. Efforts to adapt standard methods of tissue sampling, protein extraction, arraying, and identification are reviewed, with an emphasis on those appropriate to smaller samples ranging in size from several microliters down to single cells. The effects of miniaturization on these analyses are highlighted using neuroscience-related examples, as are statistical issues unique to the high-dimensional datasets generated by proteomic experiments.
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Affiliation(s)
- Howard B Gutstein
- Department of Anesthesiology, University of Texas-MD Anderson Cancer Center, 1515 Holcombe Blvd., Box 110, Houston, TX 77030-4009, USA.
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11
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Micallef J, Gajadhar A, Wiley J, DeSouza LV, Michael Siu KW, Guha A. Proteomics: present and future implications in neuro-oncology. Neurosurgery 2008; 62:539-55; discussion 539-55. [PMID: 18425004 DOI: 10.1227/01.neu.0000317302.85837.61] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
PROTEOMICS, IN ITS broadest mandate, is the study of proteins and their functions. As the "workhorses" of the genome, proteins govern normal cellular structure and function. Protein function is not just a reflection of its expression level; it is also the cumulative result of many post-transcriptional (splicing) and post-translational events that together determine cellular localization, interactions, and longevity. The composition and variability of the proteome is vastly more complex than the corresponding genome. It is this proteome variation that helps define an organism and the unique characteristics that separate one individual from another. Aberrations in protein function, which alter normal cellular structure and function, are the ultimate basis of disease, including cancer. Therefore, an understanding of protein networks through a systems biology approach of proteomics is necessary to understand normal and abnormal cellular function, with the goal of performing rational therapeutic interventions. In this review, we focus on two emerging proteomic technologies: mass spectrometry and bioluminescence resonance energy transfer. In addition to reviewing the principles and potential utilization of these two techniques, we highlight their application in neuro-oncology research.
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Affiliation(s)
- Johann Micallef
- Arthur and Sonia Labatt Brain Tumour Center, Hospital for Sick Children's Research Institute, University of Toronto, Toronto, Canada
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12
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Neubauer H, Fehm T, Schütz C, Speer R, Solomayer E, Schrattenholz A, Cahill MA, Kurek R. Proteomic expression profiling of breast cancer. Recent Results Cancer Res 2007; 176:89-120. [PMID: 17607919 DOI: 10.1007/978-3-540-46091-6_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Breast cancer is one of the most common cancers observed in women in industrialized Western countries. The development of novel diagnostic methods and the application of modern systemic therapies have significantly optimized early detection and therapy of breast cancer. However, many patients are currently overtreated. Traditionally, tumours have been categorized on the basis of histopathological criteria. However, staining pattern and intensity of cancer cells are not sufficient to reflect the molecular events driving tumour development and progression. Therefore, new genomic, transcriptomic and proteomic techniques are applied to clinical samples aiming to identify new targets for a therapy tailored for an individual patient. After an introduction to common genomic and transcriptomic profiling technologies and their relevance for clinical use, we will focus on analytical and preanalytical applications for the identification of new therapeutic targets by protein profiling, with a special emphasis on two-dimensional gel-technologies (2D-PAGE), particularly as they apply to the study of breast cancer.
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13
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Wozny W, Schroer K, Schwall GP, Poznanović S, Stegmann W, Dietz K, Rogatsch H, Schaefer G, Huebl H, Klocker H, Schrattenholz A, Cahill MA. Differential radioactive quantification of protein abundance ratios between benign and malignant prostate tissues: cancer association of annexin A3. Proteomics 2007; 7:313-22. [PMID: 17205602 DOI: 10.1002/pmic.200600646] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A differential quantitative protein expression study, comparing matched prostate cancerous and benign tissues from 31 patients, revealed proteins newly associated with prostate cancer. Average effects for 17 proteins whose abundance was significantly different (p<0.01) across patients ranged from 1.5- to 6.1-fold, and included a number of known cancer markers. The most differentially abundant proteins between cancer and benign samples were isopeptidase T, serum amyloid P (SAP), annexin A3 (ANXA3) and mitochondrial enoyl coenzyme-A hydratase. SAP is restricted to stroma in healthy tissue, and the lower abundance in tumours may be explained by the reduced stromal content. ANXA3 is present in healthy epithelial cells, exhibits strong staining in precancerous prostatic intraepithelial neoplasia, and is relatively less abundant in individual tumour cells of increasing Gleason pattern (GP), despite exhibiting higher overall tissue abundance in tumours. ANXA3 staining was predominantly cytoplasmic, yet nuclear localization was also observed. Strongly staining single cells, possibly phagocytes, were interspersed in highly dedifferentiated GP5 tumour areas among tumour cells without measurable ANXA3. Local recurrent androgen ablation therapy-resistant tumours exhibit heterogenous low levels of ANXA3 staining. Results are discussed focussing on the potential implications for tumour tissues.
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14
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Yang Z, Attygalle AB. LC/MS characterization of undesired products formed during iodoacetamide derivatization of sulfhydryl groups of peptides. JOURNAL OF MASS SPECTROMETRY : JMS 2007; 42:233-43. [PMID: 17206739 DOI: 10.1002/jms.1157] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Many undesired by-products have been noticed during alkylation with iodoacetamide, a widely used derivatization reaction in proteomics for the determination of sulfhydryl groups in peptides and proteins. We report here that iodoacetamide reacts with the N-terminal NH2 and the C-terminal carboxylic acid groups, in addition to the peripheral residues bearing protic functional groups. If sufficient reaction time is given, the N-terminal NH2 group is readily dialkylated by iodoacetamide. In fact, the N-terminal NH2 group reacts even faster than the reactive sites present in residues, such as tyrosine or histidine. LC/MS investigations with certain reactive peptides show that by-products are formed in a relatively short reaction time, even at room temperature. Interestingly, derivatives formed in this way are useful for sequence determination of peptides by MS since the intensities of y'' ions are highly suppressed in the spectra of N-terminus mono- and dialkylated peptides, whereas those of b-ions are significantly enhanced. For example, in the spectrum of N,N-dicarboxamidomethyl derivative of Val-Ala-Ala-Phe (VAAF), the y-series ions are virtually absent. On the other hand, when the derivatization takes place at the carboxylic group, the y-series ions are markedly observed in the spectra of these undesired O-carboxamidomethyl derivatives.
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Affiliation(s)
- Zhihua Yang
- Center for Mass Spectrometry, Department of Chemistry and Chemical Biology, Stevens Institute of Technology, NJ 07030, USA
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15
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Holmberg M, Stibius KB, Ndoni S, Larsen NB, Kingshott P, Hou XL. Protein aggregation and degradation during iodine labeling and its consequences for protein adsorption to biomaterials. Anal Biochem 2006; 361:120-5. [PMID: 17187752 DOI: 10.1016/j.ab.2006.11.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2006] [Revised: 11/06/2006] [Accepted: 11/10/2006] [Indexed: 11/24/2022]
Abstract
Protein adsorption on modified and unmodified polymer surfaces investigated through radiolabeling experiments showed a tendency for higher than expected albumin and immunoglobulin G (IgG) adsorption. Possible enhanced protein aggregation and degradation caused by the iodine labeling method used were analyzed through chromatography and spectroscopy techniques. Results show that the iodine labeling method using chloramine-T (CAT) as an oxidizing agent can cause both enhanced aggregation and fragmentation of proteins. Albumin shows an enhanced tendency to aggregate after iodine labeling using the CAT method, and higher amounts of fragmentation are observed for CAT-labeled IgG molecules relative to unlabeled IgG molecules as well as to IgG molecules labeled using the Iodo-Gen method. These results show that the widely applied method of radioisotope labeling for quantitative assessment of protein adsorption should be used with caution and preferably should be validated by a label-free methodology for each combination of radiolabel and protein. The results obtained in this study can be used to optimize investigation of protein adsorption on surfaces of materials for biomedical devices.
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Affiliation(s)
- Maria Holmberg
- Danish Polymer Centre, Risø National Laboratory, DK-4000 Roskilde, Denmark.
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16
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Synthesis of D-labeled naphthyliodoacetamide and application to quantitative peptide analysis by isotope differential mass spectrometry. Bioorg Med Chem Lett 2006; 16:6054-7. [DOI: 10.1016/j.bmcl.2006.08.112] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2006] [Revised: 08/28/2006] [Accepted: 08/29/2006] [Indexed: 11/19/2022]
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17
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Ou K, Kesuma D, Ganesan K, Yu K, Soon SY, Lee SY, Goh XP, Hooi M, Chen W, Jikuya H, Ichikawa T, Kuyama H, Matsuo EI, Nishimura O, Tan P. Quantitative profiling of drug-associated proteomic alterations by combined 2-nitrobenzenesulfenyl chloride (NBS) isotope labeling and 2DE/MS identification. J Proteome Res 2006; 5:2194-206. [PMID: 16944931 DOI: 10.1021/pr060115n] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The identification of drug-responsive biomarkers in complex protein mixtures is an important goal of quantitative proteomics. Here, we describe a novel approach for identifying such drug-induced protein alterations, which combines 2-nitrobenzenesulfenyl chloride (NBS) tryptophan labeling with two-dimensional gel electrophoresis (2DE)/mass spectrometry (MS). Lysates from drug-treated and control samples are labeled with light or heavy NBS moiety and separated on a common 2DE gel, and protein alterations are identified by MS through the differential intensity of paired NBS peptide peaks. Using NBS/2DE/MS, we profiled the proteomic alterations induced by tamoxifen (TAM) in the estrogen receptor (ER) positive MCF-7 breast cancer cell line. Of 88 protein spots that significantly changed upon TAM treatment, 44 spots representing 23 distinct protein species were successfully identified with NBS-paired peptides. Of these 23 TAM-altered proteins, 16 (70%) have not been previously associated with TAM or ER activity. We found the NBS labeling procedure to be both technically and biologically reproducible, and the NBS/2DE/MS alterations exhibited good concordance with conventional 2DE differential protein quantitation, with discrepancies largely due to the comigration of distinct proteins in the regular 2DE gels. To validate the NBS/2DE/MS results, we used immunoblotting to confirm GRP78, CK19, and PA2G4 as bona fide TAM-regulated proteins. Furthermore, we demonstrate that PA2G4 expression can serve as a novel prognostic factor for disease-free survival in two independent breast cancer patient cohorts. To our knowledge, this is the first report describing the proteomic changes in breast cancer cells induced by TAM, the most commonly used selective estrogen receptor modulator (SERM). Our results indicate that NBS/2DE/MS may represent a more reliable approach for cellular protein quantitation than conventional 2DE approaches.
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Affiliation(s)
- Keli Ou
- Agenica Research/National Cancer Centre/Genome Institute of Singapore, 11 Hospital Drive, Singapore 169610
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18
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Kurono S, Kurono T, Komori N, Niwayama S, Matsumoto H. Quantitative proteome analysis using D-labeled N-ethylmaleimide and 13C-labeled iodoacetanilide by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Bioorg Med Chem 2006; 14:8197-209. [PMID: 17049249 PMCID: PMC1876768 DOI: 10.1016/j.bmc.2006.09.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2006] [Revised: 09/12/2006] [Accepted: 09/12/2006] [Indexed: 11/16/2022]
Abstract
A new methodology for quantitative analysis of proteins is described, applying stable-isotope labeling by small organic molecules combined with one- or two-dimensional electrophoresis and MALDI-TOF-MS, also allowing concurrent protein identification by peptide mass fingerprinting. Our method eliminates fundamental problems in other existing isotope-tagging methods requiring liquid chromatography and MS/MS, such as isotope effects, fragmentation, and solubility. It is also anticipated to be more practical and accessible than those LC-dependent methods.
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19
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Abstract
The brain is unquestionably the most fascinating organ. Despite tremendous progress, current knowledge falls short of being able to explain its function. An emerging approach toward improved understanding of the molecular mechanisms underlying brain function is neuroproteomics. Today's neuroscientists have access to a battery of versatile technologies both in transcriptomics and proteomics. The challenge is to choose the right strategy in order to generate new hypotheses on how the brain works. The goal of this review is therefore two-fold: first we recall the bewildering cellular, molecular, and functional complexity in the brain, as this knowledge is fundamental to any study design. In fact, an impressive complexity on the molecular level has recently re-emerged as a central theme in large-scale analyses. Then we review transcriptomics and proteomics technologies, as both are complementary. Finally, we comment on the most widely used proteomics techniques and their respective strengths and drawbacks. We conclude that for the time being, neuroproteomics should focus on its strengths, namely the identification of posttranslational modifications and protein-protein interactions, as well as the characterization of highly purified subproteomes. For global expression profiling, emphasis should be put on further development to significantly increase coverage.
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Affiliation(s)
- Michael Becker
- Abteilung Tierphysiologie, Fachbereich Biologie, Technische Universität Kaiserslautern, Germany
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20
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Neubauer H, Clare SE, Kurek R, Fehm T, Wallwiener D, Sotlar K, Nordheim A, Wozny W, Schwall GP, Poznanović S, Sastri C, Hunzinger C, Stegmann W, Schrattenholz A, Cahill MA. Breast cancer proteomics by laser capture microdissection, sample pooling, 54-cm IPG IEF, and differential iodine radioisotope detection. Electrophoresis 2006; 27:1840-52. [PMID: 16645950 DOI: 10.1002/elps.200500739] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The presence of progesterone receptor (PR) in estrogen receptor (ER)-positive breast cancer is associated with a good prognosis, and indicates that tumors are likely to respond to tamoxifen. However, ER+/PR- tumors respond less well. To reveal the potential molecular mechanism of this phenomenon, we sought to identify differential protein abundances between invasive ductal carcinoma cells from cryopreserved ER+/PR+ and ER+/PR- mammary tumor specimens. Because current proteomics methods are hampered in the examination of most primary human tumor samples by the extreme tissue heterogeneity, we used laser capture microdissection (LCM) to isolate tumor cells and developed a sample pooling strategy to analyze small sample protein lysates. Proteins from LCM-harvested tumors were pooled into four sub-pools from each condition of three tumors/sub-pool, and proteins from respective paired sub-pools were co-electrophoresed by 2-DE using 54-cm IEF over pH 4-9. Abundance ratios were accurately quantified by a differential multiplex radioactive ProteoTope method at low attomole levels ( approximately 3.6 microg protein per labeling reaction, <180 ng per multiplex protein sample per 54-cm gel). Applying this approach, differentially displayed proteins were identified by MS using comigrating non-radioactively labeled tumor proteins. They include decreased cytochrome b5 and transgelin, and more abundant CRABP-II, cyclophilin A, Neudesin, and hemoglobin in ER+/PR+ tumors versus ER+/PR- providing a possible explanation for differential susceptibility against tamoxifen as a result of deregulated cytochrome b5-dependent metabolism. This study demonstrates the potential of ProteoTope and LCM to enable extremely sensitive and precise differential analyses from well-defined primary clinical specimen.
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21
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Mundinger GS, Espina V, Liotta LA, Petricoin EF, Calvo KR. Clinical phosphoproteomic profiling for personalized targeted medicine using reverse phase protein microarray. Target Oncol 2006. [DOI: 10.1007/s11523-006-0025-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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22
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Nishizuka S. Profiling cancer stem cells using protein array technology. Eur J Cancer 2006; 42:1273-82. [PMID: 16644205 DOI: 10.1016/j.ejca.2006.01.042] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2006] [Accepted: 01/23/2006] [Indexed: 11/20/2022]
Abstract
Since cancer cells and somatic stem cells share the biological characteristics of self-renewal and proliferation, it has been suggested that the principles of stem cell biology can be applied to improve our understanding of cancer biology. Recent studies have shown that the majority of cancers appear to originate from a small subset of cells that have the ability of self-renewal and to proliferate, namely 'cancer stem cells'. The isolation of cancer stem cells has been demonstrated using cell surface markers in haematopoietic and non-haematopoietic malignancies. Advances in protein array technologies have enabled the use of minuscule amounts of biological materials to profile these cells at the molecular level. Using a combination of protein arrays and cancer stem cell isolation techniques, a higher resolution molecular profiling can be performed, which might improve therapies targeting the cancer stem cells.
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Affiliation(s)
- Satoshi Nishizuka
- Molecular Translational Technologies, Molecular Therapeutics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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23
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Poznanović S, Wozny W, Schwall GP, Sastri C, Hunzinger C, Stegmann W, Schrattenholz A, Buchner A, Gangnus R, Burgemeister R, Cahill MA. Differential radioactive proteomic analysis of microdissected renal cell carcinoma tissue by 54 cm isoelectric focusing in serial immobilized pH gradient gels. J Proteome Res 2006; 4:2117-25. [PMID: 16335957 DOI: 10.1021/pr050218q] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We present a proof of principle study, using laser microdissection and pressure catapulting (LMPC) of two clinical tissue samples, each containing approximately 3.8 microg renal cell carcinoma protein and 3.8 microg normal kidney protein respectively from one patient. The study involved separate radio-iodination of each sample with both (125)I and (131)I, dual inverse replicate sample loading to high resolution 54 cm "daisy chain" serial immobilized pH gradient isoelectric focusing (IPG-IEF) 2D-PAGE gels, co-electrophoretic separation of cross-labeled proteins from different samples, and precision multiplex differential radioactive imaging to obtain signals specific for each sample coelectrophoresed within single gels but labeled with different isotopes of iodine, providing extremely precise intra-gel estimates of the abundance ratio for protein spots from both samples. Twelve multiplexed analytical radioactive SDS-gels from 4 serial IPG-IEF gels provided 24 individual radioactive images for a comprehensive analytical protein multiplex quantification study. A further 12 SDS gels containing (125)I-labeled sample were coelectrophoresed with preparative protein amounts obtained from whole tissue sections for the mass spectrometric identification of comigrating proteins. This consumed <40% of the (125)I-labeled sample, and <20% of the (131)I-labeled sample from the respective original 3.8 microg samples. Twenty-nine proteins were identified by mass spectrometry with PMF scores >70 that were >2-fold differentially abundant between the samples and t-test probabilities <0.05. We conclude that this combination of technologies provides excellent quality protein multiplex data for the differential abundance analysis of large numbers of proteins from extremely small samples, and is applicable to a broad range of clinical and related applications.
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24
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Churchward MA, Butt RH, Lang JC, Hsu KK, Coorssen JR. Enhanced detergent extraction for analysis of membrane proteomes by two-dimensional gel electrophoresis. Proteome Sci 2005; 3:5. [PMID: 15941475 PMCID: PMC1184097 DOI: 10.1186/1477-5956-3-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2005] [Accepted: 06/07/2005] [Indexed: 11/29/2022] Open
Abstract
Background The analysis of hydrophobic membrane proteins by two-dimensional gel electrophoresis has long been hampered by the concept of inherent difficulty due to solubility issues. We have optimized extraction protocols by varying the detergent composition of the solubilization buffer with a variety of commercially available non-ionic and zwitterionic detergents and detergent-like phospholipids. Results After initial analyses by one-dimensional SDS-PAGE, quantitative two-dimensional analyses of human erythrocyte membranes, mouse liver membranes, and mouse brain membranes, extracted with buffers that included the zwitterionic detergent MEGA 10 (decanoyl-N-methylglucamide) and the zwitterionic lipid LPC (1-lauroyl lysophosphatidylcholine), showed selective improvement over extraction with the common 2-DE detergent CHAPS (3 [(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate). Mixtures of the three detergents showed additive improvements in spot number, density, and resolution. Substantial improvements in the analysis of a brain membrane proteome were observed. Conclusion This study demonstrates that an optimized detergent mix, coupled with rigorous sample handling and electrophoretic protocols, enables simple and effective analysis of membrane proteomes using two-dimensional electrophoresis.
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Affiliation(s)
- Matthew A Churchward
- Dept. of Physiology and Biophysics, University of Calgary Faculty of Medicine, 3330 Hospital Drive NW, Calgary AB, T2N 4N1, CANADA
| | - R Hussain Butt
- Dept. of Physiology and Biophysics, University of Calgary Faculty of Medicine, 3330 Hospital Drive NW, Calgary AB, T2N 4N1, CANADA
| | - John C Lang
- Dept. of Physiology and Biophysics, University of Calgary Faculty of Medicine, 3330 Hospital Drive NW, Calgary AB, T2N 4N1, CANADA
| | - Kimberly K Hsu
- Dept. of Physiology and Biophysics, University of Calgary Faculty of Medicine, 3330 Hospital Drive NW, Calgary AB, T2N 4N1, CANADA
| | - Jens R Coorssen
- Dept. of Physiology and Biophysics, University of Calgary Faculty of Medicine, 3330 Hospital Drive NW, Calgary AB, T2N 4N1, CANADA
- Dept. of Biochemistry and Molecular Biology, University of Calgary Faculty of Medicine, 3330 Hospital Drive NW, Calgary AB, T2N 4N1, CANADA
- Hotchkiss Brain Institute, University of Calgary Faculty of Medicine, 3330 Hospital Drive NW, Calgary AB, T2N 4N1, CANADA
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25
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Barrier M, Mirkes PE. Proteomics in developmental toxicology. Reprod Toxicol 2005; 19:291-304. [PMID: 15686865 DOI: 10.1016/j.reprotox.2004.09.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2004] [Revised: 07/26/2004] [Accepted: 09/03/2004] [Indexed: 10/26/2022]
Abstract
The objective of this presentation is to review the major proteomic technologies available to developmental toxicologists and, when possible, to provide examples of how various proteomic technologies have been used in developmental toxicology or toxicology in general. The field of proteomics is too broad for us to go into great depth about each technology, so we have attempted to provide brief overviews supplemented with many references that cover the subjects in more detail. Proteomics tools produce a global view of complex biological systems by examining complex protein mixtures using large-scale, high-throughput technologies. These technologies speed up the process of protein separation, quantification, and identification. As an important complement to genomics, proteomics allows for the examination of the entire complement of proteins in an organism, tissue, or cell-type. Current proteomics technologies not only identify protein expression, but also post-translational modifications and protein interactions. The field of proteomics is expanding rapidly to provide greater volume and quality of protein information to help understand the multifaceted nature of biological systems.
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Affiliation(s)
- Marianne Barrier
- Birth Defects Research Laboratory, Division of Genetics and Developmental Medicine, Department of Pediatrics, University of Washington, Box 356320, 1959 NE Pacific Street, Seattle, WA 98195, USA
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Abstract
The human genome contains about 30,000 genes, each creating several transcripts per gene. Transcript structures and expression are studied by high-throughput transcriptomic techniques using microarrays. Generally, transcripts are not directly operating molecules, but are translated into functional proteins, post-translationally modified by proteolysis, glycosylation, phosphorylation, etc., sometimes with great functional impact. Proteins need to be analyzed by proteomic techniques, less suited for high-throughput. Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), separating thousands of proteins has developed slowly over the past quarter of a century. This technique is now quite reproducible and suitable for differential proteomics, comparing normal and diseased cells/tissues revealing differentially regulated proteins. 2D-PAGE is combined with protein-identification methods, currently mass spectrometry (MS), which has been significantly improved over the last decade. Other proteomic techniques studying protein-protein interactions are now either established or still being developed, such as peptide or protein arrays, phage display, and the yeast two-hybrid system. The strengths and weaknesses of these techniques are discussed.
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Affiliation(s)
- Bent Honoré
- Department of Medical Biochemistry, University of Aarhus, Aarhus C, Denmark.
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28
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Schrattenholz A, Klemm M, Cahill M. Potential of comprehensive toxico-proteomics: quantitative and differential mining of functional proteomes from native samples. Altern Lab Anim 2004; 32 Suppl 1A:123-31. [PMID: 23577445 DOI: 10.1177/026119290403201s19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
It is becoming increasingly clear that the interactions of targets and biomarkers, drug modes of action and molecular mechanisms of side-effects and toxic effects are much more complex than previously anticipated, basically due to physiological compensation and cross-talk. Single genes often lead to hundreds or even thousands of functional protein molecules, modified at the post-translational level. Thus, the comprehensive analysis of proteins (proteomics) teaches us that physiological activity means dynamic, multidimensional processes among many thousands of different proteins within higher systems of organisation and correlation. Crucial for control and relevant reduction of this enormous complexity, which will enable new kinds of molecular drug screening, as well as a new type of molecular toxicology, is a consequently differential and quantitative protein analysis. Precise knowledge of key protein isoforms with specific post-translational modifications within kinetic and contextual relationships is accessible by powerful new technologies, which have emerged to analyse the surprisingly ambiguous world of proteins, where single molecular modules are involved in a diversity of often opposing signal transduction pathways in a most flexible way.
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29
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Issaq HJ. Application of separation technologies to proteomics research. ADVANCES IN PROTEIN CHEMISTRY 2004; 65:249-69. [PMID: 12964372 DOI: 10.1016/s0065-3233(03)01022-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Haleem J Issaq
- Separation Technology Group, Analytical Chemistry Laboratory, SAIC-Frederick, National Cancer Institute at Frederick, Frederick, Maryland 21702, USA
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30
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Zagursky RJ, Olmsted SB, Russell DP, Wooters JL. Bioinformatics: how it is being used to identify bacterial vaccine candidates. Expert Rev Vaccines 2003; 2:417-36. [PMID: 12903807 DOI: 10.1586/14760584.2.3.417] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Genomic sequencing has provided a tremendous amount of information that can be useful in vaccine target identification. The sheer volume of information available necessitates the use of new research disciplines and techniques. Using bioinformatics, researchers sift through available data to identify appropriate candidates for biological analysis. This review provides an overview of available bioinformatic techniques for vaccine candidate identification and a few examples of how these techniques are being applied to specific bacterial pathogens.
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31
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Shin BK, Wang H, Yim AM, Le Naour F, Brichory F, Jang JH, Zhao R, Puravs E, Tra J, Michael CW, Misek DE, Hanash SM. Global profiling of the cell surface proteome of cancer cells uncovers an abundance of proteins with chaperone function. J Biol Chem 2003; 278:7607-16. [PMID: 12493773 DOI: 10.1074/jbc.m210455200] [Citation(s) in RCA: 396] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
There is currently limited data available pertaining to the global characterization of the cell surface proteome. We have implemented a strategy for the comprehensive profiling and identification of surface membrane proteins. This strategy has been applied to cancer cells, including the SH-SY5Y neuroblastoma, the A549 lung adenocarcinoma, the LoVo colon adenocarcinoma, and the Sup-B15 acute lymphoblastic leukemia (B cell) cell lines and ovarian tumor cells. Surface membrane proteins of viable, intact cells were subjected to biotinylation then affinity-captured and purified on monomeric avidin columns. The biotinylated proteins were eluted from the monomeric avidin columns as intact proteins and were subsequently separated by two-dimensional PAGE, transferred to polyvinylidene difluoride membranes, and visualized by hybridization with streptavidin-horseradish peroxidase. Highly reproducible, but distinct, two-dimensional patterns consisting of several hundred biotinylated proteins were obtained for the different cell populations analyzed. Identification of a subset of biotinylated proteins among the different cell populations analyzed using matrix-assisted laser desorption ionization and tandem mass spectrometry uncovered proteins with a restricted expression pattern in some cell line(s), such as CD87 and the activin receptor type IIB. We also identified more widely expressed proteins, such as CD98, and a sushi repeat-containing protein, a member of the selectin family. Remarkably, a set of proteins identified as chaperone proteins were found to be highly abundant on the cell surface, including GRP78, GRP75, HSP70, HSP60, HSP54, HSP27, and protein disulfide isomerase. Comprehensive profiling of the cell surface proteome provides an effective approach for the identification of commonly occurring proteins as well as proteins with restricted expression patterns in this compartment.
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MESH Headings
- Activin Receptors, Type II/metabolism
- Amino Acid Sequence
- Biotinylation
- Blotting, Western
- Carrier Proteins/biosynthesis
- Electrophoresis, Gel, Two-Dimensional
- Endoplasmic Reticulum Chaperone BiP
- Fusion Regulatory Protein-1/biosynthesis
- HSP70 Heat-Shock Proteins/biosynthesis
- Heat-Shock Proteins
- Humans
- Mass Spectrometry
- Microscopy, Fluorescence
- Molecular Chaperones/biosynthesis
- Molecular Chaperones/metabolism
- Molecular Sequence Data
- Neoplasms/metabolism
- Oligonucleotide Array Sequence Analysis
- Protein Array Analysis
- Protein Binding
- Protein Structure, Tertiary
- Proteome
- Receptors, Cell Surface/biosynthesis
- Receptors, Urokinase Plasminogen Activator
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Tumor Cells, Cultured
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Affiliation(s)
- Bong Kyung Shin
- Departments of Pediatrics and Pathology, University of Michigan, Ann Arbor, Michigan 48109-0656, USA
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32
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Cahill MA, Wozny W, Schwall G, Schroer K, Hölzer K, Poznanovic S, Hunzinger C, Vogt JA, Stegmann W, Matthies H, Schrattenholz A. Analysis of relative isotopologue abundances for quantitative profiling of complex protein mixtures labelled with the acrylamide/D3-acrylamide alkylation tag system. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2003; 17:1283-1290. [PMID: 12811751 DOI: 10.1002/rcm.1046] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The new method of analysis of relative isotopologue abundances (ARIA) applied here is based on the evaluation of total isotope patterns of tryptic protein fragments measured by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOFMS) to calculate the mixing ratios of composites consisting of stable isotope labelled and isotopically natural (unlabelled) proteins, as described in an accompanying paper in this issue. Recently, Sechi (Rapid Commun. Mass Spectrom. 2002; 16: 1416-1424) and Gehanne et al. (Rapid Commun. Mass Spectrom. 2002; 16: 1692-1698) introduced the use of differential quantitative mass analysis by MALDI-TOFMS using mixtures of standard proteins alkylated prior to two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) with either acrylamide (AA) or deuterium-labelled [2,3,3'-D(3)]-acrylamide (D3AA). In the present study we validate the AA/D3AA system, firstly by measuring the yield of proteins alkylated with AA, and secondly by using differential radioactive labels ((125)I and (131)I) to quantitatively establish that non-comigration in 2D-PAGE is negligible. ARIA is then applied to quantitatively estimate the relative proportions of peptides labelled with AA or D3AA in the validated system, using typical silver-stained 2D-PAGE protein spots from 2D gels loaded with 150 microg of total liver protein. The precision and limitations of ARIA quantification of peptides differentially alkylated with isotopomeric reagents are discussed.
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Affiliation(s)
| | | | | | - Klaus Schroer
- ProteoSys AG, Carl-Zeiss-Str. 51, 55129 Mainz, Germany
| | | | | | | | - Josef A Vogt
- University Hospital Ulm, Department of Anaesthesia, Parkstrasse 11, 89073 Ulm, Germany
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33
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He Y, Yeung ES, Chan KC, Issaq HJ. Two dimensional mapping of cancer cell extracts by liquid chromatography-capillary electrophoresis with ultraviolet absorbance detection. J Chromatogr A 2002; 979:81-9. [PMID: 12498235 DOI: 10.1016/s0021-9673(02)01503-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A two-dimensional liquid chromatography/capillary electrophoresis technique was developed for rapid and comprehensive mapping of cell extracts. The cell extracts were first separated by reversed-phase HPLC based on hydrophobicity. Fractions of the effluent from the HPLC system were collected into 96-well microtiter plates and dried under vacuum. The fractions were reconstituted with deionized water, separated by capillary array electrophoresis based on charge-to-size ratio, and detected by UV absorption at 214 nm. Prior to analysis by multiplexed capillary electrophoresis, the reconstituted fractions were concentrated on-column using large volume sample stacking with polarity switching. In this way, high-resolution analysis of even the minor components in the complicated mixture was possible.
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Affiliation(s)
- Yan He
- Ames Laboratory-USDOE and Department of Chemistry, Iowa State University, Ames, IA 50011, USA
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34
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Abstract
In the last few years there has been an increased effort to develop technologies capable of identifying and quantifying large numbers of proteins expressed within a cell system (i.e., the proteome). The complexity of the mixtures being analyzed has made the development of effective fractionation and separation methods a critical component of this effort. This review highlights many of the protein and peptide fractionation and separation methods, such as electrophoresis and high-performance liquid chromatography (HPLC), which have experienced significant development over the past forty years. Modern instrumental strategies for the resolution of cell proteins, based on separations employing a single high-resolution or multidimensional approach, and the relative merits of each, will be discussed. The focus of this manuscript will be on the development of multidimensional separations such as two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), HPLC/HPLC, and HPLC-capillary electrophoresis and their application to the characterization of complex proteome mixtures.
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Affiliation(s)
- Haleem J Issaq
- Analytical Chemistry Laboratory, SAIC Frederick NCI-Frederick, Frederick, MD 21702, USA.
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35
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Abstract
With the human genome sequence now determined, the field of molecular medicine is moving beyond genomics to proteomics. In the field of cancer research, the key question is: how can oncologists best use techniques of proteomics in basic research and clinical application? In the postgenomic era, proteomics promises the discovery of biomarkers and tumor markers for early detection and diagnosis, novel protein-based drug targets for anticancer therapy, and new endpoints for the assessment of therapeutic efficacy and toxicity. This review paper will explore key themes in proteomics and their application in clinical cancer research.
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Affiliation(s)
- W Wu
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030-4009, USA.
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36
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Patton WF, Schulenberg B, Steinberg TH. Two-dimensional gel electrophoresis; better than a poke in the ICAT? Curr Opin Biotechnol 2002; 13:321-8. [PMID: 12323353 DOI: 10.1016/s0958-1669(02)00333-6] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
To date, the most widely used technology for conducting proteomic studies has been two-dimensional gel electrophoresis (2DGE), but this approach does have drawbacks. Isotope-coded affinity tagging (ICAT) is starting to challenge 2DGE as a new proteomic tool for the analysis of proteins in complex biological specimens. An appraisal of these two methodologies reveals that neither ICAT nor 2DGE provide comprehensive coverage on a proteome-wide scale.
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Affiliation(s)
- Wayne F Patton
- Proteomics Section, Molecular Probes, Inc., 4849 Pitchford Avenue, Eugene, Oregon 97402, USA.
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37
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Rabilloud T. Two-dimensional gel electrophoresis in proteomics: old, old fashioned, but it still climbs up the mountains. Proteomics 2002. [PMID: 11788986 DOI: 10.1002/1615-9861(200201)2:1%3c3::aid-prot3%3e3.0.co;2-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Proteomics has traditionally used the separating power of two-dimensional electrophoresis for the quantitative analysis of protein amounts in complex extracts. However, the limitations of this approach in terms of throughput and analyzable protein range have elicited the development of other proteomics approaches, based either on peptide separations instead of protein separations, or based on direct protein recognition and selection on dedicated arrays (protein chips). These recent methods seem very promising, and probably look more promising than they will ultimately be, just because their weaknesses are not fully characterized yet. The purpose of this paper is thus to highlight the strengths and weaknesses of all the proteomics approaches proposed to date and to try to deduce the respective niches in proteomics that these approaches will have in the future.
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Affiliation(s)
- Thierry Rabilloud
- CEA-Laboratoire de Bioénergétique Cellulaire et Pathologique, Grenoble, France.
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Abstract
Global analysis of biological systems is becoming increasingly feasible as technologies that facilitate genome-wide analyses of gene expression are developed. Proteomics is the global analysis of expressed proteins (including posttranslational modifications) and seeks to establish the relationship between genome sequence, expressed proteins, protein-protein interactions, and cell and tissue phenotype. While the relative abundance of transcripts can be quantified using gene expression microarrays, the identification and quantitation of expressed proteins is more challenging. Nevertheless, the potential payoff for global protein analyses is immense because identification of distinctive protein signatures associated with cell function may provide novel therapeutic targets, molecular markers of disease, and increased understanding of determinants of cell phenotype. The challenges and promises of applications of established and emerging proteome strategies to detect and quantify differentially expressed proteins in culture cells are discussed.
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Affiliation(s)
- Ellen A Panisko
- Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
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Abstract
In the last few years there has been an increased effort into the separation, quantification and identification of all proteins in a cell or tissue. This is a review of the role gel electrophoresis, high performance liquid chromatography (HPLC), and capillary electrophoresis (CE) play in proteomics research. The capabilities and limitations of each separation technique have been pointed out. Instrumental strategies for the resolution of cell proteins which are based on efficient separation employing either a single high-resolution procedure or a multidimensional approach on-line or off-line, and a mass spectrometer for protein identification have been reviewed. A comparison of the advantages of multi-dimensional separations such as two-dimensional polyacrylamide gel electrophoresis, HPLC-HPLC, and HPLC-CE to the separation of cell and tissue proteins are discussed. Also, a discussion of novel approaches to protein concentration, separation, detection, and quantification is given.
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Affiliation(s)
- H J Issaq
- Separation Technology Group, SAIC-Frederick/NCI-Frederick, MD 21702, USA.
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41
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Abstract
2D gel electrophoresis is the technology that everyone loves to hate-it requires manual dexterity and precision to reproduce precisely and is thus not well-suited as a high-throughput technology. Although almost everyone would like to replace it, the resolution and sensitivity it offers are exquisite and unsurpassed if one wants a global view of cellular activity. There have been several recent developments, for example, the detection of low abundance proteins, and the resolution possible with narrow-range IPG gels.
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Affiliation(s)
- S J Fey
- Centre for Proteome Analysis, University of Southern Denmark, International Science Park Odense, Forskerparken 10B, DK-5230, Odense M, Denmark.
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