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Credle JJ, Gunn J, Sangkhapreecha P, Monaco DR, Zheng XA, Tsai HJ, Wilbon A, Morgenlander WR, Dong Y, Jayaraman S, Tosi L, Parekkadan B, Baer AN, Roederer M, Bloch EM, Tobian AAR, Zyskind I, Silverberg JI, Rosenberg AZ, Cox AL, Lloyd T, Mammen AL, Larman HB. Neutralizing IFNL3 Autoantibodies in Severe COVID-19 Identified Using Molecular Indexing of Proteins by Self-Assembly. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.03.02.432977. [PMID: 33688651 PMCID: PMC7941622 DOI: 10.1101/2021.03.02.432977] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Unbiased antibody profiling can identify the targets of an immune reaction. A number of likely pathogenic autoreactive antibodies have been associated with life-threatening SARS-CoV-2 infection; yet, many additional autoantibodies likely remain unknown. Here we present Molecular Indexing of Proteins by Self Assembly (MIPSA), a technique that produces ORFeome-scale libraries of proteins covalently coupled to uniquely identifying DNA barcodes for analysis by sequencing. We used MIPSA to profile circulating autoantibodies from 55 patients with severe COVID-19 against 11,076 DNA-barcoded proteins of the human ORFeome library. MIPSA identified previously known autoreactivities, and also detected undescribed neutralizing interferon lambda 3 (IFN-λ3) autoantibodies. At-risk individuals with anti- IFN-λ3 antibodies may benefit from interferon supplementation therapies, such as those currently undergoing clinical evaluation.
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Affiliation(s)
- Joel J. Credle
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine; Baltimore, MD, USA
| | - Jonathan Gunn
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine; Baltimore, MD, USA
| | - Puwanat Sangkhapreecha
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine; Baltimore, MD, USA
| | - Daniel R. Monaco
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine; Baltimore, MD, USA
| | - Xuwen Alice Zheng
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine; Baltimore, MD, USA
| | - Hung-Ji Tsai
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston; Birmingham, United Kingdom
| | - Azaan Wilbon
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine; Baltimore, MD, USA
| | - William R. Morgenlander
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine; Baltimore, MD, USA
| | - Yi Dong
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine; Baltimore, MD, USA
| | - Sahana Jayaraman
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine; Baltimore, MD, USA
| | - Lorenzo Tosi
- Department of Biomedical Engineering, Rutgers University; Piscataway, NJ, USA
| | - Biju Parekkadan
- Department of Biomedical Engineering, Rutgers University; Piscataway, NJ, USA
| | - Alan N. Baer
- Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine; Baltimore, MD, USA
| | - Mario Roederer
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH; Bethesda, MD, USA
| | - Evan M. Bloch
- Division of Transfusion Medicine, Department of Pathology, Johns Hopkins University School of Medicine; Baltimore, MD, USA
| | - Aaron A. R. Tobian
- Division of Transfusion Medicine, Department of Pathology, Johns Hopkins University School of Medicine; Baltimore, MD, USA
| | - Israel Zyskind
- Department of Pediatrics, NYU Langone Medical Center, New York, NY and Maimonides Medical Center; Brooklyn, NY, USA
| | - Jonathan I. Silverberg
- Department of Dermatology, George Washington University School of Medicine and Health Sciences; Washington, DC, USA
| | - Avi Z. Rosenberg
- Division of Transfusion Medicine, Department of Pathology, Johns Hopkins University; Baltimore, MD, USA
| | - Andrea L. Cox
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins University; Baltimore, MD, USA
| | - Tom Lloyd
- Departments of Neurology and Neuroscience, Johns Hopkins University School of Medicine; Baltimore, MD, USA
| | - Andrew L. Mammen
- Muscle Disease Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH; Bethesda, MD, USA and Departments of Neurology and Medicine, Johns Hopkins University School of Medicine; Baltimore, MD, USA
| | - H. Benjamin Larman
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine; Baltimore, MD, USA
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Kerrigan JJ, Xie Q, Ames RS, Lu Q. Production of protein complexes via co-expression. Protein Expr Purif 2010; 75:1-14. [PMID: 20692346 DOI: 10.1016/j.pep.2010.07.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Revised: 07/22/2010] [Accepted: 07/31/2010] [Indexed: 12/21/2022]
Abstract
Multi-protein complexes are involved in essentially all cellular processes. A protein's function is defined by a combination of its own properties, its interacting partners, and the stoichiometry of each. Depending on binding partners, a transcription factor can function as an activator in one instance and a repressor in another. The study of protein function or malfunction is best performed in the relevant context. While many protein complexes can be reconstituted from individual component proteins after being produced individually, many others require co-expression of their native partners in the host cells for proper folding, stability, and activity. Protein co-expression has led to the production of a variety of biological active complexes in sufficient quantities for biochemical, biophysical, structural studies, and high throughput screens. This article summarizes examples of such cases and discusses critical considerations in selecting co-expression partners, and strategies to achieve successful production of protein complexes.
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Affiliation(s)
- John J Kerrigan
- Biological Reagents & Assay Development, Platform Technology & Science, GlaxoSmithKline R&D, 1250 South Collegeville Road, Collegeville, PA 19426, USA
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Stapleton JA, Swartz JR. A cell-free microtiter plate screen for improved [FeFe] hydrogenases. PLoS One 2010; 5:e10554. [PMID: 20479937 PMCID: PMC2866662 DOI: 10.1371/journal.pone.0010554] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2010] [Accepted: 04/09/2010] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND [FeFe] hydrogenase enzymes catalyze the production and dissociation of H(2), a potential renewable fuel. Attempts to exploit these catalysts in engineered systems have been hindered by the biotechnologically inconvenient properties of the natural enzymes, including their extreme oxygen sensitivity. Directed evolution has been used to improve the characteristics of a range of natural catalysts, but has been largely unsuccessful for [FeFe] hydrogenases because of a lack of convenient screening platforms. METHODOLOGY/PRINCIPAL FINDINGS Here we describe an in vitro screening technology for oxygen-tolerant and highly active [FeFe] hydrogenases. Despite the complexity of the protocol, we demonstrate a level of reproducibility that allows moderately improved mutants to be isolated. We have used the platform to identify a mutant of the Chlamydomonas reinhardtii [FeFe] hydrogenase HydA1 with a specific activity approximately 4 times that of the wild-type enzyme. CONCLUSIONS/SIGNIFICANCE Our results demonstrate the feasibility of using the screen presented here for large-scale efforts to identify improved biocatalysts for energy applications. The system is based on our ability to activate these complex enzymes in E. coli cell extracts, which allows unhindered access to the protein maturation and assay environment.
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Affiliation(s)
- James A. Stapleton
- Department of Chemical Engineering, Stanford University, Stanford, California, United States of America
| | - James R. Swartz
- Department of Chemical Engineering, Stanford University, Stanford, California, United States of America
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
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Directed evolution of angiotensin II-inhibiting peptides using a microbead display. J Biosci Bioeng 2009; 109:411-7. [PMID: 20226387 DOI: 10.1016/j.jbiosc.2009.10.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Revised: 10/10/2009] [Accepted: 10/13/2009] [Indexed: 11/22/2022]
Abstract
Angiotensin II (ang II), an octapeptide (DRVYVHPF), can regulate blood pressure by binding specifically to its receptor, AT1. A peptide (VVIVIY) in the first transmembrane of AT1 has been found, via peptide array technology, to have an affinity for ang II. In this study, the peptide P2, which contained the VVIVIY sequence, was mutated and screened using microbead display technology that utilized emulsion PCR and cell-free protein synthesis. After one round of screening, the binding activities of collected mutants were estimated using flow cytometry and a peptide array. Two of these exhibited improved association rate constants to ang II, compared to the P2 peptide.
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