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May C, Brosseron F, Pfeiffer K, Fuchs K, Meyer HE, Sitek B, Marcus K. Proteome Analysis with Classical 2D-PAGE. Methods Mol Biol 2021; 2228:53-62. [PMID: 33950483 DOI: 10.1007/978-1-0716-1024-4_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) is based on the combination of two orthogonal separation techniques. In the first dimension, proteins are separated by their isoelectric point, a technique known as isoelectric focusing (IEF). There are two important variants of IEF, which are carrier-ampholine (CA)-based IEF and immobilized pH-gradient (IPG)-based IEF. In the second dimension, proteins are further separated by their electrophoretic mobility using SDS-PAGE. Finally, proteins can be visualized and quantified by different staining procedures such as Coomassie, silver staining, or fluorescence labeling. This article gives detailed protocols for 2D-PAGE, using both CA- and IPG-based separation in the first dimension.
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Affiliation(s)
- Caroline May
- Medizinisches Proteom-Center (MPC), Medical Faculty, Ruhr-University Bochum, Bochum, Germany
- Medical Proteome Analysis, Center for Proteindiagnostics (PRODI) Ruhr-University Bochum, Bochum, Germany
| | - Frederic Brosseron
- Medizinisches Proteom-Center (MPC), Medical Faculty, Ruhr-University Bochum, Bochum, Germany
| | - Kathy Pfeiffer
- Medizinisches Proteom-Center (MPC), Medical Faculty, Ruhr-University Bochum, Bochum, Germany
- Medical Proteome Analysis, Center for Proteindiagnostics (PRODI) Ruhr-University Bochum, Bochum, Germany
| | - Kristin Fuchs
- Medizinisches Proteom-Center (MPC), Medical Faculty, Ruhr-University Bochum, Bochum, Germany
- Medical Proteome Analysis, Center for Proteindiagnostics (PRODI) Ruhr-University Bochum, Bochum, Germany
- Klinik für Anästhesiologie, Intensivmedizin und Schmerztherapie, Universitätsklinikum Knappschaftskrankenhaus Bochum, Bochum, Germany
| | - Helmut E Meyer
- Medizinisches Proteom-Center (MPC), Medical Faculty, Ruhr-University Bochum, Bochum, Germany
| | - Barbara Sitek
- Medizinisches Proteom-Center (MPC), Medical Faculty, Ruhr-University Bochum, Bochum, Germany
- Medical Proteome Analysis, Center for Proteindiagnostics (PRODI) Ruhr-University Bochum, Bochum, Germany
- Klinik für Anästhesiologie, Intensivmedizin und Schmerztherapie, Universitätsklinikum Knappschaftskrankenhaus Bochum, Bochum, Germany
| | - Katrin Marcus
- Medizinisches Proteom-Center (MPC), Medical Faculty, Ruhr-University Bochum, Bochum, Germany.
- Medical Proteome Analysis, Center for Proteindiagnostics (PRODI) Ruhr-University Bochum, Bochum, Germany.
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Torres VM, Popovic L, Vaz F, Penque D. Proteomics in the Assessment of the Therapeutic Response of Antineoplastic Drugs: Strategies and Practical Applications. Methods Mol Biol 2016; 1395:281-298. [PMID: 26910080 DOI: 10.1007/978-1-4939-3347-1_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Uncovering unknown pathological mechanisms and body response to applied medication are the driving forces toward personalized medicine. In this post-genomic era, all eyes are turned to the proteomics field, searching for answers and explanations by investigating the gene end point functional units-proteins and their proteoforms. The development of cutting-edge mass spectrometric technologies and bioinformatics tools have allowed the life-science community to discover disease-specific proteins as biomarkers, which are often concealed by high sample complexity and dynamic range of abundance. Currently, there are several proteomics-based approaches to investigate the proteome. This chapter focuses on gold standard proteomics strategies and related issues toward candidate biomarker discovery, which may have diagnostic/prognostic as well as mechanistic utility in cancer drug resistance.
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Affiliation(s)
- Vukosava Milic Torres
- Laboratory of Proteomics, Human Genetics Departament, Instituto Nacional de Saúde Dr Ricardo Jorge, Av. Padre Cruz, Lisbon, 1649-016, Portugal
- ToxOmics-Centre of Toxicogenomics and Human Health, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Lazar Popovic
- Medical Oncology Department, Oncology Institute of Vojvodina, Sremska Kamenica, Serbia
- Medical Faculty, University of Novi Sad, Novi Sad, Serbia
| | - Fátima Vaz
- Laboratory of Proteomics, Human Genetics Departament, Instituto Nacional de Saúde Dr Ricardo Jorge, Av. Padre Cruz, Lisbon, 1649-016, Portugal
- ToxOmics-Centre of Toxicogenomics and Human Health, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Deborah Penque
- Laboratory of Proteomics, Human Genetics Departament, Instituto Nacional de Saúde Dr Ricardo Jorge, Av. Padre Cruz, Lisbon, 1649-016, Portugal.
- ToxOmics-Centre of Toxicogenomics and Human Health, Universidade Nova de Lisboa, Lisboa, Portugal.
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Frantzi M, Latosinska A, Merseburger AS, Mischak H. Recent progress in urinary proteome analysis for prostate cancer diagnosis and management. Expert Rev Mol Diagn 2015; 15:1539-54. [PMID: 26491818 DOI: 10.1586/14737159.2015.1104248] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Prostate cancer (PCa) is fifth leading cause of cancer-associated deaths in men worldwide. Although the application of the serum prostate-specific antigen (PSA) screening test resulted in an increase in the PCa diagnosed cases, it demonstrated a negligible benefit regarding the associated mortality. Treatment options vary, with active surveillance to be preferable for patients with low-risk PCa and therapy of advanced castration-resistant PCa to rely on α-emitters and cytotoxic chemotherapy. Although recent developments have led to the approval of novel drugs for the treatment of castration-resistant PCa, the optimal sequence and timing of medication have not been yet determined. New screening modalities could improve the discriminatory accuracy between tumors with favorable clinical prognosis. Implementation of proteomic-based biomarkers appears to be a promising improvement, which could enable a more accurate diagnosis, guide treatment and improve patient outcome. Reviewed here are urinary proteome-based approaches for detection of PCa and patient management.
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Affiliation(s)
- Maria Frantzi
- a Mosaiques diagnostics GmbH , Hannover , Germany.,b Biotechnology Division , Biomedical Research Foundation Academy of Athens , Athens , Greece
| | - Agnieszka Latosinska
- b Biotechnology Division , Biomedical Research Foundation Academy of Athens , Athens , Greece
| | | | - Harald Mischak
- a Mosaiques diagnostics GmbH , Hannover , Germany.,d Institute of Cardiovascular and Medical Sciences , University of Glasgow , Glasgow , UK
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Frantzi M, Bhat A, Latosinska A. Clinical proteomic biomarkers: relevant issues on study design & technical considerations in biomarker development. Clin Transl Med 2014; 3:7. [PMID: 24679154 PMCID: PMC3994249 DOI: 10.1186/2001-1326-3-7] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 03/06/2014] [Indexed: 12/11/2022] Open
Abstract
Biomarker research is continuously expanding in the field of clinical proteomics. A combination of different proteomic-based methodologies can be applied depending on the specific clinical context of use. Moreover, current advancements in proteomic analytical platforms are leading to an expansion of biomarker candidates that can be identified. Specifically, mass spectrometric techniques could provide highly valuable tools for biomarker research. Ideally, these advances could provide with biomarkers that are clinically applicable for disease diagnosis and/ or prognosis. Unfortunately, in general the biomarker candidates fail to be implemented in clinical decision making. To improve on this current situation, a well-defined study design has to be established driven by a clear clinical need, while several checkpoints between the different phases of discovery, verification and validation have to be passed in order to increase the probability of establishing valid biomarkers. In this review, we summarize the technical proteomic platforms that are available along the different stages in the biomarker discovery pipeline, exemplified by clinical applications in the field of bladder cancer biomarker research.
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Affiliation(s)
- Maria Frantzi
- Mosaiques Diagnostics GmbH, Mellendorfer Strasse 7-9, D-30625 Hannover, Germany
- Biotechnology Division, Biomedical Research Foundation Academy of Athens, Soranou Ephessiou 4, 115 27 Athens, Greece
| | - Akshay Bhat
- Mosaiques Diagnostics GmbH, Mellendorfer Strasse 7-9, D-30625 Hannover, Germany
- Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Agnieszka Latosinska
- Biotechnology Division, Biomedical Research Foundation Academy of Athens, Soranou Ephessiou 4, 115 27 Athens, Greece
- Charité-Universitätsmedizin Berlin, Berlin, Germany
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Di Michele M, Van Geet C, Freson K. Recent advances in platelet proteomics. Expert Rev Proteomics 2014; 9:451-66. [DOI: 10.1586/epr.12.31] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Brosseron F, May C, Schoenebeck B, Tippler B, Woitalla D, Kauth M, Brockmann K, Meyer HE, Berg D, Bufe A, Marcus K. Stepwise isolation of human peripheral erythrocytes, T lymphocytes, and monocytes for blood cell proteomics. Proteomics Clin Appl 2012; 6:497-501. [DOI: 10.1002/prca.201200032] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Revised: 06/14/2012] [Accepted: 07/05/2012] [Indexed: 01/02/2023]
Affiliation(s)
- Frederic Brosseron
- Abteilung für Funktionelle Proteomik; Medizinisches Proteom-Center; Ruhr-University Bochum; Bochum; Germany
| | - Caroline May
- Abteilung für Medizinische Proteomik/Bioanalytik; Medizinisches Proteom-Center; Ruhr-University Bochum; Bochum; Germany
| | - Bodo Schoenebeck
- Abteilung für Funktionelle Proteomik; Medizinisches Proteom-Center; Ruhr-University Bochum; Bochum; Germany
| | - Bettina Tippler
- Abteilung für Molekulare und Medizinische Virologie; Ruhr-University Bochum; Bochum; Germany
| | - Dirk Woitalla
- St. Josef-Hospital; Ruhr-University Bochum; Bochum; Germany
| | - Marion Kauth
- Experimentelle Pneumologie; Ruhr-University Bochum; Bochum; Germany
| | - Kathrin Brockmann
- Neurologische UNI-Klinik; Universitätsklinikum Tübingen; Tübingen; Germany
| | - Helmut E. Meyer
- Abteilung für Medizinische Proteomik/Bioanalytik; Medizinisches Proteom-Center; Ruhr-University Bochum; Bochum; Germany
| | - Daniela Berg
- Neurologische UNI-Klinik; Universitätsklinikum Tübingen; Tübingen; Germany
| | - Albrecht Bufe
- Experimentelle Pneumologie; Ruhr-University Bochum; Bochum; Germany
| | - Katrin Marcus
- Abteilung für Funktionelle Proteomik; Medizinisches Proteom-Center; Ruhr-University Bochum; Bochum; Germany
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Abstract
Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) is based on the combination of two orthogonal separation techniques. In the first dimension, proteins are separated by their isoelectric point, a technique known as isoelectric focusing (IEF). There are two important variants of IEF, which are carrier-ampholine (CA)-based IEF and immobilized pH gradient (IPG)-based IEF. In the second dimension, proteins are further separated by their electrophoretic mobility using SDS-PAGE. Finally, proteins can be visualized and quantified by different staining procedures, such as Coomassie, silver, or fluorescence staining. This chapter gives detailed protocols for 2D-PAGE, using both CA- and IPG-based separation in the first dimension.
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Affiliation(s)
- Caroline May
- Department of Medical Proteomics/Bionalaytics, Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany.
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May C, Brosseron F, Chartowski P, Schumbrutzki C, Schoenebeck B, Marcus K. Instruments and methods in proteomics. Methods Mol Biol 2011; 696:3-26. [PMID: 21063938 DOI: 10.1007/978-1-60761-987-1_1] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
In the past decade, major developments in instrumentation and methodology have been achieved in proteomics. For proteome investigations of complex biological samples derived from cell cultures, tissues, or whole organisms, several techniques are state of the art. Especially, many improvements have been undertaken to quantify differences in protein expression between samples from, e.g., treated vs. untreated cells and healthy vs. control patients. In this review, we give a brief insight into the main techniques, including gel-based protein separation techniques, and the growing field of mass spectrometry.
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Affiliation(s)
- Caroline May
- Department of Functional Proteomics, Medizinisches Proteom-Center, Ruhr-Universität Bochum, Bochum, Germany
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Even-Desrumeaux K, Baty D, Chames P. Strong and oriented immobilization of single domain antibodies from crude bacterial lysates for high-throughput compatible cost-effective antibody array generation. MOLECULAR BIOSYSTEMS 2010; 6:2241-8. [PMID: 20859568 DOI: 10.1039/c005279e] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Antibody microarrays are among the novel class of rapidly emerging proteomic technologies that will allow us to efficiently perform specific diagnoses and proteomic analysis. Recombinant antibody fragments are especially suited for this approach but their stability is often a limiting factor. Camelids produce functional antibodies devoid of light chains (HCAbs) of which the single N-terminal domain is fully capable of antigen binding. When produced as an independent domain, these so-called single domain antibody fragments (sdAbs) have several advantages for biotechnological applications thanks to their unique properties of size (15 kDa), stability, solubility, and expression yield. These features should allow sdAbs to outperform other antibody formats in a number of applications, notably as capture molecules for antibody arrays. In this study, we have produced antibody microarrays using direct and oriented immobilization of sdAbs, produced in crude bacterial lysates, to generate a proof-of-principle of a high-throughput compatible array design. Several sdAb immobilization strategies have been explored. Immobilization of in vivo biotinylated sdAbs by direct spotting of bacterial lysate on streptavidin and sandwich detection was developed to achieve high sensitivity and specificity, whereas immobilization of "multi-tagged" sdAbs via anti-tag antibodies and a direct labeled sample detection strategy was optimized for the design of high-density antibody arrays for high-throughput proteomics and identification of potential biomarkers.
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