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Carlton LH, McGregor R, Moreland NJ. Human antibody profiling technologies for autoimmune disease. Immunol Res 2023; 71:516-527. [PMID: 36690876 PMCID: PMC9870766 DOI: 10.1007/s12026-023-09362-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 01/12/2023] [Indexed: 01/25/2023]
Abstract
Autoimmune diseases are caused by the break-down in self-tolerance mechanisms and can result in the generation of autoantibodies specific to human antigens. Human autoantigen profiling technologies such as solid surface arrays and display technologies are powerful high-throughput technologies utilised to discover and map novel autoantigens associated with disease. This review compares human autoantigen profiling technologies including the application of these approaches in chronic and post-infectious autoimmune disease. Each technology has advantages and limitations that should be considered when designing new projects to profile autoantibodies. Recent studies that have utilised these technologies across a range of diseases have highlighted marked heterogeneity in autoantibody specificity between individuals as a frequent feature. This individual heterogeneity suggests that epitope spreading maybe an important mechanism in the pathogenesis of autoimmune disease in general and likely contributes to inflammatory tissue damage and symptoms. Studies focused on identifying autoantibody biomarkers for diagnosis should use targeted data analysis to identify the rarer public epitopes and antigens, common between individuals. Thus, utilisation of human autoantigen profiling technology, combined with different analysis approaches, can illuminate both pathogenesis and biomarker discovery.
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Affiliation(s)
- Lauren H Carlton
- School of Medical Sciences, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.
- Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand.
| | - Reuben McGregor
- School of Medical Sciences, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
| | - Nicole J Moreland
- School of Medical Sciences, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.
- Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand.
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2
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Arve-Butler S, Mossberg A, Kahn F, Najibi SM, Berthold E, Król P, Månsson B, Kahn R. Identification of novel autoantigens as potential biomarkers in juvenile idiopathic arthritis associated uveitis. Front Pediatr 2022; 10:1091308. [PMID: 36699287 PMCID: PMC9869058 DOI: 10.3389/fped.2022.1091308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 12/16/2022] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Many children with juvenile idiopathic arthritis (JIA) have autoantibodies, targeting nuclear components (anti-nuclear antibodies, ANA). ANA in JIA is associated with uveitis, an eye inflammation which may cause permanent vision impairment if not detected and treated. However, ANA-testing is neither specific nor sensitive enough to be a clinically reliable predictor of uveitis risk, and the precise autoantigens targeted by ANA in JIA are largely unknown. If identified, specific autoantibodies highly associated with uveitis could be used as biomarkers to facilitate identification of JIA patients at risk. METHODS Antibodies from six ANA-positive, oligoarticular JIA patients, with and without uveitis, were explored by two large-scale methods: (1) screening against 42,100 peptides on an autoimmunity profiling planar array, and (2) immunoprecipitations from cell lysates with antigen identification by mass spectrometry. Three hundred thirty-five peptide antigens, selected from proteins identified in the large-scale methods and the scientific literature were investigated using a bead-based array in a cohort of 56 patients with oligoarticular- or RF-negative polyarticular JIA, eight of which were having current or previous uveitis. RESULTS In the planar array, reactivity was detected against 332 peptide antigens. The immunoprecipitations identified reactivity towards 131 proteins. Only two proteins were identified by both methods. In the bead-based array of selected peptide antigens, patients with uveitis had a generally higher autoreactivity, seen as higher median fluorescence intensity (MFI) across all antigens, compared to patients without uveitis. Reactivity towards 17 specific antigens was significantly higher in patients with uveitis compared to patients without uveitis. Hierarchical clustering revealed that patients with uveitis clustered together. CONCLUSION This study investigated autoantigens in JIA and uveitis, by combining two exploratory methods and confirmation in a targeted array. JIA patients with current or a history of uveitis had significantly higher reactivity towards 17 autoantigens and a generally higher autoreactivity compared to JIA patients without uveitis. Hierarchical clustering suggests that a combination of certain autoantibodies, rather than reactivity towards one specific antigen, is associated with uveitis. Our analysis of autoantibodies associated with uveitis in JIA could be a starting point for identification of prognostic biomarkers useful in JIA clinical care.
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Affiliation(s)
- Sabine Arve-Butler
- Department of Rheumatology, Clinical Sciences Lund, Lund University, Lund, Sweden.,Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden
| | - Anki Mossberg
- Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden.,Department of Pediatrics, Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Fredrik Kahn
- Department of Infection Medicine, Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Seyed Morteza Najibi
- Department of Rheumatology, Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Elisabet Berthold
- Department of Rheumatology, Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Petra Król
- Department of Pediatrics, Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Bengt Månsson
- Department of Rheumatology, Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Robin Kahn
- Wallenberg Center for Molecular Medicine, Lund University, Lund, Sweden.,Department of Pediatrics, Clinical Sciences Lund, Lund University, Lund, Sweden
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3
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Li S, Song G, Bai Y, Song N, Zhao J, Liu J, Hu C. Applications of Protein Microarrays in Biomarker Discovery for Autoimmune Diseases. Front Immunol 2021; 12:645632. [PMID: 34012435 PMCID: PMC8126629 DOI: 10.3389/fimmu.2021.645632] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/13/2021] [Indexed: 01/18/2023] Open
Abstract
Dysregulated autoantibodies and cytokines were deemed to provide important cues for potential illnesses, such as various carcinomas and autoimmune diseases. Increasing biotechnological approaches have been applied to screen and identify the specific alterations of these biomolecules as distinctive biomarkers in diseases, especially autoimmune diseases. As a versatile and robust platform, protein microarray technology allows researchers to easily profile dysregulated autoantibodies and cytokines associated with autoimmune diseases using various biological specimens, mainly serum samples. Here, we summarize the applications of protein microarrays in biomarker discovery for autoimmune diseases. In addition, the key issues in the process of using this approach are presented for improving future studies.
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Affiliation(s)
- Siting Li
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China.,Department of Rheumatology, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Beijing, China
| | - Guang Song
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Yina Bai
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China.,Department of Rheumatology, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Beijing, China
| | - Ning Song
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China.,Department of Rheumatology, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Beijing, China
| | - Jiuliang Zhao
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China.,Department of Rheumatology, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Beijing, China
| | - Jian Liu
- Department of Rheumatology, Aerospace Center Hospital, Aerospace, Clinical Medical College, Peking University, Beijing, China
| | - Chaojun Hu
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China.,Department of Rheumatology, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Beijing, China
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Juanes-Velasco P, Landeira-Viñuela A, Hernandez AP, Fuentes M. Systematic and Rational Design of Protein Arrays in Noncontact Printers: Pipeline and Critical Aspects. Methods Mol Biol 2021; 2344:9-29. [PMID: 34115349 DOI: 10.1007/978-1-0716-1562-1_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The systematic design and construction of customized protein microarrays are critical for the further successful screening of biological samples in biomedical research projects. In general protein microarrays are classified according to the content, detection method, and printing methodology, among others. Here, we are focused on the type of printing: contact and noncontact. Both approaches have advantages and disadvantages; however, in any of the approaches, a prior well design and systematic preparation of materials and/or instruments required for the customized antibody arrays is critical. In this chapter, the process for an antibody microarray by a noncontact printer is described in detail from the preparation of array content to the analysis, including quality control steps.
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Affiliation(s)
- Pablo Juanes-Velasco
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Avda. Universidad de Coimbra S/N, Salamanca, Spain
| | - Alicia Landeira-Viñuela
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Avda. Universidad de Coimbra S/N, Salamanca, Spain
| | - Angela-Patricia Hernandez
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Avda. Universidad de Coimbra S/N, Salamanca, Spain.
| | - Manuel Fuentes
- Department of Medicine and Cytometry General Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Avda. Universidad de Coimbra S/N, Salamanca, Spain.
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain.
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Syu GD, Dunn J, Zhu H. Developments and Applications of Functional Protein Microarrays. Mol Cell Proteomics 2020; 19:916-927. [PMID: 32303587 PMCID: PMC7261817 DOI: 10.1074/mcp.r120.001936] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/24/2020] [Indexed: 12/19/2022] Open
Abstract
Protein microarrays are crucial tools in the study of proteins in an unbiased, high-throughput manner, as they allow for characterization of up to thousands of individually purified proteins in parallel. The adaptability of this technology has enabled its use in a wide variety of applications, including the study of proteome-wide molecular interactions, analysis of post-translational modifications, identification of novel drug targets, and examination of pathogen-host interactions. In addition, the technology has also been shown to be useful in profiling antibody specificity, as well as in the discovery of novel biomarkers, especially for autoimmune diseases and cancers. In this review, we will summarize the developments that have been made in protein microarray technology in both in basic and translational research over the past decade. We will also introduce a novel membrane protein array, the GPCR-VirD array, and discuss the future directions of functional protein microarrays.
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Affiliation(s)
- Guan-Da Syu
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan 701, Taiwan R.O.C..
| | - Jessica Dunn
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; Center for High-Throughput Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; Viral Oncology Program, Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231.
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Kobayashi M, Katayama H, Fahrmann JF, Hanash SM. Development of autoantibody signatures for common cancers. Semin Immunol 2020; 47:101388. [DOI: 10.1016/j.smim.2020.101388] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/01/2020] [Indexed: 12/14/2022]
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Camacho-Encina M, Balboa-Barreiro V, Rego-Perez I, Picchi F, VanDuin J, Qiu J, Fuentes M, Oreiro N, LaBaer J, Ruiz-Romero C, Blanco FJ. Discovery of an autoantibody signature for the early diagnosis of knee osteoarthritis: data from the Osteoarthritis Initiative. Ann Rheum Dis 2019; 78:1699-1705. [PMID: 31471297 PMCID: PMC6900252 DOI: 10.1136/annrheumdis-2019-215325] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 07/23/2019] [Accepted: 08/22/2019] [Indexed: 11/27/2022]
Abstract
Objective To find autoantibodies (AAbs) in serum that could be useful to predict incidence of radiographic knee osteoarthritis (KOA). Design A Nucleic-acid Programmable Protein Arrays (NAPPA) platform was used to screen AAbs against 2125 human proteins in sera at baseline from participants free of radiographic KOA belonging to the incidence and non-exposed subcohorts of the Osteoarthritis Initiative (OAI) who developed or not, radiographic KOA during a follow-up period of 96 months. NAPPA-ELISA were performed to analyse reactivity against methionine adenosyltransferase two beta (MAT2β) and verify the results in 327 participants from the same subcohorts. The association of MAT2β-AAb levels with KOA incidence was assessed by combining several robust biostatistics analysis (logistic regression, Receiver Operating Characteristic and Kaplan-Meier curves). The proposed prognostic model was replicated in samples from the progression subcohort of the OAI. Results In the screening phase, six AAbs were found significantly different at baseline in samples from incident compared with non-incident participants. In the verification phase, high levels of MAT2β-AAb were significantly associated with the future incidence of KOA and with an earlier development of the disease. The incorporation of this AAb in a clinical model for the prognosis of incident radiographic KOA significantly improved the identification/classification of patients who will develop the disorder. The usefulness of the model to predict radiographic KOA was confirmed on a different OAI subcohort. Conclusions The measurement of AAbs against MAT2β in serum might be highly useful to improve the prediction of OA development, and also to estimate the time to incidence.
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Affiliation(s)
- María Camacho-Encina
- Grupo de Investigación de Reumatología, Unidad de Proteomica, INIBIC-Complejo Hospitalario Universitario A Coruña, SERGAS, Universidad de A Coruña, A Coruña, Spain
| | - Vanesa Balboa-Barreiro
- Grupo de Epidemiología Clínica y Bioestadística, INIBIC-Complejo Hospitalario Universitario A Coruña, SERGAS, Universidad de A Coruña, A Coruña, Spain
| | - Ignacio Rego-Perez
- Grupo de Investigacion de Reumatologia, Unidad de Genomica, INIBIC-Complexo Hospitalario Universitario de A Coruña, SERGAS, Universidad de A Coruña, A Coruña, Spain
| | - Florencia Picchi
- Grupo de Investigación de Reumatología, Unidad de Proteomica, INIBIC-Complejo Hospitalario Universitario A Coruña, SERGAS, Universidad de A Coruña, A Coruña, Spain
| | - Jennifer VanDuin
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute-Arizona State University, Tempe, Arizona, USA
| | - Ji Qiu
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute-Arizona State University, Tempe, Arizona, USA
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus. Proteomics Unit. CIBER-ONC, Cancer Research Center (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Natividad Oreiro
- Grupo de Investigacion Reumatologia, Unidad de Investigacion Clinica, INIBIC-Complejo Hospitalario Universitario A Coruña, SERGAS, Universidad de A Coruña, A Coruña, Spain
| | - Joshua LaBaer
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute-Arizona State University, Tempe, Arizona, USA
| | - Cristina Ruiz-Romero
- Grupo de Investigación de Reumatología, Unidad de Proteomica, INIBIC-Complejo Hospitalario Universitario A Coruña, SERGAS, Universidad de A Coruña, A Coruña, Spain
| | - Francisco J Blanco
- Grupo de Investigacion de Reumatologia, INIBIC-Complejo Hospitalario Universitario A Coruña, SERGAS, Departamento de Medicina, Universidad de A Coruña, A Coruña, Spain
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8
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Mahmud SA, Binstadt BA. Autoantibodies in the Pathogenesis, Diagnosis, and Prognosis of Juvenile Idiopathic Arthritis. Front Immunol 2019; 9:3168. [PMID: 30693002 PMCID: PMC6339949 DOI: 10.3389/fimmu.2018.03168] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 12/24/2018] [Indexed: 12/26/2022] Open
Abstract
Autoantibody production occurs in juvenile idiopathic arthritis (JIA) and numerous other autoimmune diseases. In some conditions, the autoantibodies are clearly pathogenic, whereas in others the roles are less defined. Here we review various autoantibodies associated with JIA, with a particular focus on antinuclear antibodies and antibodies recognizing citrullinated self-antigens. We explore potential mechanisms that lead to the development of autoantibodies and the use of autoantibody testing in diagnosis and prognosis. Finally, we compare and contrast JIA-associated autoantibodies with those found in adults with rheumatoid arthritis (RA).
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Affiliation(s)
- Shawn A Mahmud
- Division of Pediatric Rheumatology, Department of Pediatrics, and the Center for Immunology, University of Minnesota, Minneapolis, MN, United States
| | - Bryce A Binstadt
- Division of Pediatric Rheumatology, Department of Pediatrics, and the Center for Immunology, University of Minnesota, Minneapolis, MN, United States
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9
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Contreras-Llano LE, Tan C. High-throughput screening of biomolecules using cell-free gene expression systems. Synth Biol (Oxf) 2018; 3:ysy012. [PMID: 32995520 PMCID: PMC7445777 DOI: 10.1093/synbio/ysy012] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 05/31/2018] [Accepted: 06/25/2018] [Indexed: 01/13/2023] Open
Abstract
The incorporation of cell-free transcription and translation systems into high-throughput screening applications enables the in situ and on-demand expression of peptides and proteins. Coupled with modern microfluidic technology, the cell-free methods allow the screening, directed evolution and selection of desired biomolecules in minimal volumes within a short timescale. Cell-free high-throughput screening applications are classified broadly into in vitro display and on-chip technologies. In this review, we outline the development of cell-free high-throughput screening methods. We further discuss operating principles and representative applications of each screening method. The cell-free high-throughput screening methods may be advanced by the future development of new cell-free systems, miniaturization approaches, and automation technologies.
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Affiliation(s)
| | - Cheemeng Tan
- Department of Biomedical Engineering, University of California Davis, Davis, CA, USA
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10
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Abstract
INTRODUCTION High-content protein microarrays in principle enable the functional interrogation of the human proteome in a broad range of applications, including biomarker discovery, profiling of immune responses, identification of enzyme substrates, and quantifying protein-small molecule, protein-protein and protein-DNA/RNA interactions. As with other microarrays, the underlying proteomic platforms are under active technological development and a range of different protein microarrays are now commercially available. However, deciphering the differences between these platforms to identify the most suitable protein microarray for the specific research question is not always straightforward. Areas covered: This review provides an overview of the technological basis, applications and limitations of some of the most commonly used full-length, recombinant protein and protein fragment microarray platforms, including ProtoArray Human Protein Microarrays, HuProt Human Proteome Microarrays, Human Protein Atlas Protein Fragment Arrays, Nucleic Acid Programmable Arrays and Immunome Protein Arrays. Expert commentary: The choice of appropriate protein microarray platform depends on the specific biological application in hand, with both more focused, lower density and higher density arrays having distinct advantages. Full-length protein arrays offer advantages in biomarker discovery profiling applications, although care is required in ensuring that the protein production and array fabrication methodology is compatible with the required downstream functionality.
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Affiliation(s)
- Jessica G Duarte
- a Cancer Immunobiology Laboratory, Olivia Newton-John Cancer Research Institute/School of Cancer Medicine , La Trobe University , Heidelberg , Australia
| | - Jonathan M Blackburn
- b Institute of Infectious Disease and Molecular Medicine & Department of Integrative Biomedical Sciences, Faculty of Health Sciences , University of Cape Town , Observatory, South Africa
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Abstract
INTRODUCTION Cell-free protein microarrays represent a special form of protein microarray which display proteins made fresh at the time of the experiment, avoiding storage and denaturation. They have been used increasingly in basic and translational research over the past decade to study protein-protein interactions, the pathogen-host relationship, post-translational modifications, and antibody biomarkers of different human diseases. Their role in the first blood-based diagnostic test for early stage breast cancer highlights their value in managing human health. Cell-free protein microarrays will continue to evolve to become widespread tools for research and clinical management. Areas covered: We review the advantages and disadvantages of different cell-free protein arrays, with an emphasis on the methods that have been studied in the last five years. We also discuss the applications of each microarray method. Expert commentary: Given the growing roles and impact of cell-free protein microarrays in research and medicine, we discuss: 1) the current technical and practical limitations of cell-free protein microarrays; 2) the biomarker discovery and verification pipeline using protein microarrays; and 3) how cell-free protein microarrays will advance over the next five years, both in their technology and applications.
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Affiliation(s)
- Xiaobo Yu
- a State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences , Beijing Institute of Lifeomics , Beijing , China
| | - Brianne Petritis
- b The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute , Arizona State University , Tempe , AZ , USA
| | - Hu Duan
- a State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences , Beijing Institute of Lifeomics , Beijing , China
| | - Danke Xu
- c State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing , China
| | - Joshua LaBaer
- b The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute , Arizona State University , Tempe , AZ , USA
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Wang H, Demirkan G, Bian X, Wallstrom G, Barker K, Karthikeyan K, Tang Y, Pasha SF, Leighton JA, Qiu J, LaBaer J. Identification of Antibody Against SNRPB, Small Nuclear Ribonucleoprotein-Associated Proteins B and B', as an Autoantibody Marker in Crohn's Disease using an Immunoproteomics Approach. J Crohns Colitis 2017; 11:848-856. [PMID: 28204086 DOI: 10.1093/ecco-jcc/jjx019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
BACKGROUND Current non-invasive biomarkers for Crohn's disease are limited in their utility. Progress in identifying individual autoantigens and autoantibodies in Crohn's disease has been challenging due to limitations of available immunoassays. AIMS Our aim was to identify autoantibodies associated with Crohn's disease that may be useful in diagnosis and management using an innovative protein array technology, namely nucleic acid programmable protein arrays [NAPPA]. METHODS Serum samples of 96 patients with established Crohn's disease and 96 healthy controls were included and evenly split into discovery and validation sets randomly. Autoantibodies of both IgG and IgA classes were profiled against ~1900 human proteins in the discovery set on NAPPA. Autoantibodies discovered to be Crohn's disease-specific were further validated in the independent validation set by enzyme-linked immunosorbent assay. RESULTS Overall, reactivity of IgG autoantibodies was stronger than that of IgA autoantibodies; however, IgA autoantibodies showed greater differential reactivity between cases and controls. Four IgA autoantibodies against SNRPB, PRPH, PTTG1 and SNAI1 were newly identified with sensitivities above 15% at 95% specificity, among which anti-SNRPB-IgA had the highest sensitivity of 24.0%. Autoantibodies associated with specific disease subtypes were also found. CONCLUSIONS As one of the first studies to use immunoproteomics for the identification of autoantibodies in Crohn's disease, our results support the utility of NAPPA in implementing future expanded studies with better coverage of the human proteome and microbial proteomes relevant to Crohn's disease and identifying antibody markers that may have clinical impact in diagnosis and management.
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Affiliation(s)
- Haoyu Wang
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Gokhan Demirkan
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Xiaofang Bian
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Garrick Wallstrom
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Kristi Barker
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Kailash Karthikeyan
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Yanyang Tang
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Shabana F Pasha
- Division of Gastroenterology and Hepatology, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Jonathan A Leighton
- Division of Gastroenterology and Hepatology, Mayo Clinic Arizona, Scottsdale, AZ, USA
| | - Ji Qiu
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Joshua LaBaer
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
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Pantazes RJ, Reifert J, Bozekowski J, Ibsen KN, Murray JA, Daugherty PS. Identification of disease-specific motifs in the antibody specificity repertoire via next-generation sequencing. Sci Rep 2016; 6:30312. [PMID: 27481573 PMCID: PMC4969583 DOI: 10.1038/srep30312] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 07/04/2016] [Indexed: 12/12/2022] Open
Abstract
Disease-specific antibodies can serve as highly effective biomarkers but have been identified for only a relatively small number of autoimmune diseases. A method was developed to identify disease-specific binding motifs through integration of bacterial display peptide library screening, next-generation sequencing (NGS) and computational analysis. Antibody specificity repertoires were determined by identifying bound peptide library members for each specimen using cell sorting and performing NGS. A computational algorithm, termed Identifying Motifs Using Next- generation sequencing Experiments (IMUNE), was developed and applied to discover disease- and healthy control-specific motifs. IMUNE performs comprehensive pattern searches, identifies patterns statistically enriched in the disease or control groups and clusters the patterns to generate motifs. Using celiac disease sera as a discovery set, IMUNE identified a consensus motif (QPEQPF[PS]E) with high diagnostic sensitivity and specificity in a validation sera set, in addition to novel motifs. Peptide display and sequencing (Display-Seq) coupled with IMUNE analysis may thus be useful to characterize antibody repertoires and identify disease-specific antibody epitopes and biomarkers.
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Affiliation(s)
- Robert J Pantazes
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA.,Serimmune, Inc, Santa Barbara, CA 93105, USA
| | - Jack Reifert
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA.,Serimmune, Inc, Santa Barbara, CA 93105, USA
| | - Joel Bozekowski
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA
| | - Kelly N Ibsen
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA
| | - Joseph A Murray
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Patrick S Daugherty
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA.,Serimmune, Inc, Santa Barbara, CA 93105, USA
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14
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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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15
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Clement CC, Moncrieffe H, Lele A, Janow G, Becerra A, Bauli F, Saad FA, Perino G, Montagna C, Cobelli N, Hardin J, Stern LJ, Ilowite N, Porcelli SA, Santambrogio L. Autoimmune response to transthyretin in juvenile idiopathic arthritis. JCI Insight 2016; 1:85633. [PMID: 26973882 DOI: 10.1172/jci.insight.85633] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Juvenile idiopathic arthritis (JIA) is the most common pediatric rheumatological condition. Although it has been proposed that JIA has an autoimmune component, the autoantigens are still unknown. Using biochemical and proteomic approaches, we identified the molecular chaperone transthyretin (TTR) as an antigenic target for B and T cell immune responses. TTR was eluted from IgG complexes and affinity purified from 3 JIA patients, and a statistically significant increase in TTR autoantibodies was observed in a group of 43 JIA patients. Three cryptic, HLA-DR1-restricted TTR peptides, which induced CD4+ T cell expansion and IFN-γ and TNF-α production in 3 out of 17 analyzed patients, were also identified. Misfolding, aggregation and oxidation of TTR, as observed in the synovial fluid of all JIA patients, enhanced its immunogenicity in HLA-DR1 transgenic mice. Our data point to TTR as an autoantigen potentially involved in the pathogenesis of JIA and to oxidation and aggregation as a mechanism facilitating TTR autoimmunity.
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Affiliation(s)
- Cristina C Clement
- Department of Pathology, Albert Einstein College of Medicine, New York, New York, USA
| | - Halima Moncrieffe
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Aditi Lele
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Ginger Janow
- Department of Pediatric Rheumatology, Montefiore Medical Center, New York, New York, USA
| | - Aniuska Becerra
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Francesco Bauli
- Department of Pathology, Albert Einstein College of Medicine, New York, New York, USA
| | - Fawzy A Saad
- Department of Pathology, Albert Einstein College of Medicine, New York, New York, USA
| | - Giorgio Perino
- Department of Pathology, Hospital for Special Surgery, New York, New York, USA
| | - Cristina Montagna
- Department of Genetics, Albert Einstein College of Medicine, New York, New York, USA
| | - Neil Cobelli
- Department of Orthopedic Surgery, Montefiore Medical Center, New York, New York, USA
| | - John Hardin
- Department of Orthopedic Surgery, Montefiore Medical Center, New York, New York, USA
| | - Lawrence J Stern
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Norman Ilowite
- Department of Pediatric Rheumatology, Montefiore Medical Center, New York, New York, USA
| | - Steven A Porcelli
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, New York, USA
| | - Laura Santambrogio
- Department of Pathology, Albert Einstein College of Medicine, New York, New York, USA.,Department of Orthopedic Surgery, Montefiore Medical Center, New York, New York, USA.,Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, New York, USA
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16
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Araujo GR, Fujimura PT, Vaz ER, Silva TA, Rodovalho VR, Britto-Madurro AG, Madurro JM, Fonseca JE, Silva CHM, Santos PS, Mourão AF, Canhão H, Goulart LR, Gonçalves J, Ueira-Vieira C. A novel reactive epitope-based antigen targeted by serum autoantibodies in oligoarticular and polyarticular juvenile idiopathic arthritis and development of an electrochemical biosensor. Immunobiology 2016; 221:634-40. [PMID: 26806845 DOI: 10.1016/j.imbio.2016.01.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 01/12/2016] [Accepted: 01/12/2016] [Indexed: 12/17/2022]
Abstract
Currently, there are no specific markers for juvenile idiopathic arthritis (JIA) diagnosis, which is based on clinical symptoms and some blood tests for diseases' exclusion. Aiming to select new epitope-based antigens (mimotopes) that could recognize circulating autoantibodies in most JIA forms, we screened a phage displayed random peptide library against IgG antibodies purified from serum of JIA patients. ELISA assay was carried out to confirm immunoreactivity of selected peptides against sera IgG antibodies from JIA patients, healthy children and patients with other autoimmune diseases. The mimotope PRF+1 fused to phage particles was able to efficiently discriminate JIA patients from controls, and for this reason was chosen to be chemically synthesized for validation in a larger sample size. The synthetic peptide was immobilized onto bioelectrodes' surface for antibody detection by electrochemical analyses through differential pulse voltammetry. The PRF+1 synthetic peptide has efficiently discriminated JIA patients from control groups (p<0.0001) with a very good accuracy (AUC>0.84; sensitivity=61%; specificity=91%). The electrochemical platform proved to be fast, low cost and effective in detecting anti-PRF+1 antibodies from JIA patients compared to healthy controls (p=0.0049). Our study describes a novel and promising epitope-based biomarker for JIA diagnosis that can become a useful tool for screening tests, which was successfully incorporated onto an electrochemical biosensor and could be promptly used in field diagnostics.
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Affiliation(s)
- Galber R Araujo
- Laboratório de Nanobiotecnologia, Instituto de Genética e Bioquímica, Universidade Federal de Uberlândia, Av. Amazonas, Bloco 2E, sala 248, Uberlândia 38400-902, Minas Gerais, Brazil.
| | - Patricia T Fujimura
- Laboratório de Nanobiotecnologia, Instituto de Genética e Bioquímica, Universidade Federal de Uberlândia, Av. Amazonas, Bloco 2E, sala 248, Uberlândia 38400-902, Minas Gerais, Brazil
| | - Emília R Vaz
- Laboratório de Nanobiotecnologia, Instituto de Genética e Bioquímica, Universidade Federal de Uberlândia, Av. Amazonas, Bloco 2E, sala 248, Uberlândia 38400-902, Minas Gerais, Brazil
| | - Tamiris A Silva
- Laboratório de Nanobiotecnologia, Instituto de Genética e Bioquímica, Universidade Federal de Uberlândia, Av. Amazonas, Bloco 2E, sala 248, Uberlândia 38400-902, Minas Gerais, Brazil
| | - Vinícius R Rodovalho
- Laboratório de Biomateriais, Instituto de Genética e Bioquímica, Universidade Federal de Uberlândia, Av. Amazonas, Bloco 2E, Uberlândia 38400-902, Minas Gerais, Brazil
| | - Ana Graci Britto-Madurro
- Laboratório de Biomateriais, Instituto de Genética e Bioquímica, Universidade Federal de Uberlândia, Av. Amazonas, Bloco 2E, Uberlândia 38400-902, Minas Gerais, Brazil
| | - João M Madurro
- Laboratório de Filmes Poliméricos e Nanotecnologia, Instituto de Química, Universidade Federal de Uberlândia, Av. João Naves de Ávila 2121, Uberlândia 38408-100, Minas Gerais, Brazil
| | - João E Fonseca
- Unidade de Investigação em Reumatologia, Instituto de Medicina Molecular, Av. Prof. Egas Moniz, Lisboa 1649-028, Portugal
| | - Carlos H M Silva
- Unidade de Reumatologia Pediátrica, Hospital de Clínicas, Faculdade de Medicina da Universidade Federal de Uberlândia, Av. Pará 1720, Bloco 2U, Uberlândia 38400-902, Brazil
| | - Paula S Santos
- Laboratório de Nanobiotecnologia, Instituto de Genética e Bioquímica, Universidade Federal de Uberlândia, Av. Amazonas, Bloco 2E, sala 248, Uberlândia 38400-902, Minas Gerais, Brazil
| | - Ana F Mourão
- Unidade de Investigação em Reumatologia, Instituto de Medicina Molecular, Av. Prof. Egas Moniz, Lisboa 1649-028, Portugal
| | - Helena Canhão
- Unidade de Investigação em Reumatologia, Instituto de Medicina Molecular, Av. Prof. Egas Moniz, Lisboa 1649-028, Portugal
| | - Luiz R Goulart
- Laboratório de Nanobiotecnologia, Instituto de Genética e Bioquímica, Universidade Federal de Uberlândia, Av. Amazonas, Bloco 2E, sala 248, Uberlândia 38400-902, Minas Gerais, Brazil; Department of Medical Microbiology and Immunology, University of California Davis, 1 Shields Avenue, Tupper Hall, Rm. 3146, Davis, CA 95616, USA
| | - João Gonçalves
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Av. Prof. Egas Moniz, Lisboa 1649-028, Portugal
| | - Carlos Ueira-Vieira
- Laboratório de Nanobiotecnologia, Instituto de Genética e Bioquímica, Universidade Federal de Uberlândia, Av. Amazonas, Bloco 2E, sala 248, Uberlândia 38400-902, Minas Gerais, Brazil
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17
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New autoantibody detection technologies yield novel insights into autoimmune disease. Curr Opin Rheumatol 2015; 26:717-23. [PMID: 25203116 DOI: 10.1097/bor.0000000000000107] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
PURPOSE OF REVIEW The purpose of this review is to highlight recent progress in autoantibody detection technologies and describe how these methods are providing novel information and insights into autoimmune disorders. RECENT FINDINGS In recent years, alternative methods such as comprehensive phage display, fluid-phase immunoassays, and antigen microarrays have been developed for autoantigen discovery and profiling autoantibody responses. Compared with classic approaches such as Western blot and ELISA, these methods show improved diagnostic performance, the ability to measure antibody responses to multiple targets, and/or allow more quantitative analyses. Specific notable findings include uncovering previously unrecognized autoantigens, the improved classification of patient clinical phenotypes, and the discovery of pathogenic autoantibodies promoting disease. SUMMARY Advances in immunoassay technologies offer many opportunities for understanding the relationship between autoantibody detection and the myriad complex, clinical phenotypes characteristic of most autoimmune diseases. Further simplification and standardization of these technologies may allow routine integration into clinical practice with improved diagnostic and therapeutic outcomes.
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18
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Bian X, Wiktor P, Kahn P, Brunner A, Khela A, Karthikeyan K, Barker K, Yu X, Magee M, Wasserfall CH, Gibson D, Rooney ME, Qiu J, LaBaer J. Antiviral antibody profiling by high-density protein arrays. Proteomics 2015; 15:2136-45. [PMID: 25758251 PMCID: PMC4545592 DOI: 10.1002/pmic.201400612] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 02/12/2015] [Accepted: 03/07/2015] [Indexed: 12/14/2022]
Abstract
Viral infections elicit antiviral antibodies and have been associated with various chronic diseases. Detection of these antibodies can facilitate diagnosis, treatment of infection, and understanding of the mechanisms of virus-associated diseases. In this work, we assayed antiviral antibodies using a novel high-density nucleic acid programmable protein array (HD-NAPPA) platform. Individual viral proteins were expressed in situ directly from plasmids encoding proteins in an array of microscopic reaction chambers. Quality of protein display and serum response was assured by comparing intra- and inter-array correlation within or between printing batches with average correlation coefficients of 0.91 and 0.96, respectively. HD-NAPPA showed higher signal-to-background ratio compared with standard NAPPA on planar glass slides and ELISA. Antibody responses to 761 antigens from 25 different viruses were profiled among patients with juvenile idiopathic arthritis and type 1 diabetes. Common and unique antibody reactivity patterns were detected between patients and healthy controls. We believe HD-viral-NAPPA will enable the study of host-pathogen interactions at unprecedented dimensions and elucidate the role of pathogen infections in disease development.
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Affiliation(s)
- Xiaofang Bian
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Peter Wiktor
- Center for Bioelectronics and Biosensors, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Peter Kahn
- Engineering Arts LLC, Tempe, AZ, 85281, USA
| | - Al Brunner
- Engineering Arts LLC, Tempe, AZ, 85281, USA
| | - Amritpal Khela
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Kailash Karthikeyan
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Kristi Barker
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Xiaobo Yu
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Mitch Magee
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Clive H. Wasserfall
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL 32603, USA
| | - David Gibson
- Northern Ireland Centre for Stratified Medicine, Ulster University, C-TRIC, Glenshane Road, Londonderry, BT47 6SB, UK
| | - Madeleine E Rooney
- Arthritis Research Group, Centre for Infection and Immunity, Health Science Building, Queen’s University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, UK
| | - Ji Qiu
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Joshua LaBaer
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
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19
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Díez P, González-González M, Lourido L, Dégano RM, Ibarrola N, Casado-Vela J, LaBaer J, Fuentes M. NAPPA as a Real New Method for Protein Microarray Generation. MICROARRAYS 2015; 4:214-27. [PMID: 27600221 PMCID: PMC4996395 DOI: 10.3390/microarrays4020214] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 03/30/2015] [Accepted: 04/14/2015] [Indexed: 11/16/2022]
Abstract
Nucleic Acid Programmable Protein Arrays (NAPPA) have emerged as a powerful and innovative technology for the screening of biomarkers and the study of protein-protein interactions, among others possible applications. The principal advantages are the high specificity and sensitivity that this platform offers. Moreover, compared to conventional protein microarrays, NAPPA technology avoids the necessity of protein purification, which is expensive and time-consuming, by substituting expression in situ with an in vitro transcription/translation kit. In summary, NAPPA arrays have been broadly employed in different studies improving knowledge about diseases and responses to treatments. Here, we review the principal advances and applications performed using this platform during the last years.
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Affiliation(s)
- Paula Díez
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca 37007, Spain.
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca 37007, Spain.
| | - María González-González
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca 37007, Spain.
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca 37007, Spain.
| | - Lucía Lourido
- Rheumatology Division, ProteoRed/ISCIII Proteomics Group, INIBIC, Hospital Universitario de A Coruña, A Coruña 15006, Spain.
| | - Rosa M Dégano
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca 37007, Spain.
| | - Nieves Ibarrola
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca 37007, Spain.
| | - Juan Casado-Vela
- Biotechnology National Centre, Spanish National Research Council (CSIC), Madrid 28049, Spain.
| | - Joshua LaBaer
- Biodesign Institute, Arizona State University, 1001 South McAllister Avenue, Tempe, AZ 85287, USA.
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca 37007, Spain.
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca 37007, Spain.
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20
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Yu X, Decker KB, Barker K, Neunuebel MR, Saul J, Graves M, Westcott N, Hang H, LaBaer J, Qiu J, Machner MP. Host-pathogen interaction profiling using self-assembling human protein arrays. J Proteome Res 2015; 14:1920-36. [PMID: 25739981 DOI: 10.1021/pr5013015] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Host-pathogen protein interactions are fundamental to every microbial infection, yet their identification has remained challenging due to the lack of simple detection tools that avoid abundance biases while providing an open format for experimental modifications. Here, we applied the Nucleic Acid-Programmable Protein Array and a HaloTag-Halo ligand detection system to determine the interaction network of Legionella pneumophila effectors (SidM and LidA) with 10 000 unique human proteins. We identified known targets of these L. pneumophila proteins and potentially novel interaction candidates. In addition, we applied our Click chemistry-based NAPPA platform to identify the substrates for SidM, an effector with an adenylyl transferase domain that catalyzes AMPylation (adenylylation), the covalent addition of adenosine monophosphate (AMP). We confirmed a subset of the novel SidM and LidA targets in independent in vitro pull-down and in vivo cell-based assays, and provided further insight into how these effectors may discriminate between different host Rab GTPases. Our method circumvents the purification of thousands of human and pathogen proteins, and does not require antibodies against or prelabeling of query proteins. This system is amenable to high-throughput analysis of effectors from a wide variety of human pathogens that may bind to and/or post-translationally modify targets within the human proteome.
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Affiliation(s)
- Xiaobo Yu
- †Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Kimberly B Decker
- ‡Unit on Microbial Pathogenesis, Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Kristi Barker
- †Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - M Ramona Neunuebel
- ‡Unit on Microbial Pathogenesis, Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Justin Saul
- †Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Morgan Graves
- †Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Nathan Westcott
- §The Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, New York 10065, United States
| | - Howard Hang
- §The Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York, New York 10065, United States
| | - Joshua LaBaer
- †Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Ji Qiu
- †Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Matthias P Machner
- ‡Unit on Microbial Pathogenesis, Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
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21
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Wiktor P, Brunner A, Kahn P, Qiu J, Magee M, Bian X, Karthikeyan K, LaBaer J. Microreactor array device. Sci Rep 2015; 5:8736. [PMID: 25736721 PMCID: PMC4348619 DOI: 10.1038/srep08736] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 01/28/2015] [Indexed: 11/22/2022] Open
Abstract
We report a device to fill an array of small chemical reaction chambers (microreactors) with reagent and then seal them using pressurized viscous liquid acting through a flexible membrane. The device enables multiple, independent chemical reactions involving free floating intermediate molecules without interference from neighboring reactions or external environments. The device is validated by protein expressed in situ directly from DNA in a microarray of ~10,000 spots with no diffusion during three hours incubation. Using the device to probe for an autoantibody cancer biomarker in blood serum sample gave five times higher signal to background ratio compared to standard protein microarray expressed on a flat microscope slide. Physical design principles to effectively fill the array of microreactors with reagent and experimental results of alternate methods for sealing the microreactors are presented.
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Affiliation(s)
- Peter Wiktor
- 1] Engineering Arts LLC, Tempe, Arizona, U.S.A [2] The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, U.S.A
| | - Al Brunner
- Engineering Arts LLC, Tempe, Arizona, U.S.A
| | - Peter Kahn
- Engineering Arts LLC, Tempe, Arizona, U.S.A
| | - Ji Qiu
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, U.S.A
| | - Mitch Magee
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, U.S.A
| | - Xiaofang Bian
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, U.S.A
| | - Kailash Karthikeyan
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, U.S.A
| | - Joshua LaBaer
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona, U.S.A
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22
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Utility of Autoantibodies as Biomarkers for Diagnosis and Staging of Neurodegenerative Diseases. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2015; 122:1-51. [DOI: 10.1016/bs.irn.2015.05.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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23
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Kilb N, Burger J, Roth G. Protein microarray generation by in situ protein expression from template DNA. Eng Life Sci 2014. [DOI: 10.1002/elsc.201300052] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Normann Kilb
- Laboratory for Microarray Copying, Centre for Biological Systems Analysis (ZBSA) University of Freiburg Freiburg Germany
| | - Jürgen Burger
- Laboratory for Microarray Copying, Centre for Biological Systems Analysis (ZBSA) University of Freiburg Freiburg Germany
- Laboratory for MEMS Applications, Department of Microsystems Engineering—IMTEK University of Freiburg Freiburg Germany
| | - Günter Roth
- Laboratory for Microarray Copying, Centre for Biological Systems Analysis (ZBSA) University of Freiburg Freiburg Germany
- BIOSS—Centre for Biological Signalling Studies University of Freiburg Freiburg Germany
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24
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Yu X, Bian X, Throop A, Song L, Moral LD, Park J, Seiler C, Fiacco M, Steel J, Hunter P, Saul J, Wang J, Qiu J, Pipas JM, LaBaer J. Exploration of panviral proteome: high-throughput cloning and functional implications in virus-host interactions. Am J Cancer Res 2014; 4:808-22. [PMID: 24955142 PMCID: PMC4063979 DOI: 10.7150/thno.8255] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Accepted: 04/27/2014] [Indexed: 12/24/2022] Open
Abstract
Throughout the long history of virus-host co-evolution, viruses have developed delicate strategies to facilitate their invasion and replication of their genome, while silencing the host immune responses through various mechanisms. The systematic characterization of viral protein-host interactions would yield invaluable information in the understanding of viral invasion/evasion, diagnosis and therapeutic treatment of a viral infection, and mechanisms of host biology. With more than 2,000 viral genomes sequenced, only a small percent of them are well investigated. The access of these viral open reading frames (ORFs) in a flexible cloning format would greatly facilitate both in vitro and in vivo virus-host interaction studies. However, the overall progress of viral ORF cloning has been slow. To facilitate viral studies, we are releasing the initiation of our panviral proteome collection of 2,035 ORF clones from 830 viral genes in the Gateway® recombinational cloning system. Here, we demonstrate several uses of our viral collection including highly efficient production of viral proteins using human cell-free expression system in vitro, global identification of host targets for rubella virus using Nucleic Acid Programmable Protein Arrays (NAPPA) containing 10,000 unique human proteins, and detection of host serological responses using micro-fluidic multiplexed immunoassays. The studies presented here begin to elucidate host-viral protein interactions with our systemic utilization of viral ORFs, high-throughput cloning, and proteomic technologies. These valuable plasmid resources will be available to the research community to enable continued viral functional studies.
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25
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Bragazzi NL, Pechkova E, Nicolini C. Proteomics and Proteogenomics Approaches for Oral Diseases. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 95:125-62. [DOI: 10.1016/b978-0-12-800453-1.00004-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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26
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Miersch S, Bian X, Wallstrom G, Sibani S, Logvinenko T, Wasserfall CH, Schatz D, Atkinson M, Qiu J, LaBaer J. Serological autoantibody profiling of type 1 diabetes by protein arrays. J Proteomics 2013; 94:486-96. [PMID: 24148850 DOI: 10.1016/j.jprot.2013.10.018] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 09/04/2013] [Accepted: 10/01/2013] [Indexed: 12/30/2022]
Abstract
The need for biomarkers that illuminate the pathophysiology of type 1 diabetes (T1D), enhance early diagnosis and provide additional avenues for therapeutic intervention is well recognized in the scientific community. We conducted a proteome-scale, two-stage serological AAb screening followed by an independent validation study. In the first stage, the immunoreactivity was compared between T1D cases and healthy controls against ~6000 human proteins using the nucleic acid programmable protein array (NAPPA). Genes identified with higher signal intensities in patients were challenged with a larger sample set during the second stage. Statistical analysis revealed 26 novel autoantigens and a known T1D-associated autoantigen. During validation, we verified the presence of AAbs to dual specificity tyrosine-phosphorylation-regulated kinase 2 (DYRK2) using the Luciferase ImmunoPrecipitation System (LIPS) assay (36% sensitivity, 98% specificity). The AUC for a combination of DYRK2A and the classical T1D AAb IA-2A was 0.90 compared to 0.72 for DYRK2A and 0.64 for IA-2A alone. This is the first systematic screening for seroreactivity against a large number of human proteins in T1D patients. We demonstrated the application of protein microarrays to identify novel autoantigens in T1D, expanded the current T1D "autoantigenome" and help fulfill the goal of searching for novel biomarker candidates for T1D. BIOLOGICAL SIGNIFICANCE Protein microarrays provide a high-throughput platform that enables the profiling of serum antibodies to a large number of protein antigens. The value of AAb biomarkers in diagnosis, prognosis and treatment is well recognized in autoimmune diseases including T1D. We performed a systematic screening for new T1D-associated autoantigens by adapting the innovative protein array platform NAPPA. We believe that the discovery in this study will add information on candidate autoantigens that could potentially improve the diagnosis and help uncover the pathophysiology of T1D. The successful use of NAPPA for T1D AAb profiling will open the window for larger studies including more human antigen genes and other autoimmune diseases.
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Affiliation(s)
- Shane Miersch
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
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Wingren C. Novel type of protein chip for multiplex detection of autoantibodies. Expert Rev Proteomics 2013; 10:417-20. [PMID: 24088012 DOI: 10.1586/14789450.2013.842900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Evaluation of: Akada J, Kamei S, Ito A et al. A new type of protein chip to detect hepatocellular carcinoma-related autoimmune antibodies in the sera of hepatitis C virus-positive patients. Proteome Sci. 11(1), 33 (2013). Unlocking the proteome and delivering biomarkers to the clinic will be critical for early and improved diagnosis and prognosis. Conventional protein microarrays have evolved as a promising proteomic technology with great potential for protein expression profiling in health and disease. In this study, Akada et al. explore a new type of protein chip, interfaced with a dual-color fluorescence-based read-out, for screening of autoantibodies in serum. Uniquely, the recombinant antigens were microarray adapted by molecular design to contain a five-cysteine tag for immobilization and green fluorescent protein for detection (color 1). The engineered antigens were immobilized on in-house-designed maleimide-incorporated diamond-like carbon substrates and subsequently heat treated in a solution of denaturing and reducing agents before any specifically bound serum autoantibodies were detected (color 2). The authors used a 4-plex array targeting hepatocellular carcinoma-related autoantibodies in the sera of hepatitis C virus-positive patients as model system to demonstrate proof-of-concept.
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Affiliation(s)
- Christer Wingren
- Department of Immunotechnology, Lund University, Medicon Village, SE-22381 Lund, Sweden
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28
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Ayoglu B, Häggmark A, Khademi M, Olsson T, Uhlén M, Schwenk JM, Nilsson P. Autoantibody profiling in multiple sclerosis using arrays of human protein fragments. Mol Cell Proteomics 2013; 12:2657-72. [PMID: 23732997 PMCID: PMC3769337 DOI: 10.1074/mcp.m112.026757] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Profiling the autoantibody repertoire with large antigen collections is emerging as a powerful tool for the identification of biomarkers for autoimmune diseases. Here, a systematic and undirected approach was taken to screen for profiles of IgG in human plasma from 90 individuals with multiple sclerosis related diagnoses. Reactivity pattern of 11,520 protein fragments (representing ∼38% of all human protein encoding genes) were generated on planar protein microarrays built within the Human Protein Atlas. For more than 2,000 antigens IgG reactivity was observed, among which 64% were found only in single individuals. We used reactivity distributions among multiple sclerosis subgroups to select 384 antigens, which were then re-evaluated on planar microarrays, corroborated with suspension bead arrays in a larger cohort (n = 376) and confirmed for specificity in inhibition assays. Among the heterogeneous pattern within and across multiple sclerosis subtypes, differences in recognition frequencies were found for 51 antigens, which were enriched for proteins of transcriptional regulation. In conclusion, using protein fragments and complementary high-throughput protein array platforms facilitated an alternative route to discovery and verification of potentially disease-associated autoimmunity signatures, that are now proposed as additional antigens for large-scale validation studies across multiple sclerosis biobanks.
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Affiliation(s)
- Burcu Ayoglu
- SciLifeLab Stockholm, School of Biotechnology, KTH-Royal Institute of Technology, Stockholm, Sweden
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Takulapalli BR, Qiu J, Magee DM, Kahn P, Brunner A, Barker K, Means S, Miersch S, Bian X, Mendoza A, Festa F, Syal K, Park JG, LaBaer J, Wiktor P. High density diffusion-free nanowell arrays. J Proteome Res 2012; 11:4382-91. [PMID: 22742968 DOI: 10.1021/pr300467q] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Proteomics aspires to elucidate the functions of all proteins. Protein microarrays provide an important step by enabling high-throughput studies of displayed proteins. However, many functional assays of proteins include untethered intermediates or products, which could frustrate the use of planar arrays at very high densities because of diffusion to neighboring features. The nucleic acid programmable protein array (NAPPA) is a robust in situ synthesis method for producing functional proteins just-in-time, which includes steps with diffusible intermediates. We determined that diffusion of expressed proteins led to cross-binding at neighboring spots at very high densities with reduced interspot spacing. To address this limitation, we have developed an innovative platform using photolithographically etched discrete silicon nanowells and used NAPPA as a test case. This arrested protein diffusion and cross-binding. We present confined high density protein expression and display, as well as functional protein-protein interactions, in 8000 nanowell arrays. This is the highest density of individual proteins in nanovessels demonstrated on a single slide. We further present proof of principle results on ultrahigh density protein arrays capable of up to 24000 nanowells on a single slide.
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Affiliation(s)
- Bharath R Takulapalli
- Biodesign Institute, Center for Personal Diagnostics, Arizona State University, Tempe, Arizona 85287, United States
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