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Koy C, Röwer C, Thiesen HJ, Neamtu A, Glocker MO. Intact Transition Epitope Mapping-Force Interferences by Variable Extensions (ITEM-FIVE). Biomolecules 2024; 14:454. [PMID: 38672470 PMCID: PMC11048379 DOI: 10.3390/biom14040454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
Investigations on binding strength differences of non-covalent protein complex components were performed by mass spectrometry. T4 fibritin foldon (T4Ff) is a well-studied miniprotein, which together with its biotinylated version served as model system to represent a compactly folded protein to which an Intrinsically Disordered Region (IDR) was attached. The apparent enthalpies of the gas phase dissociation reactions of the homo-trimeric foldon F-F-F and of the homo-trimeric triply biotinylated foldon bF-bF-bF have been determined to be rather similar (3.32 kJ/mol and 3.85 kJ/mol) but quite distinct from those of the singly and doubly biotinylated hetero-trimers F-F-bF and F-bF-bF (1.86 kJ/mol and 1.08 kJ/mol). Molecular dynamics simulations suggest that the ground states of the (biotinylated) T4Ff trimers are highly symmetric and well comparable to each other, indicating that the energy levels of all four (biotinylated) T4Ff trimer ground states are nearly indistinguishable. The experimentally determined differences and/or similarities in enthalpies of the complex dissociation reactions are explained by entropic spring effects, which are noticeable in the T4Ff hetero-trimers but not in the T4Ff homo-trimers. A lowering of the transition state energy levels of the T4Ff hetero-trimers seems likely because the biotin moieties, mimicking intrinsically disordered regions (IDRs), induced asymmetries in the transition states of the biotinylated T4Ff hetero-trimers. This transition state energy level lowering effect is absent in the T4Ff homo-trimer, as well as in the triply biotinylated T4Ff homo-trimer. In the latter, the IDR-associated entropic spring effects on complex stability cancel each other out. ITEM-FIVE enabled semi-quantitative determination of energy differences of complex dissociation reactions, whose differences were modulated by IDRs attached to compactly folded proteins.
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Affiliation(s)
- Cornelia Koy
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock Schillingallee 69, 18057 Rostock, Germany; (C.K.)
| | - Claudia Röwer
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock Schillingallee 69, 18057 Rostock, Germany; (C.K.)
| | - Hans-Jürgen Thiesen
- Institute for Immunology, Medical Faculty, University of Rostock, Schillingallee 70, 18057 Rostock, Germany;
| | - Andrei Neamtu
- Department of Physiology, “Gr. T. Popa” University of Medicine and Pharmacy, Str. Universitatii nr. 16, 700115 Iasi, Romania
- TRANSCEND Centre, Regional Institute of Oncology (IRO) Iasi, Str. General Henri Mathias Berthelot, Nr. 2–4, 700483 Iasi, Romania
| | - Michael O. Glocker
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock Schillingallee 69, 18057 Rostock, Germany; (C.K.)
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Röwer C, Olaleye OO, Bischoff R, Glocker MO. Mass Spectrometric ITEM-ONE and ITEM-TWO Analyses Confirm and Refine an Assembled Epitope of an Anti-Pertuzumab Affimer. Biomolecules 2023; 14:24. [PMID: 38254624 PMCID: PMC10813730 DOI: 10.3390/biom14010024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/13/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024] Open
Abstract
Intact Transition Epitope Mapping-One-step Non-covalent force Exploitation (ITEM-ONE) analysis reveals an assembled epitope on the surface of Pertuzumab, which is recognized by the anti-Pertuzumab affimer 00557_709097. It encompasses amino acid residues NSGGSIYNQRFKGR, which are part of CDR2, as well as residues FTLSVDR, which are located on the variable region of Pertuzumab's heavy chain and together form a surface area of 1381.46 Å2. Despite not being part of Pertuzumab's CDR2, the partial sequence FTLSVDR marks a unique proteotypic Pertuzumab peptide. Binding between intact Pertuzumab and the anti-Pertuzumab affimer was further investigated using the Intact Transition Epitope Mapping-Thermodynamic Weak-force Order (ITEM-TWO) approach. Quantitative analysis of the complex dissociation reaction in the gas phase afforded a quasi-equilibrium constant (KD m0g#) of 3.07 × 10-12. The experimentally determined apparent enthalpy (ΔHm0g#) and apparent free energy (ΔGm0g#) of the complex dissociation reaction indicate that the opposite reaction-complex formation-is spontaneous at room temperature. Due to strong binding to Pertuzumab and because of recognizing Pertuzumab's unique partial amino acid sequences, the anti-Pertuzumab affimer 00557_709097 is considered excellently suitable for implementation in Pertuzumab quantitation assays as well as for the accurate therapeutic drug monitoring of Pertuzumab in biological fluids.
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Affiliation(s)
- Claudia Röwer
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, 18057 Rostock, Germany
| | - Oladapo O. Olaleye
- Department of Analytical Biochemistry, Faculty of Science & Engineering, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Rainer Bischoff
- Department of Analytical Biochemistry, Faculty of Science & Engineering, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Michael O. Glocker
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, 18057 Rostock, Germany
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Qin S, Zhu J, Zhang G, Sui Q, Niu Y, Ye W, Ma G, Liu H. Research progress of functional motifs based on growth factors in cartilage tissue engineering: A review. Front Bioeng Biotechnol 2023; 11:1127949. [PMID: 36824354 PMCID: PMC9941568 DOI: 10.3389/fbioe.2023.1127949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 01/20/2023] [Indexed: 02/10/2023] Open
Abstract
Osteoarthritis is a chronic degenerative joint disease that exerts significant impacts on personal life quality, and cartilage tissue engineering is a practical treatment in clinical. Various growth factors are involved in cartilage regeneration and play important roles therein, which is the focus of current cartilage repair strategy. To compensate for the purification difficulty, high cost, poor metabolic stability, and circulating dilution of natural growth factors, the concept of functional motifs (also known as mimetic peptides) from original growth factor was introduced in recent studies. Here, we reviewed the selection mechanisms, biological functions, carrier scaffolds, and modification methods of growth factor-related functional motifs, and evaluated the repair performance in cartilage tissue engineering. Finally, the prospects of functional motifs in researches and clinical application were discussed.
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Affiliation(s)
- Shengao Qin
- School of Stomatology, Dalian Medical University, Dalian, China,Academician Laboratory of Immune and Oral Development and Regeneration, Dalian Medical University, Dalian, China
| | - Jiaman Zhu
- Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, China,Department of Stomatology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Guangyong Zhang
- School of Stomatology, Dalian Medical University, Dalian, China,Academician Laboratory of Immune and Oral Development and Regeneration, Dalian Medical University, Dalian, China
| | - Qijia Sui
- School of Stomatology, Dalian Medical University, Dalian, China,Academician Laboratory of Immune and Oral Development and Regeneration, Dalian Medical University, Dalian, China
| | - Yimeng Niu
- School of Stomatology, Dalian Medical University, Dalian, China,Academician Laboratory of Immune and Oral Development and Regeneration, Dalian Medical University, Dalian, China
| | - Weilong Ye
- School of Stomatology, Dalian Medical University, Dalian, China,Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Beijing Stomatological Hospital, School of Stomatology, Capital Medical University, Beijing, China,*Correspondence: Weilong Ye, ; Guowu Ma, ; Huiying Liu,
| | - Guowu Ma
- School of Stomatology, Dalian Medical University, Dalian, China,Academician Laboratory of Immune and Oral Development and Regeneration, Dalian Medical University, Dalian, China,*Correspondence: Weilong Ye, ; Guowu Ma, ; Huiying Liu,
| | - Huiying Liu
- School of Stomatology, Dalian Medical University, Dalian, China,Academician Laboratory of Immune and Oral Development and Regeneration, Dalian Medical University, Dalian, China,*Correspondence: Weilong Ye, ; Guowu Ma, ; Huiying Liu,
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Intact Transition Epitope Mapping-Force Differences between Original and Unusual Residues (ITEM-FOUR). Biomolecules 2023; 13:biom13010187. [PMID: 36671572 PMCID: PMC9856199 DOI: 10.3390/biom13010187] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/06/2023] [Accepted: 01/13/2023] [Indexed: 01/19/2023] Open
Abstract
Antibody-based point-of-care diagnostics have become indispensable for modern medicine. In-depth analysis of antibody recognition mechanisms is the key to tailoring the accuracy and precision of test results, which themselves are crucial for targeted and personalized therapy. A rapid and robust method is desired by which binding strengths between antigens and antibodies of concern can be fine-mapped with amino acid residue resolution to examine the assumedly serious effects of single amino acid polymorphisms on insufficiencies of antibody-based detection capabilities of, e.g., life-threatening conditions such as myocardial infarction. The experimental ITEM-FOUR approach makes use of modern mass spectrometry instrumentation to investigate intact immune complexes in the gas phase. ITEM-FOUR together with molecular dynamics simulations, enables the determination of the influences of individually exchanged amino acid residues within a defined epitope on an immune complex's binding strength. Wild-type and mutated epitope peptides were ranked according to their experimentally determined dissociation enthalpies relative to each other, thereby revealing which single amino acid polymorphism caused weakened, impaired, and even abolished antibody binding. Investigating a diagnostically relevant human cardiac Troponin I epitope for which seven nonsynonymous single nucleotide polymorphisms are known to exist in the human population tackles a medically relevant but hitherto unsolved problem of current antibody-based point-of-care diagnostics.
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Grötzinger C. Applications of Peptide Microarrays in Autoantibody, Infection, and Cancer Detection. Methods Mol Biol 2023; 2578:1-15. [PMID: 36152276 DOI: 10.1007/978-1-0716-2732-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The diversity of the antigen-specific humoral immune response reflects the interaction of the immune system with pathogens and autoantigens. Peptide microarray analysis opens up new perspectives for the use of antibodies as diagnostic biomarkers and provides unique access to a more differentiated view on humoral responses to disease. This review focuses on the latest applications of peptide microarrays for the serologic medical diagnosis of autoimmunity, infectious diseases (including COVID-19), and cancer.
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Affiliation(s)
- Carsten Grötzinger
- Department of Hepatology and Gastroenterology, Charité - Universitätsmedizin Berlin, Berlin, Germany.
- Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
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Lupu LM, Wiegand P, Holdschick D, Mihoc D, Maeser S, Rawer S, Völklein F, Malek E, Barka F, Knauer S, Uth C, Hennermann J, Kleinekofort W, Hahn A, Barka G, Przybylski M. Identification and Affinity Determination of Protein-Antibody and Protein-Aptamer Epitopes by Biosensor-Mass Spectrometry Combination. Int J Mol Sci 2021; 22:12832. [PMID: 34884636 PMCID: PMC8657952 DOI: 10.3390/ijms222312832] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/17/2021] [Accepted: 11/17/2021] [Indexed: 12/24/2022] Open
Abstract
Analytical methods for molecular characterization of diagnostic or therapeutic targets have recently gained high interest. This review summarizes the combination of mass spectrometry and surface plasmon resonance (SPR) biosensor analysis for identification and affinity determination of protein interactions with antibodies and DNA-aptamers. The binding constant (KD) of a protein-antibody complex is first determined by immobilizing an antibody or DNA-aptamer on an SPR chip. A proteolytic peptide mixture is then applied to the chip, and following removal of unbound material by washing, the epitope(s) peptide(s) are eluted and identified by MALDI-MS. The SPR-MS combination was applied to a wide range of affinity pairs. Distinct epitope peptides were identified for the cardiac biomarker myoglobin (MG) both from monoclonal and polyclonal antibodies, and binding constants determined for equine and human MG provided molecular assessment of cross immunoreactivities. Mass spectrometric epitope identifications were obtained for linear, as well as for assembled ("conformational") antibody epitopes, e.g., for the polypeptide chemokine Interleukin-8. Immobilization using protein G substantially improved surface fixation and antibody stabilities for epitope identification and affinity determination. Moreover, epitopes were successfully determined for polyclonal antibodies from biological material, such as from patient antisera upon enzyme replacement therapy of lysosomal diseases. The SPR-MS combination was also successfully applied to identify linear and assembled epitopes for DNA-aptamer interaction complexes of the tumor diagnostic protein C-Met. In summary, the SPR-MS combination has been established as a powerful molecular tool for identification of protein interaction epitopes.
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Affiliation(s)
- Loredana-Mirela Lupu
- Centre for Analytical Biochemistry and Biomedical Mass Spectrometry (AffyMSLifeChem), and Steinbeis Transfer Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstrasse 29, 65428 Rüsselsheim am Main, Germany; (L.-M.L.); (P.W.); (D.H.); (D.M.); (S.M.); (S.R.); (E.M.); (W.K.)
| | - Pascal Wiegand
- Centre for Analytical Biochemistry and Biomedical Mass Spectrometry (AffyMSLifeChem), and Steinbeis Transfer Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstrasse 29, 65428 Rüsselsheim am Main, Germany; (L.-M.L.); (P.W.); (D.H.); (D.M.); (S.M.); (S.R.); (E.M.); (W.K.)
| | - Daria Holdschick
- Centre for Analytical Biochemistry and Biomedical Mass Spectrometry (AffyMSLifeChem), and Steinbeis Transfer Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstrasse 29, 65428 Rüsselsheim am Main, Germany; (L.-M.L.); (P.W.); (D.H.); (D.M.); (S.M.); (S.R.); (E.M.); (W.K.)
- Department of Engineering & Institute for Microtechnologies (IMTECH), RheinMain University, 65428 Rüsselsheim am Main, Germany;
| | - Delia Mihoc
- Centre for Analytical Biochemistry and Biomedical Mass Spectrometry (AffyMSLifeChem), and Steinbeis Transfer Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstrasse 29, 65428 Rüsselsheim am Main, Germany; (L.-M.L.); (P.W.); (D.H.); (D.M.); (S.M.); (S.R.); (E.M.); (W.K.)
| | - Stefan Maeser
- Centre for Analytical Biochemistry and Biomedical Mass Spectrometry (AffyMSLifeChem), and Steinbeis Transfer Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstrasse 29, 65428 Rüsselsheim am Main, Germany; (L.-M.L.); (P.W.); (D.H.); (D.M.); (S.M.); (S.R.); (E.M.); (W.K.)
| | - Stephan Rawer
- Centre for Analytical Biochemistry and Biomedical Mass Spectrometry (AffyMSLifeChem), and Steinbeis Transfer Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstrasse 29, 65428 Rüsselsheim am Main, Germany; (L.-M.L.); (P.W.); (D.H.); (D.M.); (S.M.); (S.R.); (E.M.); (W.K.)
| | - Friedemann Völklein
- Department of Engineering & Institute for Microtechnologies (IMTECH), RheinMain University, 65428 Rüsselsheim am Main, Germany;
| | - Ebrahim Malek
- Centre for Analytical Biochemistry and Biomedical Mass Spectrometry (AffyMSLifeChem), and Steinbeis Transfer Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstrasse 29, 65428 Rüsselsheim am Main, Germany; (L.-M.L.); (P.W.); (D.H.); (D.M.); (S.M.); (S.R.); (E.M.); (W.K.)
- Department of Engineering & Institute for Microtechnologies (IMTECH), RheinMain University, 65428 Rüsselsheim am Main, Germany;
| | - Frederik Barka
- Sunchrom GmbH, Industriestr. 18, 61381 Friedrichsdorf, Germany; (F.B.); (G.B.)
| | - Sascha Knauer
- Sulfotools GmbH, Bahnhofsplatz 1, 65428 Rüsselsheim am Main, Germany; (S.K.); (C.U.)
| | - Christina Uth
- Sulfotools GmbH, Bahnhofsplatz 1, 65428 Rüsselsheim am Main, Germany; (S.K.); (C.U.)
| | - Julia Hennermann
- Department of Pediatrics, Universitätsmedizin Mainz, 55130 Mainz, Germany;
| | - Wolfgang Kleinekofort
- Centre for Analytical Biochemistry and Biomedical Mass Spectrometry (AffyMSLifeChem), and Steinbeis Transfer Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstrasse 29, 65428 Rüsselsheim am Main, Germany; (L.-M.L.); (P.W.); (D.H.); (D.M.); (S.M.); (S.R.); (E.M.); (W.K.)
- Department of Engineering & Institute for Microtechnologies (IMTECH), RheinMain University, 65428 Rüsselsheim am Main, Germany;
| | - Andreas Hahn
- Department of Child Neurology, Justus-Liebig-University Giessen, Feulgenstraße 10-12, 35389 Giessen, Germany;
| | - Günes Barka
- Sunchrom GmbH, Industriestr. 18, 61381 Friedrichsdorf, Germany; (F.B.); (G.B.)
| | - Michael Przybylski
- Centre for Analytical Biochemistry and Biomedical Mass Spectrometry (AffyMSLifeChem), and Steinbeis Transfer Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstrasse 29, 65428 Rüsselsheim am Main, Germany; (L.-M.L.); (P.W.); (D.H.); (D.M.); (S.M.); (S.R.); (E.M.); (W.K.)
- Department of Engineering & Institute for Microtechnologies (IMTECH), RheinMain University, 65428 Rüsselsheim am Main, Germany;
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Opuni KFM, Koy C, Russ M, Reepmeyer M, Danquah BD, Weresow M, Alef A, Lorenz P, Thiesen HJ, Glocker MO. ITEM-THREE analysis of a monoclonal anti-malaria antibody reveals its assembled epitope on the pfMSP1 19 antigen. J Biol Chem 2020; 295:14987-14997. [PMID: 32848020 DOI: 10.1074/jbc.ra120.014802] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/18/2020] [Indexed: 11/06/2022] Open
Abstract
Rapid diagnostic tests are first-line assays for diagnosing infectious diseases, such as malaria. To minimize false positive and false negative test results in population-screening assays, high-quality reagents and well-characterized antigens and antibodies are needed. An important property of antigen-antibody binding is recognition specificity, which best can be estimated by mapping an antibody's epitope on the respective antigen. We have cloned a malarial antigen-containing fusion protein, MBP-pfMSP119, in Escherichia coli, which then was structurally and functionally characterized before and after high pressure-assisted enzymatic digestion. We then used our previously developed method, intact transition epitope mapping-targeted high-energy rupture of extracted epitopes (ITEM-THREE), to map the area on the MBP-pfMSP119 antigen surface that is recognized by the anti-pfMSP119 antibody G17.12. We identified three epitope-carrying peptides, 386GRNISQHQCVKKQCPQNSGCFRHLDE411, 386GRNISQHQCVKKQCPQNSGCFRHLDEREE414, and 415CKCLLNYKQE424, from the GluC-derived peptide mixture. These peptides belong to an assembled (conformational) epitope on the MBP-pfMSP119 antigen whose identification was substantiated by positive and negative control experiments. In conclusion, our data help to establish a workflow to obtain high-quality control data for diagnostic assays, including the use of ITEM-THREE as a powerful analytical tool. Data are available via ProteomeXchange: PXD019717.
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Affiliation(s)
- Kwabena F M Opuni
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Rostock, Germany; Department of Pharmaceutical Chemistry, School of Pharmacy, College of Health, University of Ghana, Legon, Ghana
| | - Cornelia Koy
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Rostock, Germany
| | - Manuela Russ
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Rostock, Germany
| | - Maren Reepmeyer
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Rostock, Germany
| | - Bright D Danquah
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Rostock, Germany
| | | | | | - Peter Lorenz
- Institute for Immunology, University Medicine Rostock, Rostock, Germany
| | | | - Michael O Glocker
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Rostock, Germany.
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8
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Safonova TN, Zaitseva GV, Loginov VI, Burdenniy AM, Lukina SS. [Association of polymorphisms of the TRIM21 gene with the severity of dry keratoconjunctivitis in rheumatoid arthritis and Sjogren's disease]. Vestn Oftalmol 2019; 135:192-198. [PMID: 31691659 DOI: 10.17116/oftalma2019135052192] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Ophthalmologic manifestation of Sjogren's disease (SD) and rheumatoid arthritis (RA) is dry keratoconjunctivitis (dry eye disease; DED). PURPOSE To study the relationship of polymorphic markers rs7947461 (C/T), rs915956 (C/T), rs4144331 (C/A) of the TRIM21 gene with the severity of DED in patients with RA and SD. MATERIAL AND METHODS The study included 70 patients with RA (n=27) and SD (n=43). The control group consisted of volunteers without a history of RA or SD (n=35). Alleles of the polymorphic marker C660T rs7947461 of the TRIM21 gene were identified using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method; alleles of the polymorphic marker rs915956 (C/T) and rs4144331 (C/A) of the TRIM21 gene were identified by analyzing DNA melting curves. RESULTS An association was found between the predisposing genotype (TT) of rs7947461 polymorphic marker and the risk of developing severe DED. The AA genotype of rs4144331 polymorphic marker was found only in severe DED (c2=7.74; OR=17.46, CI95%=1.96-318.38, p=0.02). CONCLUSION An association was established between rs7947461 (rs660) and rs4144331 and the risk of developing severe DED.
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Affiliation(s)
- T N Safonova
- Research Institute of Eye Diseases, 11A Rossolimo St., Moscow, Russian Federation, 119021
| | - G V Zaitseva
- Research Institute of Eye Diseases, 11A Rossolimo St., Moscow, Russian Federation, 119021
| | - V I Loginov
- Institute of General Pathology and Pathophysiology, 8 Baltiiskaya St., Moscow, Russian Federation, 125315
| | - A M Burdenniy
- Institute of General Pathology and Pathophysiology, 8 Baltiiskaya St., Moscow, Russian Federation, 125315
| | - S S Lukina
- Institute of General Pathology and Pathophysiology, 8 Baltiiskaya St., Moscow, Russian Federation, 125315; I.M. Sechenov First Moscow State Medical University, Department of Ophthalmology, 8-2 Trubetskaya St., Moscow, Russian Federation, 119991
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9
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Safonova TN, Zaitseva GV, Burdenniy AM. [Polymorphic markers of certain genes in the development of dry keratoconjunctivitis in patients with rheumatoid arthritis and Sjogren's syndrome]. Vestn Oftalmol 2019; 135:254-259. [PMID: 31691669 DOI: 10.17116/oftalma2019135052254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The article reviews literature on relationships between polymorphic variants of the genes THBS1, GTF2I, MUC1, TRIM21, STAT4, PTPN22 with clinical features of dry keratoconjunctivitis in rheumatoid arthritis and Sjogren's syndrome. The development and implementation of a method for analyzing polymorphic gene variants used to diagnose dry keratoconjunctivitis in rheumatoid arthritis and Sjogren's syndrome will allow assessment of the possibility of developing dry keratoconjunctivitis and/or its progression in patients with autoimmune diseases or in people at risk. Determination of clinical and morphological regularities of dry keratoconjunctivitis in accordance with the revealed molecular and genetic changes will contribute to better understanding of the etiology and pathogenesis of ophthalmological manifestations of autoimmune diseases, and will also help improve the diagnostics and prognosis of dry keratoconjunctivitis.
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Affiliation(s)
- T N Safonova
- Research Institute of Eye Diseases, 11A Rossolimo St., Moscow, Russian Federation, 119021
| | - G V Zaitseva
- Research Institute of Eye Diseases, 11A Rossolimo St., Moscow, Russian Federation, 119021
| | - A M Burdenniy
- Institute of General Pathology and Pathophysiology, 8 Baltiyskaya St., Moscow, Russian Federation, 125315
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10
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Danquah BD, Yefremova Y, Opuni KFM, Röwer C, Koy C, Glocker MO. Intact Transition Epitope Mapping - Thermodynamic Weak-force Order (ITEM - TWO). J Proteomics 2019; 212:103572. [PMID: 31683061 DOI: 10.1016/j.jprot.2019.103572] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 10/25/2019] [Accepted: 10/27/2019] [Indexed: 01/17/2023]
Abstract
We have developed an electrospray mass spectrometry method which is capable to determine antibody affinity in a gas phase experiment. A solution with the immune complex is electrosprayed and multiply charged ions are translated into the gas phase. Then, the intact immune-complex ions are separated from unbound peptide ions. Increasing the voltage difference in a collision cell results in collision induced dissociation of the immune-complex by which bound peptide ions are released. When analyzing a peptide mixture, measuring the mass of the complex-released peptide ions identifies which of the peptides contains the epitope. A step-wise increase in the collision cell voltage difference changes the intensity ratios of the surviving immune complex ions, the released peptide ions, and the antibody ions. From all the ions´ normalized intensity ratios are deduced the thermodynamic quasi equilibrium dissociation constants (KDm0g#) from which are calculated the apparent gas phase Gibbs energies of activation over temperature (ΔGm0g#T). The order of the apparent gas phase dissociation constants of four antibody - epitope peptide pairs matched well with those obtained from in-solution measurements. The determined gas phase values for antibody affinities are independent from the source of the investigated peptides and from the applied instrument. Data are available via ProteomeXchange with identifier PXD016024. SIGNIFICANCE: ITEM - TWO enables rapid epitope mapping and determination of apparent dissociation energies of immune complexes with minimal in-solution handling. Mixing of antibody and antigen peptide solutions initiates immune complex formation in solution. Epitope binding strengths are determined in the gas phase after electrospraying the antibody / antigen peptide mixtures and mass spectrometric analysis of immune complexes under different collision induced dissociation conditions. Since the order of binding strengths in the gas phase is the same as that in solution, ITEM - TWO characterizes two most important antibody properties, specificity and affinity.
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Affiliation(s)
- Bright D Danquah
- Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | - Yelena Yefremova
- Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | | | - Claudia Röwer
- Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | - Cornelia Koy
- Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | - Michael O Glocker
- Proteome Center Rostock, University Medicine Rostock, Rostock, Germany.
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11
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Danquah BD, Röwer C, Opuni KM, El-Kased R, Frommholz D, Illges H, Koy C, Glocker MO. Intact Transition Epitope Mapping - Targeted High-Energy Rupture of Extracted Epitopes (ITEM-THREE). Mol Cell Proteomics 2019; 18:1543-1555. [PMID: 31147491 PMCID: PMC6683010 DOI: 10.1074/mcp.ra119.001429] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 05/14/2019] [Indexed: 12/31/2022] Open
Abstract
Epitope mapping, which is the identification of antigenic determinants, is essential for the design of novel antibody-based therapeutics and diagnostic tools. ITEM-THREE is a mass spectrometry-based epitope mapping method that can identify epitopes on antigens upon generating an immune complex in electrospray-compatible solutions by adding an antibody of interest to a mixture of peptides from which at least one holds the antibody's epitope. This mixture is nano-electrosprayed without purification. Identification of the epitope peptide is performed within a mass spectrometer that provides an ion mobility cell sandwiched in-between two collision cells and where this ion manipulation setup is flanked by a quadrupole mass analyzer on one side and a time-of-flight mass analyzer on the other side. In a stepwise fashion, immune-complex ions are separated from unbound peptide ions and dissociated to release epitope peptide ions. Immune complex-released peptide ions are separated from antibody ions and fragmented by collision induced dissociation. Epitope-containing peptide fragment ions are recorded, and mass lists are submitted to unsupervised data base search thereby retrieving both, the amino acid sequence of the epitope peptide and the originating antigen. ITEM-THREE was developed with antiTRIM21 and antiRA33 antibodies for which the epitopes were known, subjecting them to mixtures of synthetic peptides of which one contained the respective epitope. ITEM-THREE was then successfully tested with an enzymatic digest of His-tagged recombinant human β-actin and an antiHis-tag antibody, as well as with an enzymatic digest of recombinant human TNFα and an antiTNFα antibody whose epitope was previously unknown.
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Affiliation(s)
- Bright D Danquah
- ‡Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | - Claudia Röwer
- ‡Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | | | - Reham El-Kased
- ¶Microbiology and Immunology Faculty of Pharmacy, The British University in Egypt, Cairo, Egypt
| | - David Frommholz
- ‖University of Applied Sciences Bonn-Rhein-Sieg, Immunology and Cell Biology, Rheinbach, Germany
| | - Harald Illges
- ‖University of Applied Sciences Bonn-Rhein-Sieg, Immunology and Cell Biology, Rheinbach, Germany;; **University of Applied Sciences Bonn-Rhein-Sieg, Institute for Functional Gene Analytics, Rheinbach, Germany
| | - Cornelia Koy
- ‡Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | - Michael O Glocker
- ‡Proteome Center Rostock, University Medicine Rostock, Rostock, Germany.
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12
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Kong W, Hayashi T, Fiches G, Xu Q, Li MZ, Que J, Liu S, Zhang W, Qi J, Santoso N, Elledge SJ, Zhu J. Diversified Application of Barcoded PLATO (PLATO-BC) Platform for Identification of Protein Interactions. GENOMICS, PROTEOMICS & BIOINFORMATICS 2019; 17:319-331. [PMID: 31494268 PMCID: PMC6818353 DOI: 10.1016/j.gpb.2018.12.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 10/24/2018] [Accepted: 12/21/2018] [Indexed: 11/29/2022]
Abstract
Proteins usually associate with other molecules physically to execute their functions. Identifying these interactions is important for the functional analysis of proteins. Previously, we reported the parallel analysis of translated ORFs (PLATO) to couple ribosome display of full-length ORFs with affinity enrichment of mRNA/protein/ribosome complexes for the "bait" molecules, followed by the deep sequencing analysis of mRNA. However, the sample processing, from extraction of precipitated mRNA to generation of DNA libraries, includes numerous steps, which is tedious and may cause the loss of materials. Barcoded PLATO (PLATO-BC), an improved platform was further developed to test its application for protein interaction discovery. In this report, we tested the antisera-antigen interaction using serum samples from patients with inclusion body myositis (IBM). Tripartite motif containing 21 (TRIM21) was identified as a potentially new IBM autoantigen. We also expanded the application of PLATO-BC to identify protein interactions for JQ1, single ubiquitin peptide, and NS5 protein of Zika virus. From PLATO-BC analyses, we identified new protein interactions for these "bait" molecules. We demonstrate that Ewing sarcoma breakpoint region 1 (EWSR1) binds to JQ1 and their interactions may interrupt the EWSR1 association with acetylated histone H4. RIO kinase 3 (RIOK3), a newly identified ubiquitin-binding protein, is preferentially associated with K63-ubiquitin chain. We also find that Zika NS5 protein interacts with two previously unreported host proteins, par-3 family cell polarity regulator (PARD3) and chromosome 19 open reading frame 53 (C19orf53), whose attenuated expression benefits the replication of Zika virus. These results further demonstrate that PLATO-BC is capable of identifying novel protein interactions for various types of "bait" molecules.
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Affiliation(s)
- Weili Kong
- Department of Microbiology and Immunology, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Tsuyoshi Hayashi
- Department of Microbiology and Immunology, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Guillaume Fiches
- Department of Microbiology and Immunology, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Qikai Xu
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Mamie Z Li
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Jianwen Que
- Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Shuai Liu
- Department of Chemistry, College of Science and Mathematics, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Wei Zhang
- Department of Chemistry, College of Science and Mathematics, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Jun Qi
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Netty Santoso
- Department of Microbiology and Immunology, Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Stephen J Elledge
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Jian Zhu
- Department of Pathology, Ohio State University Wexner Medical Center, Columbus, OH 43210, USA.
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13
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Opuni KFM, Al-Majdoub M, Yefremova Y, El-Kased RF, Koy C, Glocker MO. Mass spectrometric epitope mapping. MASS SPECTROMETRY REVIEWS 2018; 37:229-241. [PMID: 27403762 DOI: 10.1002/mas.21516] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 06/23/2016] [Indexed: 06/06/2023]
Abstract
Mass spectrometric epitope mapping has become a versatile method to precisely determine a soluble antigen's partial structure that directly interacts with an antibody in solution. Typical lengths of investigated antigens have increased up to several 100 amino acids while experimentally determined epitope peptides have decreased in length to on average 10-15 amino acids. Since the early 1990s more and more sophisticated methods have been developed and have forwarded a bouquet of suitable approaches for epitope mapping with immobilized, temporarily immobilized, and free-floating antibodies. While up to now monoclonal antibodies have been mostly used in epitope mapping experiments, the applicability of polyclonal antibodies has been proven. The antibody's resistance towards enzymatic proteolysis has been of key importance for the two mostly applied methods: epitope excision and epitope extraction. Sample consumption has dropped to low pmol amounts on both, the antigen and the antibody. While adequate in-solution sample handling has been most important for successful epitope mapping, mass spectrometric analysis has been found the most suitable read-out method from early on. The rapidity by which mass spectrometric epitope mapping nowadays is executed outperforms all alternative methods. Thus, it can be asserted that mass spectrometric epitope mapping has reached a state of maturity, which allows it to be used in any mass spectrometry laboratory. After 25 years of constant and steady improvements, its application to clinical samples, for example, for patient characterization and stratification, is anticipated in the near future. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 37:229-241, 2018.
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Affiliation(s)
- Kwabena F M Opuni
- Proteome Center Rostock, University Medicine and Natural Science Faculty, University of Rostock, Rostock, Germany
| | - Mahmoud Al-Majdoub
- Proteome Center Rostock, University Medicine and Natural Science Faculty, University of Rostock, Rostock, Germany
| | - Yelena Yefremova
- Proteome Center Rostock, University Medicine and Natural Science Faculty, University of Rostock, Rostock, Germany
| | - Reham F El-Kased
- Microbiology and Immunology Faculty of Pharmacy, The British University in Egypt, Cairo, Egypt
| | - Cornelia Koy
- Proteome Center Rostock, University Medicine and Natural Science Faculty, University of Rostock, Rostock, Germany
| | - Michael O Glocker
- Proteome Center Rostock, University Medicine and Natural Science Faculty, University of Rostock, Rostock, Germany
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14
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Abstract
The article reviews the results of Russian and foreign studies concerning the search of susceptibility genes for widespread multifactorial diseases: Sjogren's syndrome and rheumatoid arthritis. Studying regularity patterns of genome changes in autoimmune processes with ophthalmic manifestations and their correlation with the severity of dry keratoconjunctivitis will contribute to a better understanding of the etiology and pathogenesis of eye manifestations of the diseases, and will also allow the development of new effective methods of diagnosis and targeted therapy.
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Affiliation(s)
- T N Safonova
- Research Institute of Eye Diseases, 11 A, B Rossolimo St., Moscow, Russian Federation, 119021
| | - G V Zaitseva
- Research Institute of Eye Diseases, 11 A, B Rossolimo St., Moscow, Russian Federation, 119021
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15
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Abstract
Primary Sjögren’s syndrome (pSS) is an autoimmune disease characterized by inflammation in exocrine glands, resulting in reduced secretion of tears and saliva, manifesting as xerophthalmia and xerostomia, respectively. It is commonly associated with Sjögren’s syndrome type A (Ro) and Sjögren’s syndrome type B (La) antigens. However, in most patients, the identity of the triggering antigen is not known. Factors such as genetics of histocompatibility, dysregulation of T-cells, B-cells and viral infections have been implicated. Several important studies on autoantigens in pSS have been published since a review in 2012, and the aim of this review is to provide an update on further peer-reviewed original articles in this field. Oxidative damage of Ro60 antigen may explain the epitope spreading during the immune activation in pSS. Immune-mediated destruction of the muscarinic receptor-3-expressing cells has been associated with a reduction in parasympathetic function, which could cause reduced secretory function of exocrine glands. Such a process also activates reactive oxidative species and antioxidants, which are linked to the triggering of inflammatory responses. Elevated levels of kallikrein, yet another antigen present in the lacrimal gland and other tissues, are similarly involved in triggering an autoimmune T-cell response against target glands. Studying additional antigens, the platelet-selectin and vasoactive intestinal peptides, in patients with pSS can help to elucidate the origin and process of autoimmunity, or even lead to potential biomarkers. In conclusion, the understanding of autoantigens has led to exciting major advances in the biology of pSS and may influence diagnosis and management of pSS in future.
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Affiliation(s)
- Louis Tong
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore.,Corneal and External Eye Disease, Singapore National Eye Centre.,Ocular Surface Research Group, Singapore Eye Research Institute.,Eye Academic Clinical Program, Duke-NUS Medical School
| | - Vanessa Koh
- Ocular Surface Research Group, Singapore Eye Research Institute
| | - Bernard Yu-Hor Thong
- Department of Rheumatology, Allergy and Immunology, Tan Tock Seng Hospital, Singapore
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16
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Yefremova Y, Opuni KFM, Danquah BD, Thiesen HJ, Glocker MO. Intact Transition Epitope Mapping (ITEM). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1612-1622. [PMID: 28616748 DOI: 10.1007/s13361-017-1654-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 03/06/2017] [Accepted: 03/07/2017] [Indexed: 06/07/2023]
Abstract
Intact transition epitope mapping (ITEM) enables rapid and accurate determination of protein antigen-derived epitopes by either epitope extraction or epitope excision. Upon formation of the antigen peptide-containing immune complex in solution, the entire mixture is electrosprayed to translate all constituents as protonated ions into the gas phase. There, ions from antibody-peptide complexes are separated from unbound peptide ions according to their masses, charges, and shapes either by ion mobility drift or by quadrupole ion filtering. Subsequently, immune complexes are dissociated by collision induced fragmentation and the ion signals of the "complex-released peptides," which in effect are the epitope peptides, are recorded in the time-of-flight analyzer of the mass spectrometer. Mixing of an antibody solution with a solution in which antigens or antigen-derived peptides are dissolved is, together with antigen proteolysis, the only required in-solution handling step. Simplicity of sample handling and speed of analysis together with very low sample consumption makes ITEM faster and easier to perform than other experimental epitope mapping methods. Graphical Abstract ᅟ.
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Affiliation(s)
- Yelena Yefremova
- Proteome Center Rostock, University Medicine Rostock, Schillingallee 69, 18057, Rostock, Germany
| | - Kwabena F M Opuni
- Proteome Center Rostock, University Medicine Rostock, Schillingallee 69, 18057, Rostock, Germany
| | - Bright D Danquah
- Proteome Center Rostock, University Medicine Rostock, Schillingallee 69, 18057, Rostock, Germany
| | - Hans-Juergen Thiesen
- Institute of Immunology, University Medicine Rostock, Schillingallee 70, 18057, Rostock, Germany
| | - Michael O Glocker
- Proteome Center Rostock, University Medicine Rostock, Schillingallee 69, 18057, Rostock, Germany.
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17
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Hecker M, Fitzner B, Wendt M, Lorenz P, Flechtner K, Steinbeck F, Schröder I, Thiesen HJ, Zettl UK. High-Density Peptide Microarray Analysis of IgG Autoantibody Reactivities in Serum and Cerebrospinal Fluid of Multiple Sclerosis Patients. Mol Cell Proteomics 2016; 15:1360-80. [PMID: 26831522 DOI: 10.1074/mcp.m115.051664] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Indexed: 11/06/2022] Open
Abstract
Intrathecal immunoglobulin G (IgG) synthesis and oligoclonal IgG bands in cerebrospinal fluid (CSF) are hallmarks of multiple sclerosis (MS), but the antigen specificities remain enigmatic. Our study is the first investigating the autoantibody repertoire in paired serum and CSF samples from patients with relapsing-remitting MS (RRMS), primary progressive MS (PPMS), and other neurological diseases by the use of high-density peptide microarrays. Protein sequences of 45 presumed MS autoantigens (e.g.MOG, MBP, and MAG) were represented on the microarrays by overlapping 15mer peptides. IgG reactivities were screened against a total of 3991 peptides, including also selected viral epitopes. The measured antibody reactivities were highly individual but correlated for matched serum and CSF samples. We found 54 peptides to be recognized significantly more often by serum or CSF antibodies from MS patients compared with controls (pvalues <0.05). The results for RRMS and PPMS clearly overlapped. However, PPMS patients presented a broader peptide-antibody signature. The highest signals were detected for a peptide mapping to a region of the Epstein-Barr virus protein EBNA1 (amino acids 392-411), which is homologous to the N-terminal part of human crystallin alpha-B. Our data confirmed several known MS-associated antigens and epitopes, and they delivered additional potential linear epitopes, which await further validation. The peripheral and intrathecal humoral immune response in MS is polyspecific and includes antibodies that are also found in serum of patients with other diseases. Further studies are required to assess the pathogenic relevance of autoreactive and anti-EBNA1 antibodies as well as their combinatorial value as biomarkers for MS.
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Affiliation(s)
- Michael Hecker
- From the ‡University of Rostock, Department of Neurology, Division of Neuroimmunology, Gehlsheimer Str. 20, 18147 Rostock, Germany; §Steinbeis Transfer Center for Proteome Analysis, Schillingallee 70, 18057 Rostock, Germany;
| | - Brit Fitzner
- From the ‡University of Rostock, Department of Neurology, Division of Neuroimmunology, Gehlsheimer Str. 20, 18147 Rostock, Germany; §Steinbeis Transfer Center for Proteome Analysis, Schillingallee 70, 18057 Rostock, Germany
| | - Matthias Wendt
- From the ‡University of Rostock, Department of Neurology, Division of Neuroimmunology, Gehlsheimer Str. 20, 18147 Rostock, Germany
| | - Peter Lorenz
- ¶University of Rostock, Institute of Immunology, Schillingallee 70, 18057 Rostock, Germany
| | - Kristin Flechtner
- ¶University of Rostock, Institute of Immunology, Schillingallee 70, 18057 Rostock, Germany
| | - Felix Steinbeck
- ¶University of Rostock, Institute of Immunology, Schillingallee 70, 18057 Rostock, Germany; ‖Gesellschaft für Individualisierte Medizin mbH (IndyMED), Lessingstr. 17, 18055 Rostock, Germany
| | - Ina Schröder
- From the ‡University of Rostock, Department of Neurology, Division of Neuroimmunology, Gehlsheimer Str. 20, 18147 Rostock, Germany
| | - Hans-Jürgen Thiesen
- §Steinbeis Transfer Center for Proteome Analysis, Schillingallee 70, 18057 Rostock, Germany; ¶University of Rostock, Institute of Immunology, Schillingallee 70, 18057 Rostock, Germany; ‖Gesellschaft für Individualisierte Medizin mbH (IndyMED), Lessingstr. 17, 18055 Rostock, Germany
| | - Uwe Klaus Zettl
- From the ‡University of Rostock, Department of Neurology, Division of Neuroimmunology, Gehlsheimer Str. 20, 18147 Rostock, Germany
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18
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Hinchliffe TE, Lin ZT, Wu T. Protein arrays for biomarker discovery in lupus. Proteomics Clin Appl 2016; 10:625-34. [PMID: 26684273 DOI: 10.1002/prca.201500060] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 11/05/2015] [Accepted: 12/09/2015] [Indexed: 11/08/2022]
Abstract
Lupus is one of the most common autoimmune diseases, yet many mechanisms of its pathogenesis are not fully known. Over the last few years, advances in protein array technology have accelerated rapidly, resulting in many promising insights toward the discovery of novel lupus biomarkers that may become useful in disease diagnosis and management. Still, only two types of analytical protein arrays thus far, being antibody and antigen arrays, have found notable usage toward lupus biomarker discovery. In this review, we summarize current protein array technologies being used for biomarker discoveries in lupus and associated biomarker findings, as well as protein arrays that are likely to be used for lupus biomarker discovery in the near future.
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Affiliation(s)
- Taylor E Hinchliffe
- Department of Biomedical Engineering, University of Houston, Houston, TX, USA
| | - Zuan-Tao Lin
- Department of Biomedical Engineering, University of Houston, Houston, TX, USA
| | - Tianfu Wu
- Department of Biomedical Engineering, University of Houston, Houston, TX, USA
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19
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Abstract
The diversity of the antigen-specific humoral immune response reflects the interaction of the immune system with pathogens and autoantigens. Peptide microarray analysis opens up new perspectives for the use of antibodies as diagnostic biomarkers and provides unique access to a more differentiated serological diagnosis. This review focusses on latest applications of peptide microarrays for the serologic medical diagnosis of autoimmunity, infectious diseases, and cancer.
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20
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Yefremova Y, Al-Majdoub M, Opuni KF, Koy C, Cui W, Yan Y, Gross M, Glocker MO. "De-novo" amino acid sequence elucidation of protein G'e by combined "top-down" and "bottom-up" mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:482-492. [PMID: 25560987 PMCID: PMC6130978 DOI: 10.1007/s13361-014-1053-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Revised: 11/20/2014] [Accepted: 11/20/2014] [Indexed: 06/04/2023]
Abstract
Mass spectrometric de-novo sequencing was applied to review the amino acid sequence of a commercially available recombinant protein G´ with great scientific and economic importance. Substantial deviations to the published amino acid sequence (Uniprot Q54181) were found by the presence of 46 additional amino acids at the N-terminus, including a so-called "His-tag" as well as an N-terminal partial α-N-gluconoylation and α-N-phosphogluconoylation, respectively. The unexpected amino acid sequence of the commercial protein G' comprised 241 amino acids and resulted in a molecular mass of 25,998.9 ± 0.2 Da for the unmodified protein. Due to the higher mass that is caused by its extended amino acid sequence compared with the original protein G' (185 amino acids), we named this protein "protein G'e." By means of mass spectrometric peptide mapping, the suggested amino acid sequence, as well as the N-terminal partial α-N-gluconoylations, was confirmed with 100% sequence coverage. After the protein G'e sequence was determined, we were able to determine the expression vector pET-28b from Novagen with the Xho I restriction enzyme cleavage site as the best option that was used for cloning and expressing the recombinant protein G'e in E. coli. A dissociation constant (K(d)) value of 9.4 nM for protein G'e was determined thermophoretically, showing that the N-terminal flanking sequence extension did not cause significant changes in the binding affinity to immunoglobulins.
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Affiliation(s)
- Yelena Yefremova
- Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | | | | | - Cornelia Koy
- Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | - Weidong Cui
- Washington University in St. Louis, St. Louis, Missouri, USA
| | - Yuetian Yan
- Washington University in St. Louis, St. Louis, Missouri, USA
| | - Michael Gross
- Washington University in St. Louis, St. Louis, Missouri, USA
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21
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Legutki JB, Zhao ZG, Greving M, Woodbury N, Johnston SA, Stafford P. Scalable high-density peptide arrays for comprehensive health monitoring. Nat Commun 2014; 5:4785. [PMID: 25183057 DOI: 10.1038/ncomms5785] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 07/23/2014] [Indexed: 11/09/2022] Open
Abstract
There is an increasing awareness that health care must move from post-symptomatic treatment to presymptomatic intervention. An ideal system would allow regular inexpensive monitoring of health status using circulating antibodies to report on health fluctuations. Recently, we demonstrated that peptide microarrays can do this through antibody signatures (immunosignatures). Unfortunately, printed microarrays are not scalable. Here we demonstrate a platform based on fabricating microarrays (~10 M peptides per slide, 330,000 peptides per assay) on silicon wafers using equipment common to semiconductor manufacturing. The potential of these microarrays for comprehensive health monitoring is verified through the simultaneous detection and classification of six different infectious diseases and six different cancers. Besides diagnostics, these high-density peptide chips have numerous other applications both in health care and elsewhere.
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Affiliation(s)
- Joseph Barten Legutki
- Center for Innovations in Medicine, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Zhan-Gong Zhao
- Center for Innovations in Medicine, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Matt Greving
- NextVal, 4186 Sorrento Valley Boulevard, Suite G, San Diego, California 92121, USA
| | - Neal Woodbury
- Center for Innovations in Medicine, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Stephen Albert Johnston
- Center for Innovations in Medicine, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Phillip Stafford
- Center for Innovations in Medicine, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
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22
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Al-Majdoub M, Opuni KFM, Yefremova Y, Koy C, Lorenz P, El-Kased RF, Thiesen HJ, Glocker MO. A novel strategy for the rapid preparation and isolation of intact immune complexes from peptide mixtures. J Mol Recognit 2014; 27:566-74. [DOI: 10.1002/jmr.2375] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 02/27/2014] [Accepted: 03/13/2014] [Indexed: 01/10/2023]
Affiliation(s)
| | | | - Yelena Yefremova
- Proteome Center Rostock; University Medicine Rostock; Rostock Germany
| | - Cornelia Koy
- Proteome Center Rostock; University Medicine Rostock; Rostock Germany
| | - Peter Lorenz
- Institute of Immunology; University Medicine Rostock; Rostock Germany
| | - Reham F. El-Kased
- Microbiology and Immunology Faculty of Pharmacy; The British University in Egypt; Cairo Egypt
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23
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Luštrek M, Lorenz P, Kreutzer M, Qian Z, Steinbeck F, Wu D, Born N, Ziems B, Hecker M, Blank M, Shoenfeld Y, Cao Z, Glocker MO, Li Y, Fuellen G, Thiesen HJ. Epitope predictions indicate the presence of two distinct types of epitope-antibody-reactivities determined by epitope profiling of intravenous immunoglobulins. PLoS One 2013; 8:e78605. [PMID: 24244326 PMCID: PMC3823795 DOI: 10.1371/journal.pone.0078605] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 09/20/2013] [Indexed: 01/23/2023] Open
Abstract
Epitope-antibody-reactivities (EAR) of intravenous immunoglobulins (IVIGs) determined for 75,534 peptides by microarray analysis demonstrate that roughly 9% of peptides derived from 870 different human protein sequences react with antibodies present in IVIG. Computational prediction of linear B cell epitopes was conducted using machine learning with an ensemble of classifiers in combination with position weight matrix (PWM) analysis. Machine learning slightly outperformed PWM with area under the curve (AUC) of 0.884 vs. 0.849. Two different types of epitope-antibody recognition-modes (Type I EAR and Type II EAR) were found. Peptides of Type I EAR are high in tyrosine, tryptophan and phenylalanine, and low in asparagine, glutamine and glutamic acid residues, whereas for peptides of Type II EAR it is the other way around. Representative crystal structures present in the Protein Data Bank (PDB) of Type I EAR are PDB 1TZI and PDB 2DD8, while PDB 2FD6 and 2J4W are typical for Type II EAR. Type I EAR peptides share predicted propensities for being presented by MHC class I and class II complexes. The latter interaction possibly favors T cell-dependent antibody responses including IgG class switching. Peptides of Type II EAR are predicted not to be preferentially presented by MHC complexes, thus implying the involvement of T cell-independent IgG class switch mechanisms. The high extent of IgG immunoglobulin reactivity with human peptides implies that circulating IgG molecules are prone to bind to human protein/peptide structures under non-pathological, non-inflammatory conditions. A webserver for predicting EAR of peptide sequences is available at www.sysmed-immun.eu/EAR.
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Affiliation(s)
- Mitja Luštrek
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Universitätsmedizin, University of Rostock, Rostock, Germany
- Department of Intelligent Systems, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Peter Lorenz
- Institute of Immunology, Universitätsmedizin Rostock, University of Rostock, Rostock, Germany
| | - Michael Kreutzer
- Institute of Immunology, Universitätsmedizin Rostock, University of Rostock, Rostock, Germany
| | - Zilliang Qian
- Institute of Immunology, Universitätsmedizin Rostock, University of Rostock, Rostock, Germany
- Shanghai Institute for Biological Sciences, Shanghai, China
| | - Felix Steinbeck
- Institute of Immunology, Universitätsmedizin Rostock, University of Rostock, Rostock, Germany
| | - Di Wu
- Institute of Immunology, Universitätsmedizin Rostock, University of Rostock, Rostock, Germany
- Shanghai Institute for Biological Sciences, Shanghai, China
| | - Nadine Born
- Institute of Immunology, Universitätsmedizin Rostock, University of Rostock, Rostock, Germany
| | - Bjoern Ziems
- Gesellschaft für Individualisierte Medizin GmbH, Rostock, Germany
| | - Michael Hecker
- Steinbeis Transfer Center for Proteome Analysis, Rostock, Germany
| | - Miri Blank
- The Zabludovicz Center for Autoimmune Diseases, Sheba Medical Center, Ramat-Gan, Israel
| | - Yehuda Shoenfeld
- The Zabludovicz Center for Autoimmune Diseases, Sheba Medical Center, Ramat-Gan, Israel
| | - Zhiwei Cao
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | | | - Yixue Li
- Shanghai Institute for Biological Sciences, Shanghai, China
| | - Georg Fuellen
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Universitätsmedizin, University of Rostock, Rostock, Germany
| | - Hans-Jürgen Thiesen
- Institute of Immunology, Universitätsmedizin Rostock, University of Rostock, Rostock, Germany
- * E-mail:
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24
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Al-Majdoub M, Opuni KFM, Koy C, Glocker MO. Facile Fabrication and Instant Application of Miniaturized Antibody-Decorated Affinity Columns for Higher-Order Structure and Functional Characterization of TRIM21 Epitope Peptides. Anal Chem 2013; 85:10479-87. [DOI: 10.1021/ac402559m] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- M. Al-Majdoub
- Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | - K. F. M. Opuni
- Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | - C. Koy
- Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | - M. O. Glocker
- Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
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