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Marcus K, Lelong C, Rabilloud T. What Room for Two-Dimensional Gel-Based Proteomics in a Shotgun Proteomics World? Proteomes 2020; 8:proteomes8030017. [PMID: 32781532 PMCID: PMC7563651 DOI: 10.3390/proteomes8030017] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 08/02/2020] [Accepted: 08/04/2020] [Indexed: 02/07/2023] Open
Abstract
Two-dimensional gel electrophoresis was instrumental in the birth of proteomics in the late 1980s. However, it is now often considered as an outdated technique for proteomics—a thing of the past. Although this opinion may be true for some biological questions, e.g., when analysis depth is of critical importance, for many others, two-dimensional gel electrophoresis-based proteomics still has a lot to offer. This is because of its robustness, its ability to separate proteoforms, and its easy interface with many powerful biochemistry techniques (including western blotting). This paper reviews where and why two-dimensional gel electrophoresis-based proteomics can still be profitably used. It emerges that, rather than being a thing of the past, two-dimensional gel electrophoresis-based proteomics is still highly valuable for many studies. Thus, its use cannot be dismissed on simple fashion arguments and, as usual, in science, the tree is to be judged by the fruit.
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Affiliation(s)
- Katrin Marcus
- Medizinisches Proteom-Center, Medical Faculty & Medical Proteome Analysis, Center for Proteindiagnostics (PRODI) Ruhr-University Bochum Gesundheitscampus, 4 44801 Bochum, Germany;
| | - Cécile Lelong
- CBM UMR CNRS5249, Université Grenoble Alpes, CEA, CNRS, 17 rue des Martyrs, CEDEX 9, 38054 Grenoble, France;
| | - Thierry Rabilloud
- Laboratory of Chemistry and Biology of Metals, UMR 5249, Université Grenoble Alpes, CNRS, 38054 Grenoble, France
- Correspondence: ; Tel.: +33-438-783-212
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Caporale A, Martin AD, Capasso D, Focà G, Sandomenico A, D'Andrea LD, Grieco P, Ruvo M, Doti N. Short
PlGF
‐derived peptides bind
VEGFR
‐1 and
VEGFR
‐2 in vitro and on the surface of endothelial cells. J Pept Sci 2019; 25:e3146. [DOI: 10.1002/psc.3146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/14/2018] [Accepted: 12/17/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Andrea Caporale
- Istituto di Biostrutture e Bioimmagini—CNR and CIRPEB Naples Italy
| | - Aaron D. Martin
- SensiQ Technologies, Inc. 800 Research Pkwy Oklahoma City OK 73104 USA
| | - Dominga Capasso
- Dipartimento di FarmaciaUniversità degli Studi di Napoli “Federico II” Naples Italy
| | - Giuseppina Focà
- Istituto di Biostrutture e Bioimmagini—CNR and CIRPEB Naples Italy
| | | | | | - Paolo Grieco
- Dipartimento di FarmaciaUniversità degli Studi di Napoli “Federico II” Naples Italy
| | - Menotti Ruvo
- Istituto di Biostrutture e Bioimmagini—CNR and CIRPEB Naples Italy
| | - Nuzianna Doti
- Istituto di Biostrutture e Bioimmagini—CNR and CIRPEB Naples Italy
- Dipartimento di FarmaciaUniversità degli Studi di Napoli “Federico II” Naples Italy
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3
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Rega C, Russo R, Focà A, Sandomenico A, Iaccarino E, Raimondo D, Milanetti E, Tornatore L, Franzoso G, Pedone PV, Ruvo M, Chambery A. Probing the interaction interface of the GADD45β/MKK7 and MKK7/DTP3 complexes by chemical cross-linking mass spectrometry. Int J Biol Macromol 2018; 114:114-123. [PMID: 29572137 PMCID: PMC5981002 DOI: 10.1016/j.ijbiomac.2018.03.090] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 03/16/2018] [Accepted: 03/19/2018] [Indexed: 02/08/2023]
Abstract
GADD45β is selectively and constitutively expressed in Multiple Myeloma cells, and this expression correlates with an unfavourable clinical outcome. GADD45β physically interacts with the JNK kinase, MKK7, inhibiting its activity to enable the survival of cancer cells. DTP3 is a small peptide inhibitor of the GADD45β/MKK7 complex and is able to restore MKK7/JNK activation, thereby promoting selective cell death of GADD45β-overexpressing cancer cells. Enzymatic MS foot-printing and diazirine-based chemical cross-linking MS (CX-MS) strategies were applied to study the interactions between GADD45β and MKK7 kinase domain (MKK7_KD) and between DTP3 and MKK7_KD. Our data show that the binding between GADD45β and MKK7 largely occurs between GADD45β loop 2 (region 103-117) and the kinase enzymatic pocket. We also show that DTP3 interferes with this GADD45β/MKK7 interaction by contacting the MKK7 peptides, 113-136 and 259-274. Accordingly, an MKK7_KD Δ(101-136) variant lacking Trp135 did not produce a fluorescence quenching effect upon the binding of DTP3. The assessment of the interaction between GADD45β and MKK7 and the elucidation of the recognition surfaces between DTP3 and MKK7 significantly advance the understanding of the mechanism underlying the inhibition of the GADD45β/MKK7 interaction by DTP3 and pave the way to the design of small-molecule DTP3 analogues.
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Affiliation(s)
- Camilla Rega
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Rosita Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | | | | | | | - Domenico Raimondo
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Roma, Italy
| | - Edoardo Milanetti
- Department of Physics, Sapienza University of Rome, 00161 Rome, Italy
| | - Laura Tornatore
- Department of Medicine, Centre for Cell Signalling and Inflammation, Imperial College London, London W12 0NN, UK
| | - Guido Franzoso
- Department of Medicine, Centre for Cell Signalling and Inflammation, Imperial College London, London W12 0NN, UK
| | - Paolo Vincenzo Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | | | - Angela Chambery
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy.
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Yao H, Wynendaele E, Xu X, Kosgei A, De Spiegeleer B. Circular dichroism in functional quality evaluation of medicines. J Pharm Biomed Anal 2018; 147:50-64. [DOI: 10.1016/j.jpba.2017.08.031] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 08/18/2017] [Accepted: 08/19/2017] [Indexed: 12/31/2022]
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5
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Rahmani F, Aghamohammadi A, Ochs HD, Rezaei N. Agammaglobulinemia: comorbidities and long-term therapeutic risks. Expert Opin Orphan Drugs 2017. [DOI: 10.1080/21678707.2017.1330145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Farzaneh Rahmani
- Research Center for Immunodeficiencies, Children’s Medical Center, Tehran University of Medical Sciences, Tehran, Iran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Asghar Aghamohammadi
- Research Center for Immunodeficiencies, Children’s Medical Center, Tehran University of Medical Sciences, Tehran, Iran
- Primary Immunodeficiency Diseases Network (PIDNet), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Hans D. Ochs
- Department of Pediatrics, University of Washington and Seattle Children’s Research Institute, Seattle, WA, USA
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Seattle, WA, USA
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children’s Medical Center, Tehran University of Medical Sciences, Tehran, Iran
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Systematic Review and Meta-Analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Sheffield, UK
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Leiria Campo V, Riul TB, Oliveira Bortot L, Martins-Teixeira MB, Fiori Marchiori M, Iaccarino E, Ruvo M, Dias-Baruffi M, Carvalho I. A Synthetic MUC1 Glycopeptide Bearing βGalNAc-Thr as a Tn Antigen Isomer Induces the Production of Antibodies against Tumor Cells. Chembiochem 2017; 18:527-538. [PMID: 28068458 DOI: 10.1002/cbic.201600473] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 01/05/2017] [Indexed: 01/01/2023]
Abstract
This study presents the synthesis of the novel protected O-glycosylated amino acid derivatives 1 and 2, containing βGalNAc-SerOBn and βGalNAc-ThrOBn units, respectively, as mimetics of the natural Tn antigen (αGalNAc-Ser/Thr), along with the solid-phase assembly of the glycopeptides NHAcSer-Ala-Pro-Asp-Thr[αGalNAc]-Arg-Pro-Ala-Pro-Gly-BSA (3-BSA) and NHAcSer-Ala-Pro-Asp-Thr[βGalNAc]-Arg-Pro-Ala-Pro-Gly-BSA (4-BSA), bearing αGalNAc-Thr or βGalNAc-Thr units, respectively, as mimetics of MUC1 tumor mucin glycoproteins. According to ELISA tests, immunizations of mice with βGalNAc-glycopeptide 4-BSA induced higher sera titers (1:320 000) than immunizations with αGalNAc-glycopeptide 3-BSA (1:40 000). Likewise, flow cytometry assays showed higher capacity of the obtained anti-glycopeptide 4-BSA antibodies to recognize MCF-7 tumor cells. Cross-recognition between immunopurified anti-βGalNAc antibodies and αGalNAc-glycopeptide and vice versa was also verified. Lastly, molecular dynamics simulations and surface plasmon resonance (SPR) showed that βGalNAc-glycopeptide 4 can interact with a model antitumor monoclonal antibody (SM3). Taken together, these data highlight the improved immunogenicity of the unnatural glycopeptide 4-BSA, bearing βGalNAc-Thr as Tn antigen isomer.
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Affiliation(s)
- Vanessa Leiria Campo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café S/N, CEP, 14040-903, Ribeirão Preto, São Paulo, Brazil
| | - Thalita B Riul
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café S/N, CEP, 14040-903, Ribeirão Preto, São Paulo, Brazil
| | - Leandro Oliveira Bortot
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café S/N, CEP, 14040-903, Ribeirão Preto, São Paulo, Brazil
| | - Maristela B Martins-Teixeira
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café S/N, CEP, 14040-903, Ribeirão Preto, São Paulo, Brazil
| | - Marcelo Fiori Marchiori
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café S/N, CEP, 14040-903, Ribeirão Preto, São Paulo, Brazil
| | - Emanuela Iaccarino
- Istituto di Biostrutture e Bioimmagini, CNR, via Mezzocannone 16, 80134, Napoli, Italy.,Second University of Naples, via Vivaldi 43, 81100, Caserta, Italy
| | - Menotti Ruvo
- Istituto di Biostrutture e Bioimmagini, CNR, via Mezzocannone 16, 80134, Napoli, Italy
| | - Marcelo Dias-Baruffi
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café S/N, CEP, 14040-903, Ribeirão Preto, São Paulo, Brazil
| | - Ivone Carvalho
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. Café S/N, CEP, 14040-903, Ribeirão Preto, São Paulo, Brazil
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Ye S, Lei M, Jiang P, Liu F, Wang Z, Cao H, Du X, Yuan J, Chen Y, Ma L, Li C. Demonstration of the IgG antibody repertoire against the bacteria Escherichia coli in Chinese intravenous immunoglobulins. J Pharm Biomed Anal 2016; 133:8-14. [PMID: 27792896 DOI: 10.1016/j.jpba.2016.10.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 10/19/2016] [Accepted: 10/20/2016] [Indexed: 12/24/2022]
Abstract
Intravenous immunoglobulin (IVIg) is produced by pooling plasma from thousands of healthy blood donors, and the diversity of the antibody is critical for the clinical efficacy of IVIg. This study investigated the antibody diversity of Chinese IVIg. Firstly, 2-dimensional gel electrophoresis and immunoblotting with protein extracts of Escherichia coli (E. coli) O157:H7 were used to study IgG antibody repertoire of 8 IVIg preparations from different Chinese manufacturers. This was followed by the identification of the antibody-reactive proteins of E. coli by mass spectrometry and the sequence similarity of the proteins was aligned by bioinformatics analysis. The results showed that all IVIg preparations expressed a large range of antibody reactivities against E. coli proteins. 94-238 antigens were recognized by the 8 IVIg preparations. 33 interesting target antigens were selected and identified as 29 different proteins, mainly including membrane proteins, molecular chaperones, metabolism enzymes, and proteins involved in cell cycle processes. Additionally, these antigens were highly conserved proteins which were found extensively in a variety of other pathogenic microorganisms. Our study indicated that Chinese IVIg preparations recognized a large range of high conserved proteins which play key roles in pathogenic microorganisms, and showed each IVIg had its own distinct antibody repertoire.
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Affiliation(s)
- Shengliang Ye
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, 26 Huacai Road, Longtan Industry Park, Chenghua District, Chengdu, 610052, China.
| | - Min Lei
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, 26 Huacai Road, Longtan Industry Park, Chenghua District, Chengdu, 610052, China.
| | - Peng Jiang
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, 26 Huacai Road, Longtan Industry Park, Chenghua District, Chengdu, 610052, China.
| | - Fengjuan Liu
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, 26 Huacai Road, Longtan Industry Park, Chenghua District, Chengdu, 610052, China.
| | - Zongkui Wang
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, 26 Huacai Road, Longtan Industry Park, Chenghua District, Chengdu, 610052, China.
| | - Haijun Cao
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, 26 Huacai Road, Longtan Industry Park, Chenghua District, Chengdu, 610052, China.
| | - Xi Du
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, 26 Huacai Road, Longtan Industry Park, Chenghua District, Chengdu, 610052, China.
| | - Jing Yuan
- Guizhou Taibang Biological Products Co., Ltd., 156 Daqian Road, Huaxi District, Guiyang,550025, China.
| | - Yunhua Chen
- Guizhou Taibang Biological Products Co., Ltd., 156 Daqian Road, Huaxi District, Guiyang,550025, China.
| | - Li Ma
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, 26 Huacai Road, Longtan Industry Park, Chenghua District, Chengdu, 610052, China.
| | - Changqing Li
- Institute of Blood Transfusion, Chinese Academy of Medical Sciences, 26 Huacai Road, Longtan Industry Park, Chenghua District, Chengdu, 610052, China.
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Pegylated Trastuzumab Fragments Acquire an Increased in Vivo Stability but Show a Largely Reduced Affinity for the Target Antigen. Int J Mol Sci 2016; 17:491. [PMID: 27043557 PMCID: PMC4848947 DOI: 10.3390/ijms17040491] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/19/2016] [Accepted: 03/24/2016] [Indexed: 12/20/2022] Open
Abstract
PEGylation of biomolecules is a major approach to increase blood stream half-life, stability and solubility of biotherapeutics and to reduce their immunogenicity, aggregation potential and unspecific interactions with other proteins and tissues. Antibodies have generally long half-lives due to high molecular mass and stability toward proteases, however their size lowers to some extent their potential because of a reduced ability to penetrate tissues, especially those of tumor origin. Fab or otherwise engineered smaller fragments are an alternative but are less stable and are much less well retained in circulation. We have here investigated the effects of various PEGylations on the binding properties and in vivo half-life of Fab fragments derived from the enzymatic splitting of Trastuzumab. We find that PEGylation increases the half-life of the molecules but also strongly affects the ability to recognize the target antigen in a way that is dependent on the extent and position of the chemical modification. Data thus support the concept that polyethylene glycol (PEG) conjugation on Trastuzumab Fabs increases half-life but reduces their affinity and this is a fine balance, which must be carefully considered for the design of strategies based on the use of antibody fragments.
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Albin S, Cunningham-Rundles C. An update on the use of immunoglobulin for the treatment of immunodeficiency disorders. Immunotherapy 2014; 6:1113-26. [PMID: 25428649 PMCID: PMC4324501 DOI: 10.2217/imt.14.67] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
For patients with significant antibody deficiencies, immunoglobulin therapy is the mainstay of treatment as it significantly reduces both the frequency and severity of infections. The formulations and delivery methods of immunoglobulin have evolved over time, and continued improvements have allowed for increased access to this effective medication. This review is an update on the current status of immunoglobulin therapy in immunodeficiency disorders, and discusses the mechanisms, forms and dosing, and indications for immunoglobulin replacement.
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Affiliation(s)
- Stephanie Albin
- Division of Allergy & Clinical Immunology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Charlotte Cunningham-Rundles
- Division of Allergy & Clinical Immunology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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