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Chandrasekharan G, Unnikrishnan M. High throughput methods to study protein-protein interactions during host-pathogen interactions. Eur J Cell Biol 2024; 103:151393. [PMID: 38306772 DOI: 10.1016/j.ejcb.2024.151393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 01/18/2024] [Accepted: 01/21/2024] [Indexed: 02/04/2024] Open
Abstract
The ability of a pathogen to survive and cause an infection is often determined by specific interactions between the host and pathogen proteins. Such interactions can be both intra- and extracellular and may define the outcome of an infection. There are a range of innovative biochemical, biophysical and bioinformatic techniques currently available to identify protein-protein interactions (PPI) between the host and the pathogen. However, the complexity and the diversity of host-pathogen PPIs has led to the development of several high throughput (HT) techniques that enable the study of multiple interactions at once and/or screen multiple samples at the same time, in an unbiased manner. We review here the major HT laboratory-based technologies employed for host-bacterial interaction studies.
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Affiliation(s)
| | - Meera Unnikrishnan
- Division of Biomedical Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom.
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2
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Harvey EP, Shin JE, Skiba MA, Nemeth GR, Hurley JD, Wellner A, Shaw AY, Miranda VG, Min JK, Liu CC, Marks DS, Kruse AC. An in silico method to assess antibody fragment polyreactivity. Nat Commun 2022; 13:7554. [PMID: 36477674 PMCID: PMC9729196 DOI: 10.1038/s41467-022-35276-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022] Open
Abstract
Antibodies are essential biological research tools and important therapeutic agents, but some exhibit non-specific binding to off-target proteins and other biomolecules. Such polyreactive antibodies compromise screening pipelines, lead to incorrect and irreproducible experimental results, and are generally intractable for clinical development. Here, we design a set of experiments using a diverse naïve synthetic camelid antibody fragment (nanobody) library to enable machine learning models to accurately assess polyreactivity from protein sequence (AUC > 0.8). Moreover, our models provide quantitative scoring metrics that predict the effect of amino acid substitutions on polyreactivity. We experimentally test our models' performance on three independent nanobody scaffolds, where over 90% of predicted substitutions successfully reduced polyreactivity. Importantly, the models allow us to diminish the polyreactivity of an angiotensin II type I receptor antagonist nanobody, without compromising its functional properties. We provide a companion web-server that offers a straightforward means of predicting polyreactivity and polyreactivity-reducing mutations for any given nanobody sequence.
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Affiliation(s)
- Edward P Harvey
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Jung-Eun Shin
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Meredith A Skiba
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Genevieve R Nemeth
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Joseph D Hurley
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Alon Wellner
- Department of Chemistry, University of California, Irvine, CA, 92697, USA
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, 92697, USA
- Department of Biomedical Engineering, University of California, Irvine, CA, 92692, USA
| | - Ada Y Shaw
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Victor G Miranda
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Joseph K Min
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Chang C Liu
- Department of Chemistry, University of California, Irvine, CA, 92697, USA
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, 92697, USA
- Department of Biomedical Engineering, University of California, Irvine, CA, 92692, USA
| | - Debora S Marks
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
| | - Andrew C Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA.
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Assessment of Therapeutic Antibody Developability by Combinations of In Vitro and In Silico Methods. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2313:57-113. [PMID: 34478132 DOI: 10.1007/978-1-0716-1450-1_4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Although antibodies have become the fastest-growing class of therapeutics on the market, it is still challenging to develop them for therapeutic applications, which often require these molecules to withstand stresses that are not present in vivo. We define developability as the likelihood of an antibody candidate with suitable functionality to be developed into a manufacturable, stable, safe, and effective drug that can be formulated to high concentrations while retaining a long shelf life. The implementation of reliable developability assessments from the early stages of antibody discovery enables flagging and deselection of potentially problematic candidates, while focussing available resources on the development of the most promising ones. Currently, however, thorough developability assessment requires multiple in vitro assays, which makes it labor intensive and time consuming to implement at early stages. Furthermore, accurate in vitro analysis at the early stage is compromised by the high number of potential candidates that are often prepared at low quantities and purity. Recent improvements in the performance of computational predictors of developability potential are beginning to change this scenario. Many computational methods only require the knowledge of the amino acid sequences and can be used to identify possible developability issues or to rank available candidates according to a range of biophysical properties. Here, we describe how the implementation of in silico tools into antibody discovery pipelines is increasingly offering time- and cost-effective alternatives to in vitro experimental screening, thus streamlining the drug development process. We discuss in particular the biophysical and biochemical properties that underpin developability potential and their trade-offs, review various in vitro assays to measure such properties or parameters that are predictive of developability, and give an overview of the growing number of in silico tools available to predict properties important for antibody development, including the CamSol method developed in our laboratory.
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MacLachlan TK, Price S, Cavagnaro J, Andrews L, Blanset D, Cosenza ME, Dempster M, Galbreath E, Giusti AM, Heinz-Taheny KM, Fleurance R, Sutter E, Leach MW. Classic and evolving approaches to evaluating cross reactivity of mAb and mAb-like molecules - A survey of industry 2008-2019. Regul Toxicol Pharmacol 2021; 121:104872. [PMID: 33485926 DOI: 10.1016/j.yrtph.2021.104872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/11/2021] [Accepted: 01/19/2021] [Indexed: 11/28/2022]
Abstract
Monoclonal antibodies (mAbs) and mAb derivatives have become mainstay pharmaceutical modalites. A critical assessment is to ascertain the specificity of these molecules prior to human clinical trials. The primary technique for determining specificity has been the immunohistochemistry (IHC)-based "Tissue Cross-Reactivity" (TCR) assay, where the candidate molecule is applied to > 30 tissues to look for unexpected staining. In the last few years, however, non-IHC array-based platforms have emerged that allow for screening 75-80% of the human membrane proteome, indicating a viable alternative and/or addition to the IHC methods. The preclinical sciences subcommittee of the Biotechnology Innovation Organization (BIO), "BioSafe", conducted a survey of 26 BIO member companies to understand current sponsor experience with the IHC and array techniques. In the last ten years, respondents noted they have conducted more than 650 IHC TCR assays, largely on full length mAbs, with varying impacts on programs. Protein/cell arrays have been utilized by almost half of the companies and sponsors are gaining familiarity and comfort with the platform. Initial experience with recent versions of these arrays has been largely positive. While most sponsors are not prepared to eliminate the IHC TCR assay, growing experience with these alternatives allows them to confidently choose other approaches with or without TCR assays.
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Affiliation(s)
| | - Shari Price
- Charles River Laboratories, 15 Worman's Mill Court, Suite I, Frederick, MD, 21701, USA
| | | | | | - Diann Blanset
- Boehringer Ingelheim, 900 Ridgebury Road, Ridgefield, CT, 06877, USA
| | | | - Maggie Dempster
- GlaxoSmithKline, 1250 South Collegeville Rd, Collegeville, PA, 19426, USA
| | | | - Anna Maria Giusti
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Zurich, Switzerland
| | | | | | - Esther Sutter
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Michael W Leach
- Drug Safety Research and Development, Pfizer, Inc, 300 Technology Square, Cambridge, MA, 02139, USA
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Wu FL, Lai DY, Ding HH, Tang YJ, Xu ZW, Ma ML, Guo SJ, Wang JF, Shen N, Zhao XD, Qi H, Li H, Tao SC. Identification of Serum Biomarkers for Systemic Lupus Erythematosus Using a Library of Phage Displayed Random Peptides and Deep Sequencing. Mol Cell Proteomics 2019; 18:1851-1863. [PMID: 31308251 PMCID: PMC6731078 DOI: 10.1074/mcp.ra119.001582] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 07/01/2019] [Indexed: 12/26/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is one of the most serious autoimmune diseases, characterized by highly diverse clinical manifestations. A biomarker is still needed for accurate diagnostics. SLE serum autoantibodies were discovered and validated using serum samples from independent sample cohorts encompassing 306 participants divided into three groups, i.e. healthy, SLE patients, and other autoimmune-related diseases. To discover biomarkers for SLE, a phage displayed random peptide library (Ph.D. 12) and deep sequencing were applied to screen specific autoantibodies in a total of 100 serum samples from 50 SLE patients and 50 healthy controls. A statistical analysis protocol was set up for the identification of peptides as potential biomarkers. For validation, 10 peptides were analyzed using enzyme-linked immunosorbent assays (ELISA). As a result, four peptides (SLE2018Val001, SLE2018Val002, SLE2018Val006, and SLE2018Val008) were discovered with high diagnostic power to differentiate SLE patients from healthy controls. Among them, two peptides, i.e. SLE2018Val001 and SLE2018Val002, were confirmed between SLE with other autoimmune patients. The procedure we established could be easily adopted for the identification of autoantibodies as biomarkers for many other diseases.
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Affiliation(s)
- Fan-Lin Wu
- ‡Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; ¶School of Agriculture, Ludong University, Yantai 264025, China
| | - Dan-Yun Lai
- ‡Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Hui-Hua Ding
- ‖Shanghai Institute of Rheumatology, Department of rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 145 Shan Dong Road (c), Shanghai 200240, China
| | - Yuan-Jia Tang
- ‖Shanghai Institute of Rheumatology, Department of rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 145 Shan Dong Road (c), Shanghai 200240, China
| | - Zhao-Wei Xu
- ‡Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Ming-Liang Ma
- ‡Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Shu-Juan Guo
- ‡Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Jing-Fang Wang
- ‡Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Nan Shen
- ‖Shanghai Institute of Rheumatology, Department of rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 145 Shan Dong Road (c), Shanghai 200240, China; **State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, 2200 Lane 25 Xietu Road, Shanghai 200240, China
| | - Xiao-Dong Zhao
- ‡Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Huan Qi
- ‡Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
| | - Hua Li
- §Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Sheng-Ce Tao
- ‡Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; §Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
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Anti-GAPDH Autoantibody Is Associated with Increased Disease Activity and Intracranial Pressure in Systemic Lupus Erythematosus. J Immunol Res 2019; 2019:7430780. [PMID: 31049359 PMCID: PMC6462327 DOI: 10.1155/2019/7430780] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 01/29/2019] [Accepted: 02/14/2019] [Indexed: 01/01/2023] Open
Abstract
Objective Systemic lupus erythematosus (SLE) is an immune disease characterized by multiorgan involvement. Neuropsychiatric systemic lupus erythematosus (NPSLE) is one of the most devastating complications of SLE, which lacks efficient diagnostic biomarkers. The recent studies on the anti-GAPDH autoantibodies suggested its potential pathogenic roles in NPSLE. However, the clinical relevance of the anti-GAPDH autoantibodies in patients with SLE is still elusive. In this study, we sought to determine the serum levels of the anti-GAPDH autoantibodies in patients with SLE to investigate the clinical significance of the anti-GAPDH autoantibodies in SLE. Methods Concentrations of the glyceraldehyde 3-phosphate dehydrogenase autoantibodies (anti-GAPDH autoantibodies) in the serum of 130 SLE patients and 55 healthy individuals were determined by enzyme-linked immunosorbent assay (ELISA). Among the 130 SLE patients, 95 were SLE patients without neuropsychiatric symptoms and 35 had NPSLE. White blood cell (WBC) count, hemoglobin (HB), platelet count (PLT), IgG, IgA, IgM, anti-dsDNA, C3, C4, erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), RF, anti-cardiolipin (Acl), ANA, AnuA, anti-SSA, anti-SSB, β2-GPI, urinalysis, and 24 h urine protein were measured by standard laboratory techniques. Systemic lupus erythematosus disease activity index 2000 (SLEDAI-2K) and Systemic Lupus International Collaborating Clinics/American College of Rheumatology (SLICC/ACR) damage index scores were evaluated accordingly. Results The serum levels of the anti-GAPDH autoantibodies were significantly elevated in the SLE patients, especially in the patients with NPSLE (P = 0.0011). Elevated serum anti-GAPDH was correlated with increased SLEDAI-2K (P = 0.017), ESR, IgG, and IgM and associated with increased intracranial pressure and incidence of cerebrovascular lesions, but it was protective for seizure disorder incidence. Conclusions Serum anti-GAPDH autoantibody was increased in both groups of SLE patients with or without neuropsychiatric symptoms and associated with disease severity. It could become an indicator of tissue damages in the brain for the future clinical practice.
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Cox E, Hwang W, Uzoma I, Hu J, Guzzo CM, Jeong J, Matunis MJ, Qian J, Zhu H, Blackshaw S. Global Analysis of SUMO-Binding Proteins Identifies SUMOylation as a Key Regulator of the INO80 Chromatin Remodeling Complex. Mol Cell Proteomics 2017; 16:812-823. [PMID: 28254775 PMCID: PMC5417823 DOI: 10.1074/mcp.m116.063719] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 02/14/2017] [Indexed: 12/23/2022] Open
Abstract
SUMOylation is a critical regulator of a broad range of cellular processes, and is thought to do so in part by modulation of protein interaction. To comprehensively identify human proteins whose interaction is modulated by SUMOylation, we developed an in vitro binding assay using human proteome microarrays to identify targets of SUMO1 and SUMO2. We then integrated these results with protein SUMOylation and protein-protein interaction data to perform network motif analysis. We focused on a single network motif we termed a SUMOmodPPI (SUMO-modulated Protein-Protein Interaction) that included the INO80 chromatin remodeling complex subunits TFPT and INO80E. We validated the SUMO-binding activity of INO80E, and showed that TFPT is a SUMO substrate both in vitro and in vivo We then demonstrated a key role for SUMOylation in mediating the interaction between these two proteins, both in vitro and in vivo By demonstrating a key role for SUMOylation in regulating the INO80 chromatin remodeling complex, this work illustrates the power of bioinformatics analysis of large data sets in predicting novel biological phenomena.
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Affiliation(s)
- Eric Cox
- From the ‡Biochemistry, Cellular and Molecular Biology Graduate Program
- §Solomon H. Snyder Department of Neuroscience
- ¶Department of Pharmacology and Molecular Sciences
| | | | - Ijeoma Uzoma
- ¶Department of Pharmacology and Molecular Sciences
| | | | - Catherine M Guzzo
- **Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Junseop Jeong
- ¶Department of Pharmacology and Molecular Sciences
- ‡‡Center for High-Throughput Biology
| | - Michael J Matunis
- **Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | | | - Heng Zhu
- ¶Department of Pharmacology and Molecular Sciences
- ‡‡Center for High-Throughput Biology
| | - Seth Blackshaw
- §Solomon H. Snyder Department of Neuroscience,
- ‡‡Center for High-Throughput Biology
- §§Institute for Cell Engineering
- ¶¶Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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Lomakin YA, Stepanov AV, Balabashin DS, Ponomarenko NA, Smirnov IV, Belogurov AA. Design of Chemical Conjugate for Targeted Therapy of Multiple Sclerosis Based of Constant Fragment of Human Antibody Heavy Chain and Peptoid Analog of Autoantigen MOG 35-55. Bull Exp Biol Med 2017; 162:777-780. [PMID: 28429225 DOI: 10.1007/s10517-017-3711-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Indexed: 10/19/2022]
Abstract
Elimination of B cells producing autoantibodies to neuroantigens is considered as beneficial in the treatment of multiple sclerosis. Myelin oligodendrocyte glycoprotein (MOG) is a significant autoantigen in multiple sclerosis. It was shown that MOG-like peptoid AMogP3 can bind autoantibodies produced by pathological lymphocytes. We propose a structure of an innovative drug for targeted elimination of the pool of autoreactive B cells responsible for multiple sclerosis pathogenesis; this compound is a complex of peptoid AMogP3 with Fc fragment of human immunoglobulin. The obtained Fc-PEG-AMogP3 conjugate effectively interact with autoreactive antibodies, which attests to their high therapeutic potential.
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Affiliation(s)
- Y A Lomakin
- M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry of Russian Academy of Sciences, Moscow, Russia
| | - A V Stepanov
- M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry of Russian Academy of Sciences, Moscow, Russia
| | - D S Balabashin
- M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry of Russian Academy of Sciences, Moscow, Russia
| | - N A Ponomarenko
- M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry of Russian Academy of Sciences, Moscow, Russia
| | - I V Smirnov
- M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry of Russian Academy of Sciences, Moscow, Russia
| | - A A Belogurov
- M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry of Russian Academy of Sciences, Moscow, Russia.
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Doran TM, Sarkar M, Kodadek T. Chemical Tools To Monitor and Manipulate Adaptive Immune Responses. J Am Chem Soc 2016; 138:6076-94. [PMID: 27115249 PMCID: PMC5332222 DOI: 10.1021/jacs.6b02954] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Methods to monitor and manipulate the immune system are of enormous clinical interest. For example, the development of vaccines represents one of the earliest and greatest accomplishments of the biomedical research enterprise. More recently, drugs capable of "reawakening" the immune system to cancer have generated enormous excitement. But, much remains to be done. All drugs available today that manipulate the immune system cannot distinguish between "good" and "bad" immune responses and thus drive general and systemic immune suppression or activation. Indeed, with the notable exception of vaccines, our ability to monitor and manipulate antigen-specific immune responses is in its infancy. Achieving this finer level of control would be highly desirable. For example, it might allow the pharmacological editing of pathogenic immune responses without restricting the ability of the immune system to defend against infection. On the diagnostic side, a method to comprehensively monitor the circulating, antigen-specific antibody population could provide a treasure trove of clinically useful biomarkers, since many diseases expose the immune system to characteristic molecules that are deemed foreign and elicit the production of antibodies against them. This Perspective will discuss the state-of-the-art of this area with a focus on what we consider seminal opportunities for the chemistry community to contribute to this important field.
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Affiliation(s)
- Todd M. Doran
- Departments of Chemistry & Cancer Biology, The Scripps Research
Institute, 130 Scripps Way, Jupiter, FL 33458
| | - Mohosin Sarkar
- Departments of Chemistry & Cancer Biology, The Scripps Research
Institute, 130 Scripps Way, Jupiter, FL 33458
| | - Thomas Kodadek
- Departments of Chemistry & Cancer Biology, The Scripps Research
Institute, 130 Scripps Way, Jupiter, FL 33458
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Kivity S, Shoenfeld Y, Arango MT, Cahill DJ, O'Kane SL, Zusev M, Slutsky I, Harel-Meir M, Chapman J, Matthias T, Blank M. Anti-ribosomal-phosphoprotein autoantibodies penetrate to neuronal cells via neuronal growth associated protein, affecting neuronal cells in vitro. Rheumatology (Oxford) 2016; 60:kew027. [PMID: 27155204 DOI: 10.1093/rheumatology/kew027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Indexed: 08/30/2023] Open
Abstract
OBJECTIVE Anti-ribosomal-phosphoprotein antibodies (anti-Ribos.P Abs) are detected in 10-45% of NPSLE patients. Intracerebroventricular administration of anti-ribosomal-P Abs induces depression-like behaviour in mice. We aimed to discern the mechanism by which anti-Ribos.P Abs induce behavioural changes in mice. METHODS Anti-Ribos.P Abs were exposed to human and rat neuronal cell cultures, as well as to human umbilical vein endothelial cell cultures for a control. The cellular localization of anti-Ribo.P Abs was found by an immunofluorescent technique using a confocal microscope. Identification of the target molecules was undertaken using a cDNA library. Immunohistochemistry and an inhibition assay were carried out to confirm the identity of the target molecules. Neuronal cell proliferation was measured by bromodeoxyuridine, and Akt and Erk expression by immunoblot. RESULTS Human anti-Ribos.P Abs penetrated into human neuronal cells and rat hippocampal cell cultures in vitro, but not to endothelial cells as examined. Screening a high-content human cDNA-library with anti-Ribos.P Abs identified neuronal growth-associated protein (GAP43) as a target for anti-Ribos.P Abs. Ex vivo anti-Ribos.P Abs bind to mouse brain sections of hippocampus, dentate and amygdala. Anti-Ribos.P Abs brain-binding was prevented by GAP43 protein. Interestingly, GAP43 inhibited in a dose-dependent manner the anti-Ribos.P Abs binding to recombinant-ribosomal-P0, indicating mimicry between the ribosomal-P0 protein and GAP43. Furthermore, anti-Ribos.P Abs reduced neuronal cell proliferation activity in vitro (P < 0.001), whereas GAP43 decreased this inhibitory activity by a factor of 7.6. The last was related to Akt and Erk dephosphorylation. CONCLUSION Anti-Ribos.P Abs penetrate neuronal cells in vitro by targeting GAP43. Anti -Ribos.P Abs inhibit neuronal-cell proliferation via inhibition of Akt and Erk. Our data contribute to deciphering the mechanism for anti-Ribos.P Abs' pathogenic activity in NPSLE.
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Affiliation(s)
- Shaye Kivity
- The Zabludowicz Center for Autoimmune Diseases, affiliated to Sackler Faculty of Medicine, Tel-Aviv University, Israel
| | - Yehuda Shoenfeld
- The Zabludowicz Center for Autoimmune Diseases, affiliated to Sackler Faculty of Medicine, Tel-Aviv University, Israel
| | - Maria-Teresa Arango
- The Zabludowicz Center for Autoimmune Diseases, affiliated to Sackler Faculty of Medicine, Tel-Aviv University, Israel Doctoral Program in Biomedical Sciences, Universidad del Rosario, Bogota, Colombia
| | - Dolores J Cahill
- School of Medicine and Medical Sciences, Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Belfield, Ireland
| | - Sara Louise O'Kane
- School of Medicine and Medical Sciences, Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Belfield, Ireland
| | - Margalit Zusev
- The Zabludowicz Center for Autoimmune Diseases, affiliated to Sackler Faculty of Medicine, Tel-Aviv University, Israel
| | - Inna Slutsky
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv
| | - Michal Harel-Meir
- The Zabludowicz Center for Autoimmune Diseases, affiliated to Sackler Faculty of Medicine, Tel-Aviv University, Israel
| | - Joab Chapman
- Department of Neurology, Sagol Neuroscience Center, Sheba Medical Center, Tel-Hashomer, Israel
| | | | - Miri Blank
- The Zabludowicz Center for Autoimmune Diseases, affiliated to Sackler Faculty of Medicine, Tel-Aviv University, Israel
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Abstract
Autoantibodies are a key component for the diagnosis, prognosis and monitoring of various diseases. In order to discover novel autoantibody targets, highly multiplexed assays based on antigen arrays hold a great potential and provide possibilities to analyze hundreds of body fluid samples for their reactivity pattern against thousands of antigens in parallel. Here, we provide an overview of the available technologies for producing antigen arrays, highlight some of the technical and methodological considerations and discuss their applications as discovery tools. Together with recent studies utilizing antigen arrays, we give an overview on how the different types of antigen arrays have and will continue to deliver novel insights into autoimmune diseases among several others.
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12
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Shah P, Hsiao FSH, Ho YH, Chen CS. The proteome targets of intracellular targeting antimicrobial peptides. Proteomics 2016; 16:1225-37. [PMID: 26648572 DOI: 10.1002/pmic.201500380] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 10/30/2015] [Accepted: 12/03/2015] [Indexed: 01/28/2023]
Abstract
Antimicrobial peptides have been considered well-deserving candidates to fight the battle against microorganisms due to their broad-spectrum antimicrobial activities. Several studies have suggested that membrane disruption is the basic mechanism of AMPs that leads to killing or inhibiting microorganisms. Also, AMPs have been reported to interact with macromolecules inside the microbial cells such as nucleic acids (DNA/RNA), protein synthesis, essential enzymes, membrane septum formation and cell wall synthesis. Proteins are associated with many intracellular mechanisms of cells, thus protein targets may be specifically involved in mechanisms of action of AMPs. AMPs like pyrrhocoricin, drosocin, apidecin and Bac 7 are documented to have protein targets, DnaK and GroEL. Moreover, the intracellular targeting AMPs are reported to influence more than one protein targets inside the cell, suggesting for the multiple modes of actions. This complex mechanism of intracellular targeting AMPs makes them more difficult for the development of resistance. Herein, we have summarized the current status of AMPs in terms of their mode of actions, entry to cytoplasm and inhibition of macromolecules. To reveal the mechanism of action, we have focused on AMPs with intracellular protein targets. We have also included the use of high-throughput proteome microarray to determine the unidentified AMP protein targets in this review.
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Affiliation(s)
- Pramod Shah
- Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli, Taiwan.,Department of Biomedical Science and Engineering, National Central University, Jhongli, Taiwan
| | - Felix Shih-Hsiang Hsiao
- Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli, Taiwan.,Department of Biomedical Science and Engineering, National Central University, Jhongli, Taiwan
| | - Yu-Hsuan Ho
- Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli, Taiwan.,Department of Biomedical Science and Engineering, National Central University, Jhongli, Taiwan
| | - Chien-Sheng Chen
- Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli, Taiwan.,Department of Biomedical Science and Engineering, National Central University, Jhongli, Taiwan
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13
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Doran TM, Gao Y, Simanski S, McEnaney P, Kodadek T. High affinity binding of conformationally constrained synthetic oligomers to an antigen-specific antibody: Discovery of a diagnostically useful synthetic ligand for murine Type 1 diabetes autoantibodies. Bioorg Med Chem Lett 2015; 25:4910-4917. [PMID: 26067174 PMCID: PMC4607566 DOI: 10.1016/j.bmcl.2015.05.046] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 05/18/2015] [Indexed: 10/23/2022]
Abstract
'Antigen surrogates' are synthetic, non-natural molecules that recognize the antigen-binding sites of antibodies. These molecules are of interest as replacements for native antigens as antibody 'capture agents' in ELISA-like assays of potential diagnostic utility, for example when the antibody is indicative of a disease state. Antigen surrogates for disease-related antibodies can be mined from one-bead one-compound (OBOC) libraries by first denuding the library of ligands for antibodies present in the serum of control patients or animals, followed by screening the remainder of the library against serum from individuals with a particular disease of interest. Most of the work in this area has been done with peptoids (oligomers of N-alkylated glycine), which provide antibody ligands with only modest affinity and selectivity. Here, we explore the hypothesis that this is due to the 'floppiness' of the peptoid backbone by creating libraries of peptoid-like molecules that have conformation-restricting structural elements inserted into their backbones. Indeed, we show here that these libraries can provide high affinity and selectivity antigen surrogates and that this much-improved binding is completely dependent on conformational restriction of the oligomer chain.
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Affiliation(s)
- Todd M Doran
- The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Yu Gao
- The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Scott Simanski
- The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Patrick McEnaney
- The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Thomas Kodadek
- The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, United States.
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14
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Liu S, Zhang H, Dai J, Hu S, Pino I, Eichinger DJ, Lyu H, Zhu H. Characterization of monoclonal antibody's binding kinetics using oblique-incidence reflectivity difference approach. MAbs 2015; 7:110-9. [PMID: 25530170 PMCID: PMC4622085 DOI: 10.4161/19420862.2014.985919] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Monoclonal antibodies (mAbs) against human proteins are the primary protein capture reagents for basic research, diagnosis, and molecular therapeutics. The 2 most important attributes of mAbs used in all of these applications are their specificity and avidity. While specificity of a mAb raised against a human protein can be readily defined based on its binding profile on a human proteome microarray, it has been a challenge to determine avidity values for mAbs in a high-throughput and cost-effective fashion. To undertake this challenge, we employed the oblique-incidence reflectivity difference (OIRD) platform to characterize mAbs in a protein microarray format. We first systematically determined the Kon and Koff values of 50 mAbs measured with the OIRD method and deduced the avidity values. Second, we established a multiplexed approach that simultaneously measured avidity values of a mixture of 9 mono-specific mAbs that do not cross-react to the antigens. Third, we demonstrated that avidity values of a group of mAbs could be sequentially determined using a flow-cell device. Finally, we implemented a sequential competition assay that allowed us to bin multiple mAbs that recognize the same antigens. Our study demonstrated that OIRD offers a high-throughput and cost-effective platform for characterization of the binding kinetics of mAbs.
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Affiliation(s)
- Shuang Liu
- a Institute of Physics; Chinese Academy of Sciences ; Beijing , China
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15
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Hu B, Niu X, Cheng L, Yang LN, Li Q, Wang Y, Tao SC, Zhou SM. Discovering cancer biomarkers from clinical samples by protein microarrays. Proteomics Clin Appl 2015; 9:98-110. [PMID: 25523829 DOI: 10.1002/prca.201400094] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 11/26/2014] [Accepted: 12/15/2014] [Indexed: 12/25/2022]
Abstract
Cancer biomarkers are of potential use in early cancer diagnosis, anticancer therapy development, and monitoring the responses to treatments. Protein-based cancer biomarkers are major forms in use, as they are much easier to be monitored in body fluids or tissues. For cancer biomarker discovery, high-throughput techniques such as protein microarrays hold great promises, because they are capable of global unbiased monitoring but with a miniaturized format. In doing so, novel and cancer type specific biomarkers can be systematically discovered at an affordable cost. In this review, we give a relatively complete picture on protein microarrays applied to clinical samples for cancer biomarker discovery, and conclude this review with the future perspectives.
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Affiliation(s)
- Bin Hu
- Institute for Microsurgery of Limbs, Shanghai Sixth Hospital, Shanghai Jiao Tong University, Shanghai, China
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16
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Cox E, Uzoma I, Guzzo C, Jeong JS, Matunis M, Blackshaw S, Zhu H. Identification of SUMO E3 ligase-specific substrates using the HuProt human proteome microarray. Methods Mol Biol 2015; 1295:455-463. [PMID: 25820740 PMCID: PMC5882486 DOI: 10.1007/978-1-4939-2550-6_32] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The functional protein microarray is a powerful and versatile systems biology and proteomics tool that allows the rapid activity profiling of thousands of proteins in parallel. We have recently developed a human proteome array, the HuProt array, which includes ~80 % of all the full-length proteins of the human proteome. In one recent application of the HuProt array, we identified numerous SUMO E3 ligase-dependent SUMOylation substrates. For many SUMO E3 ligases, only a small number of substrates have been identified and the target specificities of these ligases therefore remain poorly defined. In this protocol, we outline a method we developed using the HuProt array to screen the human proteome to identify novel SUMO E3 ligase substrates recognized by specific E3 ligases.
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Affiliation(s)
- Eric Cox
- Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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17
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Kodadek T. Chemical tools to monitor and manipulate the adaptive immune system. CHEMISTRY & BIOLOGY 2014; 21:1066-74. [PMID: 25237855 PMCID: PMC4171709 DOI: 10.1016/j.chembiol.2014.07.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Revised: 07/14/2014] [Accepted: 07/25/2014] [Indexed: 12/20/2022]
Abstract
The ability to monitor and manipulate antigen-specific immune responses would have a major impact on several areas of biology and medicine. In this perspective, I consider pharmacological methods to do this, with a focus on the development of abiological "antigen surrogates" capable of binding to the antigen-binding sites of antibodies and B cell receptors with high affinity and selectivity. I describe the application of combinatorial library screening to identify antigen surrogates for monoclonal antibodies of therapeutic interest using chronic lymphocytic leukemia as an example. Furthermore, I discuss the use of multiplexed assays for the quantification of antigen surrogate-antibody complexes as diagnostic tools and antigen surrogate discovery via serum screening. Although antigen surrogates are a fairly new concept, I argue that they will open new avenues for both basic and clinical research and that major advances can be expected over the next few years.
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MESH Headings
- Adaptive Immunity
- Antibodies/immunology
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/therapeutic use
- Antigen-Antibody Complex/chemistry
- Antigens/chemistry
- Antigens/immunology
- Antigens/metabolism
- B-Lymphocytes/immunology
- B-Lymphocytes/metabolism
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/immunology
- Quantum Dots/chemistry
- Recombinant Proteins/biosynthesis
- Recombinant Proteins/genetics
- Recombinant Proteins/therapeutic use
- Small Molecule Libraries/chemistry
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Affiliation(s)
- Thomas Kodadek
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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18
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Kersten B, Wanker EE, Hoheisel JD, Angenendt P. Multiplex approaches in protein microarray technology. Expert Rev Proteomics 2014; 2:499-510. [PMID: 16097884 DOI: 10.1586/14789450.2.4.499] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The success of genome sequencing projects has provided the basis for systematic analysis of protein function and has led to a shift from the description of single molecules to the characterization of complex samples. Such a task would not be possible without the provision of appropriate high-throughput technologies, such as protein microarray technology. In addition, the increasing number of samples necessitates the adaptation of such technologies to a multiplex format. This review will discuss protein microarray technology in the context of multiplex analysis and highlight its current prospects and limitations.
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Affiliation(s)
- Birgit Kersten
- Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Strasse 10, D-13125 Berlin-Buch, Germany.
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19
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Quan J, Lakhanpal A, Reddy MM, Zaman S, Li QZ, German DC, Olsen NJ, Kodadek T, Karp DR. Discovery of biomarkers for systemic lupus erythematosus using a library of synthetic autoantigen surrogates. J Immunol Methods 2013; 402:23-34. [PMID: 24269750 DOI: 10.1016/j.jim.2013.11.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 11/11/2013] [Accepted: 11/12/2013] [Indexed: 12/28/2022]
Abstract
Antibodies to a wide range of self-antigens, including those directed against nucleic acids or nucleic acid-binding proteins are the essential biomarkers for diseases such as systemic lupus erythematosus (SLE). Highly complex libraries of nonamers consisting of N-substituted glycines (peptoids) were screened for compounds that bound IgG from patients with SLE and earlier, incomplete autoimmune syndromes. Peptoids were identified that could identify subjects with SLE and related syndromes with a high sensitivity (70%) and specificity (97.5%). Immobilized peptoids were used to isolate IgG from both healthy subjects and SLE patients that reacted with known RNA-binding proteins. In the case of SLE patients, the peptoid-purified IgG reacted with several autoantigens, suggesting that the peptoids are capable of interacting with multiple, structurally similar molecules. These results show that the measurement of IgG binding to peptoids can identify subjects with high levels of pathogenic autoantibodies.
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Affiliation(s)
- Jiexia Quan
- Department of Medicine, UT Southwestern Medical Center, Dallas, TX 75390, USA; The Department of Immunology, UT Southwestern Medical Center, Dallas, TX 75390, USA; The Department of Psychiatry, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Akshai Lakhanpal
- Department of Medicine, UT Southwestern Medical Center, Dallas, TX 75390, USA; The Department of Immunology, UT Southwestern Medical Center, Dallas, TX 75390, USA; The Department of Psychiatry, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - M Muralidhar Reddy
- The Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA; Department of Cancer Biology, The Scripps Research Institute, Jupiter, FL 33458, USA; Opko Health, Inc., 555 Heritage Dr., Jupiter, FL 33458, USA
| | - Sayed Zaman
- Department of Medicine, UT Southwestern Medical Center, Dallas, TX 75390, USA; The Department of Immunology, UT Southwestern Medical Center, Dallas, TX 75390, USA; The Department of Psychiatry, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Quan-Zhen Li
- Department of Medicine, UT Southwestern Medical Center, Dallas, TX 75390, USA; The Department of Immunology, UT Southwestern Medical Center, Dallas, TX 75390, USA; The Department of Psychiatry, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Dwight C German
- Department of Medicine, UT Southwestern Medical Center, Dallas, TX 75390, USA; The Department of Immunology, UT Southwestern Medical Center, Dallas, TX 75390, USA; The Department of Psychiatry, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nancy J Olsen
- The Department of Medicine, Penn State M.S. Hershey Medical Center, Hershey, PA 17033, USA
| | - Thomas Kodadek
- The Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA; Department of Cancer Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - David R Karp
- Department of Medicine, UT Southwestern Medical Center, Dallas, TX 75390, USA; The Department of Immunology, UT Southwestern Medical Center, Dallas, TX 75390, USA; The Department of Psychiatry, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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20
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A new type of protein chip to detect hepatocellular carcinoma-related autoimmune antibodies in the sera of hepatitis C virus-positive patients. Proteome Sci 2013; 11:33. [PMID: 23866785 PMCID: PMC3750938 DOI: 10.1186/1477-5956-11-33] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 07/14/2013] [Indexed: 02/07/2023] Open
Abstract
Background We report here a new type of protein chip to detect antibodies in sera. This chip method was used to a prototype created to detect hepatocellular carcinoma (HCC) -related autoantibodies in the sera of hepatitis C virus (HCV) infected individuals. Results Five cysteine-tagged (Cys-tag) and green fluorescent protein (GFP)-fused recombinant heat shock protein 70 (HSP70), superoxide dismutase 2 (SOD2), and peroxiredoxin 6 (PRDX6), were spotted and immobilized on maleimide-incorporated diamond-like carbon (DLC) substrates. The antibodies in diluted sera were trapped by these proteins at each spot on the chip, and visualized by a fluorescence-conjugated anti-human IgG. The total immobilized protein level of each spot was detected with anti-GFP mouse IgG and a fluorescence-conjugated secondary anti-mouse IgG. The ratio between the two fluorescence intensities was used to quantify autoantibody levels in each serum sample. Heat treatment of the chip in a solution of denaturing and reducing agents, before serum-incubation, improved autoantibody detection. We tested serum samples from healthy individuals and HCC patients using the chips. The HSP70 autoantibodies were found at high levels in sera from HCV-positive HCC patients, but not in HCV-negative sera. Conclusion This protein chip system may have useful properties to capture a specific set of antibodies for predicting the onset of particular cancers such as HCC in HCV-infected individuals.
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21
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Systematic identification of novel SLE related autoantibodies responsible for type I IFN production in human plasmacytoid dendritic cells. Cell Immunol 2013; 284:119-28. [DOI: 10.1016/j.cellimm.2013.07.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 07/11/2013] [Accepted: 07/29/2013] [Indexed: 12/25/2022]
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22
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23
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Frese K, Eisenmann M, Ostendorp R, Brocks B, Pabst S. An automated immunoassay for early specificity profiling of antibodies. MAbs 2013; 5:279-87. [PMID: 23412646 DOI: 10.4161/mabs.23539] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Antibody-based therapeutics are of great value for the treatment of human diseases. In addition to functional activity, affinity or physico-chemical properties, antibody specificity is considered to be one of the most crucial attributes for safety and efficacy. Consequently, appropriate studies are required before entering clinical trials. High content protein arrays are widely applied to assess antibody specificity, but this commercial solution can only be applied to final therapeutic antibody candidates because such arrays are expensive and their throughput is limited. A flexible, high-throughput and economical assay that allows specificity testing of IgG or Fab molecules during early discovery is described here. The 384-well microtiter plate assay contains a comprehensive panel of 32 test proteins and uses electrochemiluminescence as readout. The Protein Panel Profiling ( 3P) was used to analyze marketed therapeutic antibodies that all showed highly specific binding profiles. Subsequently, 3P was applied to antibody candidates from early discovery and the results compared well with those obtained with a commercially available high content protein chip. Our results suggest that 3P can be applied as an additional filter for lead selection, allowing the identification of favorable antibody candidates in early discovery and thereby increasing the speed and possibility of success in drug development.
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Affiliation(s)
- Katrin Frese
- Protein Sciences Department, MorphoSys AG, Martinsried/Planegg, Germany
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24
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Zhu H, Cox E, Qian J. Functional protein microarray as molecular decathlete: a versatile player in clinical proteomics. Proteomics Clin Appl 2012; 6:548-62. [PMID: 23027439 PMCID: PMC3600421 DOI: 10.1002/prca.201200041] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 08/15/2012] [Accepted: 08/20/2012] [Indexed: 12/31/2022]
Abstract
Functional protein microarrays were developed as a high-throughput tool to overcome the limitations of DNA microarrays and to provide a versatile platform for protein functional analyses. Recent years have witnessed tremendous growth in the use of protein microarrays, particularly functional protein microarrays, to address important questions in the field of clinical proteomics. In this review, we will summarize some of the most innovative and exciting recent applications of protein microarrays in clinical proteomics, including biomarker identification, pathogen-host interactions, and cancer biology.
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Affiliation(s)
- Heng Zhu
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, MD, USA.
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25
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Schlichtiger A, Luppa PB, Neumeier D, Thaler M. Biosensor approaches for the detection of autoantibodies in human serum. ACTA ACUST UNITED AC 2012. [DOI: 10.1007/s12566-012-0028-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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26
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Complementing antibody profiles: Assessing antibody function on antigen microarrays. Immunol Lett 2012; 143:101-5. [DOI: 10.1016/j.imlet.2012.01.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Revised: 01/18/2012] [Accepted: 01/20/2012] [Indexed: 11/20/2022]
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27
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Jeong JS, Jiang L, Albino E, Marrero J, Rho HS, Hu J, Hu S, Vera C, Bayron-Poueymiroy D, Rivera-Pacheco ZA, Ramos L, Torres-Castro C, Qian J, Bonaventura J, Boeke JD, Yap WY, Pino I, Eichinger DJ, Zhu H, Blackshaw S. Rapid identification of monospecific monoclonal antibodies using a human proteome microarray. Mol Cell Proteomics 2012; 11:O111.016253. [PMID: 22307071 PMCID: PMC3433917 DOI: 10.1074/mcp.o111.016253] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
To broaden the range of tools available for proteomic research, we generated a library of 16,368 unique full-length human ORFs that are expressible as N-terminal GST-His6 fusion proteins. Following expression in yeast, these proteins were then individually purified and used to construct a human proteome microarray. To demonstrate the usefulness of this reagent, we developed a streamlined strategy for the production of monospecific monoclonal antibodies that used immunization with live human cells and microarray-based analysis of antibody specificity as its central components. We showed that microarray-based analysis of antibody specificity can be performed efficiently using a two-dimensional pooling strategy. We also demonstrated that our immunization and selection strategies result in a large fraction of monospecific monoclonal antibodies that are both immunoblot and immunoprecipitation grade. Our data indicate that the pipeline provides a robust platform for the generation of monoclonal antibodies of exceptional specificity.
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Affiliation(s)
- Jun Seop Jeong
- Department of Pharmacology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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28
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Beyer NH, Lueking A, Kowald A, Frederiksen JL, Heegaard NHH. Investigation of autoantibody profiles for cerebrospinal fluid biomarker discovery in patients with relapsing-remitting multiple sclerosis. J Neuroimmunol 2011; 242:26-32. [PMID: 22177943 DOI: 10.1016/j.jneuroim.2011.08.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Revised: 08/12/2011] [Accepted: 08/16/2011] [Indexed: 12/23/2022]
Abstract
Using the UNIarray® marker technology platform, cerebrospinal fluid immunoglobulin G reactivities of 15 controls and 17 RRMS patients against human recombinant proteins were investigated. Patient cerebrospinal fluids were oligoclonal band positive and reactivities were compared to that of sex- and age-matched controls. We hereby aimed at the characterization of autoreactivity in patients with RRMS. Differences in autoreactivities between control and RRMS samples were identified comprising autoantigens identified in this study only and previously reported autoantigens as well. A combination of the 10-15 most significant proteins may be investigated further as autoantigens for diagnostic purposes. Additional investigations may include minimizing the number of proteins used in such diagnostic tests.
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Affiliation(s)
- Natascha Helena Beyer
- Department of Clinical Biochemistry and Immunology, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen S, Denmark.
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29
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Tu YH, Ho YH, Chuang YC, Chen PC, Chen CS. Identification of lactoferricin B intracellular targets using an Escherichia coli proteome chip. PLoS One 2011; 6:e28197. [PMID: 22164243 PMCID: PMC3229523 DOI: 10.1371/journal.pone.0028197] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2011] [Accepted: 11/03/2011] [Indexed: 12/16/2022] Open
Abstract
Lactoferricin B (LfcinB) is a well-known antimicrobial peptide. Several studies have indicated that it can inhibit bacteria by affecting intracellular activities, but the intracellular targets of this antimicrobial peptide have not been identified. Therefore, we used E. coli proteome chips to identify the intracellular target proteins of LfcinB in a high-throughput manner. We probed LfcinB with E. coli proteome chips and further conducted normalization and Gene Ontology (GO) analyses. The results of the GO analyses showed that the identified proteins were associated with metabolic processes. Moreover, we validated the interactions between LfcinB and chip assay-identified proteins with fluorescence polarization (FP) assays. Sixteen proteins were identified, and an E. coli interaction database (EcID) analysis revealed that the majority of the proteins that interact with these 16 proteins affected the tricarboxylic acid (TCA) cycle. Knockout assays were conducted to further validate the FP assay results. These results showed that phosphoenolpyruvate carboxylase was a target of LfcinB, indicating that one of its mechanisms of action may be associated with pyruvate metabolism. Thus, we used pyruvate assays to conduct an in vivo validation of the relationship between LfcinB and pyruvate level in E. coli. These results showed that E. coli exposed to LfcinB had abnormal pyruvate amounts, indicating that LfcinB caused an accumulation of pyruvate. In conclusion, this study successfully revealed the intracellular targets of LfcinB using an E. coli proteome chip approach.
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Affiliation(s)
- Yu-Hsuan Tu
- Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli City, Taiwan
| | - Yu-Hsuan Ho
- Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli City, Taiwan
| | - Ying-Chih Chuang
- Department of Food Science, National Taiwan Ocean University, Keelung City, Taiwan
| | - Po-Chung Chen
- Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli City, Taiwan
| | - Chien-Sheng Chen
- Graduate Institute of Systems Biology and Bioinformatics, National Central University, Jhongli City, Taiwan
- * E-mail:
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30
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Földes-Papp Z, Baumann G. Fluorescence molecule counting for single-molecule studies in crowded environment of living cells without and with broken ergodicity. Curr Pharm Biotechnol 2011; 12:824-33. [PMID: 21446904 PMCID: PMC3195905 DOI: 10.2174/138920111795470949] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2011] [Accepted: 02/25/2011] [Indexed: 01/12/2023]
Abstract
We present a new approach to distinguish between non-ergodic and ergodic behavior. Performing ensemble averaging in a subpopulation of individual molecules leads to a mean value that can be similar to the mean value obtained in an ergodic system. The averaging is carried out by minimizing the variation between the sum of the temporal averaged mean square deviation of the simulated data with respect to the logarithmic scaling behavior of the subpopulation. For this reason, we first introduce a kind of Continuous Time Random Walks (CTRW), which we call Limited Continuous Time Random Walks (LCTRW) on fractal support. The random waiting time distributions are sampled at points which fulfill the condition N < 1, where N is the Poisson probability of finding a single molecule in the femtoliter-sized observation volume ΔV at the single-molecule level. Given a subpopulation of different single molecules of the same kind, the ratio T/ Tm between the measurement time T and the meaningful time Tm, which is the time for observing just one and the same single molecule, is the experimentally accessible quantity that allows to compare different molecule numbers in the subpopulation. In addition, the mean square displacement traveled by the molecule during the time t is determined by an upper limit of the geometric dimension of the living cell or its nucleus.
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Affiliation(s)
- Zeno Földes-Papp
- Medical University of Graz, Riesstrasse 58a/5, A-8047 Graz, Austria.
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31
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Abstract
Systems biology holds the key for understanding biological systems on a system level. It eventually holds the key for the treatment and cure of complex diseases such as cancer, diabetes, obesity, mental disorders, and many others. The '-omics' technologies, such as genomics, transcriptomics, proteomics, and metabonomics, are among the major driving forces of systems biology. Featured as high-throughput, miniaturized, and capable of parallel analysis, protein microarrays have already become an important technology platform for systems biology. In this review, we will focus on the system level or global analysis of biological systems using protein microarrays. Four major types of protein microarrays will be discussed: proteome microarrays, antibody microarrays, reverse-phase protein arrays, and lectin microarrays. We will also discuss the challenges and future directions of protein microarray technologies and their applications for systems biology. We strongly believe that protein microarrays will soon become an indispensable and invaluable tool for systems biology.
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Affiliation(s)
- Lina Yang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shujuan Guo
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yang Li
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shumin Zhou
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shengce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200240, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, China
- Correspondence address. Room 126, 800 Dongchuan Rd. Shanghai 200240, China. Tel: +86-21-34207069; Fax: +86-21-34207069; E-mail:
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Ge F, Tao S, Bi L, Zhang Z, Zhang X. Proteomics: addressing the challenges of multiple myeloma. Acta Biochim Biophys Sin (Shanghai) 2011; 43:89-95. [PMID: 21212069 DOI: 10.1093/abbs/gmq120] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Multiple myeloma (MM) is a malignancy of terminally differentiated B-lymphocytes that accounts for ~13% of all hematologic cancers. Despite a wealth of knowledge describing the molecular biology of MM as well as significant advances in therapeutics, this disease remains incurable. Since proteins govern the cellular structure and biological function, a wide selection of proteomic approaches holds great promise for increasing our understanding of this disease, such as by investigating the dynamic nature of protein expression, cellular and subcellular distribution, post-translational modifications, and interactions at both the cellular and subcellular levels. The aims of this review are to introduce the available and emerging proteomic technologies that have potential applications in the study of MM and to highlight the current status of proteomic studies of MM. To date, although there have been a limited number of proteomic studies in MM, those performed have provided valuable information with regard to MM diagnosis and therapy. The potential future application of proteomic technologies is expected to provide new avenues in MM diagnostics, individualized therapy design and therapy response surveillance for the clinician.
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Affiliation(s)
- Feng Ge
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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Reddy MM, Wilson R, Wilson J, Connell S, Gocke A, Hynan L, German D, Kodadek T. Identification of candidate IgG biomarkers for Alzheimer's disease via combinatorial library screening. Cell 2011; 144:132-42. [PMID: 21215375 PMCID: PMC3066439 DOI: 10.1016/j.cell.2010.11.054] [Citation(s) in RCA: 162] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Revised: 08/04/2010] [Accepted: 11/19/2010] [Indexed: 12/24/2022]
Abstract
The adaptive immune system is thought to be a rich source of protein biomarkers, but diagnostically useful antibodies remain unknown for a large number of diseases. This is, in part, because the antigens that trigger an immune response in many diseases remain unknown. We present here a general and unbiased approach to the identification of diagnostically useful antibodies that avoids the requirement for antigen identification. This method involves the comparative screening of combinatorial libraries of unnatural, synthetic molecules against serum samples obtained from cases and controls. Molecules that retain far more IgG antibodies from the case samples than the controls are identified and subsequently tested as capture agents for diagnostically useful antibodies. The utility of this method is demonstrated using a mouse model for multiple sclerosis and via the identification of two candidate IgG biomarkers for Alzheimer's disease.
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Affiliation(s)
- M. Muralidhar Reddy
- Opko Health Laboratories, 130 Scripps Way, Jupiter, FL 33458
- Departments of Chemistry & Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, #3A2, Jupiter, FL 33458
| | - Rosemary Wilson
- Opko Health Laboratories, 130 Scripps Way, Jupiter, FL 33458
| | - Johnnie Wilson
- Opko Health Laboratories, 130 Scripps Way, Jupiter, FL 33458
| | - Steven Connell
- Division of Translational Research, Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390
| | - Anne Gocke
- Division of Translational Research, Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390
| | - Linda Hynan
- Department of Psychiatry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390
| | - Dwight German
- Department of Psychiatry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390
| | - Thomas Kodadek
- Departments of Chemistry & Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, #3A2, Jupiter, FL 33458
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Abstract
Profiling the autoantibody (AAb) repertoire in serum has been routinely used for many years for the diagnosis of autoimmune diseases, including rheumatoid arthritis, scleroderma, and lupus. In recent years, AAb profiling of cancers has become a prominent field in oncology research. Protein arrays enable high-throughput screening of clinical samples, characterising the serum profile using low volumes of samples. This chapter describes the use of a protein array comprising 37,200 redundant proteins (containing over 10,000 non-redundant human recombinant proteins) for identification of the proteins bound by the antibodies in human sera using a test set of serum samples. The proteins identified have the potential to be candidate biomarkers. These recombinant proteins are expressed, purified, and robotically spotted on microarrays or chips to facilitate the screening of additional serum samples with the aim of identifying a candidate biomarker or panel of potential biomarkers for applications in disease diagnosis, stage, progression, or response to therapy.
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Affiliation(s)
- Sara L O'Kane
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin, Ireland
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Xu Z, Du W, Zhang P, Wang X, Ma X, Shi L, Song L. Development of a protein biochip to identify 6 monoclonal antibodies against subtypes of recombinant human interferons. Assay Drug Dev Technol 2010; 8:212-8. [PMID: 20230300 DOI: 10.1089/adt.2009.0228] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Recombinant human interferons (rhIFNs) are broadly used as effective therapeutic agents with antiviral, antitumor, and immune-modulating properties. Advances in protein biochip technology have benefited the medical community greatly, making true parallelism, miniaturization, and high throughput possible. In this study, 5 rhIFN proteins (IFN-alpha1b, IFN-alpha2a, IFN-alpha2b, IFN-beta, and IFN-gamma) were immobilized onto an N-hydroxysuccinimide (NHS)-modified gold-based biochip. The protein biochip was incubated with 6 specific mouse IgG antibodies (AK1, AK2, AK3, AK4, BK1, and CK1) against the human IFNs and then with Cy3-conjugated goat anti-mouse IgG antibody. The results showed that monoclonal antibody AK1 presented a unique binding characteristic to IFN-alpha1b. AK2 reacted in immunoassays equally with IFN-alpha2a and IFN-alpha2b. AK3 detected IFN-alpha1b, IFN-alpha2a, and IFN-alpha2b. AK4 had positive immunological responses directed to both IFN-alpha1b and IFN-alpha2b. Monoclonal antibodies BK1 and CK1 recognized epitope of IFN-beta and IFN-gamma, specifically. The assay specificity of the biochip was further confirmed by enzyme-linked immunosorbent assay (ELISA) and western blotting. Finally, 88 serum samples from patients treated with rhIFN-alpha2b were simultaneously tested on a single biochip. The result demonstrated that 6.8% (6 of 88 cases) presented positive reactions to anti-IFN-alpha2b antibodies, indicating that the patients under rhIFN-alpha2b therapy produced neutralized antibody against the IFN. The biochip format would offer a competitive alternative tool not only for facilitating characterization of IFN subtypes but also potentially for enabling clinical serum detection of corresponding antibodies directed against IFNs.
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Affiliation(s)
- Zhenshan Xu
- Anhui Academic Institute of Biology, Anhui, People's Republic of China
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36
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Williams R, Chung JY, Ylaya K, Whiteley G, Hewitt SM. Characterizations and validations of novel antibodies toward translational research. Proteomics Clin Appl 2010; 4:618-25. [PMID: 21137080 PMCID: PMC3839105 DOI: 10.1002/prca.200900186] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2009] [Revised: 02/01/2010] [Accepted: 03/02/2010] [Indexed: 01/26/2023]
Abstract
PURPOSE There is significant need for well-characterized antibodies to the spectrum of human proteins encoded by the genome. Advances in tissue-based proteomic profiling have led to the discovery of many candidate molecular biomarkers and therapeutic targets for which development of clinical assays is depending on high quality antibodies. We developed an antibody validation approach for screening of new mAbs. EXPERIMENTAL DESIGN We utilized a multi-stage approach of protein array and immunohistochemistry. In the first phase, we screened the NCI60 panel of cell lines by means of protein array and select antibodies based on concordance of mRNA expression to protein array signal. Results of this assay are used to predict antibody titer for immunohistochemistry on the NCI60 cell lines, presented as a tissue microarray. In the final stage, we created a tissue-based protein expression map by performing immunohistochemistry on a multi-tumor tissue microarray. RESULTS The success rate of this systematic antibody-screening tool was approximately 93% as measured by the results from the protein array. Data from the NCI60 protein array could be used to predict antibody titer for immunohistochemistry, improving the success rate of immunohistochemical assay development. CONCLUSIONS AND CLINICAL RELEVANCE The presented strategy of antibody validation and characterization can be provided a new tool for exploration of human proteome.
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Affiliation(s)
- Reginald Williams
- Tissue Array Research Program, Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Joon-Yong Chung
- Antibody Characterization Lab, Advanced Technology Program, SAIC-Frederick, Inc., Frederick, MD, USA
| | - Kris Ylaya
- Tissue Array Research Program, Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gordon Whiteley
- Antibody Characterization Lab, Advanced Technology Program, SAIC-Frederick, Inc., Frederick, MD, USA
| | - Stephen M. Hewitt
- Tissue Array Research Program, Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Antibody Characterization Lab, Advanced Technology Program, SAIC-Frederick, Inc., Frederick, MD, USA
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Song Q, Liu G, Hu S, Zhang Y, Tao Y, Han Y, Zeng H, Huang W, Li F, Chen P, Zhu J, Hu C, Zhang S, Li Y, Zhu H, Wu L. Novel autoimmune hepatitis-specific autoantigens identified using protein microarray technology. J Proteome Res 2010; 9:30-9. [PMID: 19545157 DOI: 10.1021/pr900131e] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Autoimmune hepatitis (AIH) is a chronic necroinflammatory disease of the liver with a poorly understood etiology. Detection of nonorgan-specific and liver-related autoantibodies using immunoserological approaches has been widely used for diagnosis and prognosis. However, unambiguous and accurate detection of the disease requires the identification and characterization of disease-specific autoantigens. In the present study, we have profiled the autoantigen repertoire of patients with AIH versus those with other liver diseases, identifying and validating three novel and highly specific biomarkers for AIH. In phase I, we fabricated a human protein chip of 5011 nonredundant proteins and used it to quickly identify 11 candidate autoantigens with relative small serum collection. In phase II, we fabricated an AIH-specific protein chip and obtained autoimmunogenic profiles of serum samples from 44 AIH patients, 50 healthy controls, and 184 additional patients suffering from hepatitis B, hepatitis C, systemic lupus erythematosus, primary Sjogren's syndrome, rheumatoid arthritis, or primary biliary cirrhosis. With this two-phase approach, we identified three new antigens, RPS20, Alba-like, and dUTPase, as highly AIH-specific biomarkers, with sensitivities of 47.5% (RPS20), 45.5% (Alba-like), and 22.7% (dUTPase). These potential biomarkers were further validated with additional AIH samples in a double-blind design. Finally, we demonstrated that these new biomarkers could be readily applied to ELISA-based assays for use in clinical diagnosis/prognosis.
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Affiliation(s)
- Qifeng Song
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101318, China
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38
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Maier RH, Maier CJ, Rid R, Hintner H, Bauer JW, Onder K. Epitope mapping of antibodies using a cell array-based polypeptide library. ACTA ACUST UNITED AC 2010; 15:418-26. [PMID: 20233905 DOI: 10.1177/1087057110363821] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The authors describe a technique for mapping the epitopes of protein antigens recognized by mono- or polyclonal antibodies. This method is based on a recombinant polypeptide library, expressed in a bacterial expression system, arrayed at high density, and tested on a membrane with automated procedures. The authors analyzed the epitope of a commercially available monoclonal antibody to vitamin D receptor (VDR). About 2300 overlapping VDR peptides were screened on a test array, and a contiguous stretch of 37 amino acids was identified as the epitope. Its authenticity was confirmed by Western blotting and an immunofluorescence competition assay on human skin tissue samples. The authors define the proposed method as a cell-based protein or peptide array that is adaptable to many applications, including epitope mapping of antibodies and autoantibodies, autoantigen detection from patient sera, whole-proteome approaches such as protein-peptide interactions, or selection of monoclonal antibodies from polyclonal sera. The advantages of this method are (a) its ease of protein array production based on well-established bacterial protein/peptide expression procedures; (b) the large number of printable colonies (as many as approximately 25,000) that can be arrayed per membrane; (c) there is no need for protein purification of recombinantly expressed proteins; (d) DNA, rather than protein, is the starting material to generate the arrays; and (e) its high-throughput and automatable format.
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Affiliation(s)
- Richard H Maier
- Department of Cell Biology, University of Salzburg, Salzburg, Austria.
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39
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O'Connell DJ, Bauer MC, O'Brien J, Johnson WM, Divizio CA, O'Kane SL, Berggård T, Merino A, Akerfeldt KS, Linse S, Cahill DJ. Integrated protein array screening and high throughput validation of 70 novel neural calmodulin-binding proteins. Mol Cell Proteomics 2010; 9:1118-32. [PMID: 20068228 DOI: 10.1074/mcp.m900324-mcp200] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Calmodulin is an essential regulator of intracellular processes in response to extracellular stimuli mediated by a rise in Ca(2+) ion concentration. To profile protein-protein interactions of calmodulin in human brain, we probed a high content human protein array with fluorophore-labeled calmodulin in the presence of Ca(2+). This protein array contains 37,200 redundant proteins, incorporating over 10,000 unique human neural proteins from a human brain cDNA library. We designed a screen to find high affinity (K(D) < or = 1 microm) binding partners of calmodulin and identified 76 human proteins from all intracellular compartments of which 72 are novel. We measured the binding kinetics of 74 targets with calmodulin using a high throughput surface plasmon resonance assay. Most of the novel calmodulin-target complexes identified have low dissociation rates (k(off) < or = 10(-3) s(-1)) and high affinity (K(D) </= 1 mum), consistent with the design of the screen. Many of the identified proteins are known to assemble in neural tissue, forming assemblies such as the spectrin scaffold and the postsynaptic density. We developed a microarray of the identified target proteins with which we can characterize the biochemistry of calmodulin for all targets in parallel. Four novel targets were verified in neural cells by co-immunoprecipitation, and four were selected for exploration of the calmodulin-binding regions. Using synthetic peptides and isothermal titration calorimetry, calmodulin binding motifs were identified in the potassium voltage-gated channel Kv6.1 (residues 474-493), calmodulin kinase-like vesicle-associated protein (residues 302-316), EF-hand domain family member A2 (residues 202-216), and phosphatidylinositol-4-phosphate 5-kinase, type I, gamma (residues 400-415).
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Affiliation(s)
- David J O'Connell
- Translational Research Centre, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Republic of Ireland
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40
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Diagnostic and prognostic biomarker discovery strategies for autoimmune disorders. J Proteomics 2009; 73:1045-60. [PMID: 19995622 DOI: 10.1016/j.jprot.2009.11.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Revised: 11/25/2009] [Accepted: 11/30/2009] [Indexed: 12/28/2022]
Abstract
Current clinical, laboratory or radiological parameters cannot accurately diagnose or predict disease outcomes in a range of autoimmune disorders. Biomarkers which can diagnose at an earlier time point, predict outcome or help guide therapeutic strategies in autoimmune diseases could improve clinical management of this broad group of debilitating disorders. Additionally, there is a growing need for a deeper understanding of multi-factorial autoimmune disorders. Proteomic platforms offering a multiplex approach are more likely to reflect the complexity of autoimmune disease processes. Findings from proteomic based studies of three distinct autoimmune diseases are presented and strategies compared. It is the authors' view that such approaches are likely to be fruitful in the movement of autoimmune disease treatment away from reactive decisions and towards a preventative stand point.
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41
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Kijanka G, Murphy D. Protein arrays as tools for serum autoantibody marker discovery in cancer. J Proteomics 2009; 72:936-44. [PMID: 19258055 DOI: 10.1016/j.jprot.2009.02.006] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2008] [Revised: 02/19/2009] [Accepted: 02/24/2009] [Indexed: 11/17/2022]
Abstract
Protein array technology has begun to play a significant role in the study of protein-protein interactions and in the identification of antigenic targets of serum autoantibodies in a variety of autoimmune disorders. More recently, this technology has been applied to the identification of autoantibody signatures in cancer. The identification of tumour-associated antigens (TAAs) recognised by the patient's immune response represents an exciting approach to identify novel diagnostic cancer biomarkers and may contribute towards a better understanding of the molecular mechanisms involved. Circulating autoantibodies have not only been used to identify TAAs as diagnostic/prognostic markers and potential therapeutic targets, they also represent excellent biomarkers for the early detection of tumours and potential markers for monitoring the efficacy of treatment. Protein array technology offers the ability to screen the humoral immune response in cancer against thousands of proteins in a high throughput technique, thus readily identifying new panels of TAAs. Such an approach should not only aid in improved diagnostics, but has already contributed to the identification of complex autoantibody signatures that may represent disease subgroups, early diagnostics and facilitated the analysis of vaccine trials.
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Affiliation(s)
- Gregor Kijanka
- Centre for Human Proteomics, Royal College of Surgeons in Ireland, Dublin 2, Ireland
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42
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Papp K, Végh P, Miklós K, Németh J, Rásky K, Péterfy F, Erdei A, Prechl J. Detection of Complement Activation on Antigen Microarrays Generates Functional Antibody Profiles and Helps Characterization of Disease-Associated Changes of the Antibody Repertoire. THE JOURNAL OF IMMUNOLOGY 2008; 181:8162-9. [DOI: 10.4049/jimmunol.181.11.8162] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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43
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Matsudaira T, Tsuzuki S, Wada A, Suwa A, Kohsaka H, Tomida M, Ito Y. Automated microfluidic assay system for autoantibodies found in autoimmune diseases using a photoimmobilized autoantigen microarray. Biotechnol Prog 2008; 24:1384-92. [PMID: 19194953 DOI: 10.1002/btpr.63] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Takahiro Matsudaira
- Nano Medical Enginering Laboratory, RIKEN (The Institute of Physical and Chemical Research), Wako, Saitama, Japan
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Chung JY, Lee SJ, Kris Y, Braunschweig T, Traicoff JL, Hewitt SM. A well-based reverse-phase protein array applicable to extracts from formalin-fixed paraffin-embedded tissue. Proteomics Clin Appl 2008; 2:1539-47. [PMID: 21136801 PMCID: PMC3777740 DOI: 10.1002/prca.200800005] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2008] [Indexed: 12/19/2022]
Abstract
Proteomic analysis of formalin-fixed paraffin-embedded (FFPE) tissue offers significant diagnostic utility but is complicated due to the high level of covalently crosslinked proteins arising from formalin fixation. To address these challenges, we developed a reliable protein extraction method for FFPE tissue, based on heat-induced antigen retrieval within a pressure cooker. The protein extraction yield from archival FFPE tissue section is approximately 90% of that recovered from frozen tissue. This method demonstrates preservation of immunoreactivity and recovery of full-length proteins by Western blotting. Additionally, we developed a well-based RP protein array platform utilizing an electrochemiluminescence detection system. Protein samples derived from FFPE tissue by means of laser capture dissection, with as few as 500 shots demonstrate measurable signal differences for different proteins. The lysates coated to the array plate, remain stable over 1 month at room temperature. Theses data suggest that this new protein-profiling platform coupled with the protein extraction method can be used for molecular profiling analysis in FFPE tissue, and contribute to the validation and development of biomarkers in clinical studies.
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Affiliation(s)
- Joon-Yong Chung
- Tissue Array Research Program, Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4605, USA
| | - Seo-Jin Lee
- Extracellular Matrix Pathology Section, Vascular Biology Faculty and Cell and Cancer Biology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ylaya Kris
- Tissue Array Research Program, Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4605, USA
| | - Till Braunschweig
- Tissue Array Research Program, Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4605, USA
- Institute of Pathology, RWTH Aachen University, Aachen, Germany
| | - June L. Traicoff
- Science Applications International Corporation, 1053 Patchel Street, Room 101, Fort Detrick, MD, 21702, USA
| | - Stephen M. Hewitt
- Tissue Array Research Program, Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892-4605, USA
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45
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Schofield DJ, Pope AR, Clementel V, Buckell J, Chapple SD, Clarke KF, Conquer JS, Crofts AM, Crowther SRE, Dyson MR, Flack G, Griffin GJ, Hooks Y, Howat WJ, Kolb-Kokocinski A, Kunze S, Martin CD, Maslen GL, Mitchell JN, O'Sullivan M, Perera RL, Roake W, Shadbolt SP, Vincent KJ, Warford A, Wilson WE, Xie J, Young JL, McCafferty J. Application of phage display to high throughput antibody generation and characterization. Genome Biol 2008; 8:R254. [PMID: 18047641 PMCID: PMC2258204 DOI: 10.1186/gb-2007-8-11-r254] [Citation(s) in RCA: 172] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2007] [Revised: 07/30/2007] [Accepted: 11/29/2007] [Indexed: 12/16/2022] Open
Abstract
A phage display library has been constructed containing over 1010 human antibodies, allowing the large-scale generation of antibodies. Over 38,000 recombinant antibodies against 292 antigens were selected, screened and sequenced, and 4,400 resultant unique clones characterized further. We have created a high quality phage display library containing over 1010 human antibodies and describe its use in the generation of antibodies on an unprecedented scale. We have selected, screened and sequenced over 38,000 recombinant antibodies to 292 antigens, yielding over 7,200 unique clones. 4,400 antibodies were characterized by specificity testing and detailed sequence analysis and the data/clones are available online. Sensitive detection was demonstrated in a bead based flow cytometry assay. Furthermore, positive staining by immunohistochemistry on tissue microarrays was found for 37% (143/381) of antibodies. Thus, we have demonstrated the potential of and illuminated the issues associated with genome-wide monoclonal antibody generation.
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46
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Feyen O, Lueking A, Kowald A, Stephan C, Meyer HE, Göbel U, Niehues T. Off-target activity of TNF-alpha inhibitors characterized by protein biochips. Anal Bioanal Chem 2008; 391:1713-20. [PMID: 18344017 DOI: 10.1007/s00216-008-1938-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2007] [Revised: 12/20/2007] [Accepted: 02/05/2008] [Indexed: 10/22/2022]
Abstract
Tumor necrosis factor-alpha inhibitors are widely and successfully used to treat rheumatic diseases. However, significant side effects have been reported. To detect the potential off-target activities of such inhibitors we characterized two therapeutic antibodies (adalimumab, infliximab) and one receptor fusion protein (etanercept) on protein biochips (UNIchip AV-400) containing a printed serial dilution of tumor necrosis factor-alpha and about 384 different human proteins. Etanercept binds to ten proteins (affinity: 20-33% of tumor necrosis factor-alpha recognition), and six of these proteins are related to ribosomal proteins. Interestingly, adalimumab binds to the same six proteins related to ribosomal proteins (affinity: 12-18%) as well as to four proteins crucially involved in ribosomal protein synthesis. Alignment of protein sequences indicates no significant sequence homology between these ten proteins bound by the biological drugs with the highest off-target activities. Taken together, our in vitro results demonstrate that a significant number of proteins are recognized by tumor necrosis factor-alpha inhibitors and are related to ribosome biogenesis.
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Affiliation(s)
- Oliver Feyen
- Department of Pediatric Oncology, Hematology and Clinical Immunology, Jeffrey Modell Immunodeficiency Center, University Children's Hospital Düsseldorf, 40225, Düsseldorf, Germany
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47
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Hamacher M, Hardt T, van Hall A, Stephan C, Marcus K, Meyer HE. Inside SMP proteomics: Six years German Human Brain Proteome Project (HBPP) – A summary. Proteomics 2008; 8:1118-28. [DOI: 10.1002/pmic.200700980] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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48
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Wilson R, Bateman JF. Cartilage proteomics: Challenges, solutions and recent advances. Proteomics Clin Appl 2008; 2:251-63. [DOI: 10.1002/prca.200780007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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49
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A proteome chip approach reveals new DNA damage recognition activities in Escherichia coli. Nat Methods 2007; 5:69-74. [PMID: 18084297 DOI: 10.1038/nmeth1148] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2007] [Accepted: 11/16/2007] [Indexed: 11/08/2022]
Abstract
Despite the fact that many genomes have been decoded, proteome chips comprising individually purified proteins have been reported only for budding yeast, mainly because of the complexity and difficulty of high-throughput protein purification. To facilitate proteomics studies in prokaryotes, we have developed a high-throughput protein purification protocol that allowed us to purify 4,256 proteins encoded by the Escherichia coli K12 strain within 10 h. The purified proteins were then spotted onto glass slides to create E. coli proteome chips. We used these chips to develop assays for identifying proteins involved in the recognition of potential base damage in DNA. By using a group of DNA probes, each containing a mismatched base pair or an abasic site, we found a small number of proteins that could recognize each type of probe with high affinity and specificity. We further evaluated two of these proteins, YbaZ and YbcN, by biochemical analyses. The assembly of libraries containing DNA probes with specific modifications and the availability of E. coli proteome chips have the potential to reveal important interactions between proteins and nucleic acids that are time-consuming and difficult to detect using other techniques.
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Pollard HB, Srivastava M, Eidelman O, Jozwik C, Rothwell SW, Mueller GP, Jacobowitz DM, Darling T, Guggino WB, Wright J, Zeitlin PL, Paweletz CP. Protein microarray platforms for clinical proteomics. Proteomics Clin Appl 2007; 1:934-52. [PMID: 21136748 DOI: 10.1002/prca.200700154] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2007] [Indexed: 11/12/2022]
Abstract
Proteomics for clinical applications is presently in a state of transition. It has become clear that the classical approaches based on 2-DE and/or MS need to be complemented by different kinds of technologies. The well-known problems include sample complexity, sensitivity, quantitation, reproducibility, and analysis time. We suggest that the new technologies for clinical proteomics can be supported by antibody-centric protein microarray platforms. These platforms presently include antibody microarrays and lysate, or reverse capture/reverse phase protein microarrays. Other forms of these arrays are in less mature developmental stages, including ORF and self assembling protein microarrays. Bioinformatic support for interpreting these arrays is becoming more available as the whole field of systems biology begins to mature. The present set of applications for these platforms is profoundly focused on certain common cancers, immunology, and cystic fibrosis. However, we predict that many more disease entities will become studied as knowledge of the power and availability of these platforms becomes more widely established. We anticipate that these platforms will eventually evolve to accommodate label-free detection technologies, human genome-scale numbers of analytes, and increases in analytic and bioinformatic speeds.
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Affiliation(s)
- Harvey B Pollard
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine, USUHS, Bethesda, MD, USA.
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