51
|
Lushova AA, Biazrova MG, Prilipov AG, Sadykova GK, Kopylov TA, Filatov AV. Next-Generation Techniques for Discovering Human Monoclonal Antibodies. Mol Biol 2017; 51:782-787. [PMID: 32214477 PMCID: PMC7088925 DOI: 10.1134/s0026893317060103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Accepted: 05/12/2017] [Indexed: 01/09/2023]
Abstract
Monoclonal antibodies have found wide applications in the treatment of cancer, as well as of autoimmune, infectious, and other diseases. Several dozen new antibodies are currently undergoing different stages of clinical trials, and some of them will soon be added to the list of immunotherapeutic drugs. Most of these antibodies have been generated using hybridoma technology or a phage display. In recent years, new methods of obtaining human monoclonal antibodies have been actively developing. These methods rely on sequencing immunoglobulin genes from B lymphocytes, as well as on the creation of antibody-secreting stable B-cell lines. The term next-generation antibody-discovery platforms has already been established in the literature to refer to these approaches. Our review focuses on describing the results obtained by these methods.
Collapse
Affiliation(s)
- A A Lushova
- 1Institute of Immunology, Federal Medical-Biological Agency of Russia, Moscow, 115478 Russia
| | - M G Biazrova
- 1Institute of Immunology, Federal Medical-Biological Agency of Russia, Moscow, 115478 Russia
| | - A G Prilipov
- 2Ivanovsky Institute of Virology, Gamaleya Scientific Research Institute of Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, 123098 Russia
| | - G K Sadykova
- 2Ivanovsky Institute of Virology, Gamaleya Scientific Research Institute of Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, 123098 Russia
| | - T A Kopylov
- 3Orekhovich Institute of Biomedical Chemistry, Moscow, 119121 Russia
| | - A V Filatov
- 1Institute of Immunology, Federal Medical-Biological Agency of Russia, Moscow, 115478 Russia
| |
Collapse
|
52
|
High-throughput sequencing of the immune repertoire in oncology: Applications for clinical diagnosis, monitoring, and immunotherapies. Cancer Lett 2017; 416:42-56. [PMID: 29247824 DOI: 10.1016/j.canlet.2017.12.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 12/11/2017] [Accepted: 12/11/2017] [Indexed: 12/21/2022]
Abstract
The diagnostic, monitoring and therapeutic options for cancers currently remain limited. These limitations represent a large threat to human health. Adaptive immunity, which is dependent on diverse repertoires of B cell receptors (BCRs) and T cell receptors (TCRs), plays a critical role in the anti-tumor immune response. Modulation and surveillance of adaptive immunity has become a powerful weapon to combat cancers. Recently, the high-throughput sequencing of immune repertoire (HTS-IR) technology, which provides a robust tool for deep sequencing repertoires of BCRs or TCRs, has been applied in the development of tumor biomarkers and immunotherapeutics for cancers. This review will first provide an overview of the advancement of HTS-IR technology at the population-cell and single-cell levels. It will then provide a current summary of the applications of HTS-IR technology in the diagnosis and monitoring of minimal residual disease (MRD), focusing on immune reconstitution after the treatment of allogeneic hematopoietic stem cell transplantation (allo-HSCT) in B/T-cell malignancies, and the precise detection of tumor-infiltrating lymphocytes (TILs) in non-B/T-cell malignancies. Finally, current advances of HTS-IR technology in cancer immunotherapeutic applications, such as therapeutic antibodies, CAR-T cell based-adoptive immunotherapies, and neoantigen-specific TCR-T cell-based adoptive immunotherapies, will be introduced.
Collapse
|
53
|
The state-of-play and future of antibody therapeutics. Adv Drug Deliv Rev 2017; 122:2-19. [PMID: 27916504 DOI: 10.1016/j.addr.2016.11.004] [Citation(s) in RCA: 208] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 11/26/2016] [Accepted: 11/28/2016] [Indexed: 12/22/2022]
Abstract
It has been over four decades since the development of monoclonal antibodies (mAbs) using a hybridoma cell line was first reported. Since then more than thirty therapeutic antibodies have been marketed, mostly as oncology, autoimmune and inflammatory therapeutics. While antibodies are very efficient, their cost-effectiveness has always been discussed owing to their high costs, accumulating to more than one billion dollars from preclinical development through to market approval. Because of this, therapeutic antibodies are inaccessible to some patients in both developed and developing countries. The growing interest in biosimilar antibodies as affordable versions of therapeutic antibodies may provide alternative treatment options as well potentially decreasing costs. As certain markets begin to capitalize on this opportunity, regulatory authorities continue to refine the requirements for demonstrating quality, efficacy and safety of biosimilar compared to originator products. In addition to biosimilars, innovations in antibody engineering are providing the opportunity to design biobetter antibodies with improved properties to maximize efficacy. Enhancing effector function, antibody drug conjugates (ADC) or targeting multiple disease pathways via multi-specific antibodies are being explored. The manufacturing process of antibodies is also moving forward with advancements relating to host cell production and purification processes. Studies into the physical and chemical degradation pathways of antibodies are contributing to the design of more stable proteins guided by computational tools. Moreover, the delivery and pharmacokinetics of antibody-based therapeutics are improving as optimized formulations are pursued through the implementation of recent innovations in the field.
Collapse
|
54
|
Chen J, Zheng Q, Hammers CM, Ellebrecht CT, Mukherjee EM, Tang HY, Lin C, Yuan H, Pan M, Langenhan J, Komorowski L, Siegel DL, Payne AS, Stanley JR. Proteomic Analysis of Pemphigus Autoantibodies Indicates a Larger, More Diverse, and More Dynamic Repertoire than Determined by B Cell Genetics. Cell Rep 2017; 18:237-247. [PMID: 28052253 DOI: 10.1016/j.celrep.2016.12.013] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 11/15/2016] [Accepted: 12/05/2016] [Indexed: 11/19/2022] Open
Abstract
In autoantibody-mediated diseases such as pemphigus, serum antibodies lead to disease. Genetic analysis of B cells has allowed characterization of antibody repertoires in such diseases but would be complemented by proteomic analysis of serum autoantibodies. Here, we show using proteomic analysis that the serum autoantibody repertoire in pemphigus is much more polyclonal than that found by genetic studies of B cells. In addition, many B cells encode pemphigus autoantibodies that are not secreted into the serum. Heavy chain variable gene usage of serum autoantibodies is not shared among patients, implying targeting of the coded proteins will not be a useful therapeutic strategy. Analysis of autoantibodies in individual patients over several years indicates that many antibody clones persist but the proportion of each changes. These studies indicate a dynamic and diverse autoantibody response not revealed by genetic studies and explain why similar overall autoantibody titers may give variable disease activity.
Collapse
Affiliation(s)
- Jing Chen
- Department of Dermatology, 1008 BRB, 421 Curie Boulevard, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Qi Zheng
- Department of Dermatology, 1008 BRB, 421 Curie Boulevard, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christoph M Hammers
- Department of Dermatology, 1008 BRB, 421 Curie Boulevard, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Christoph T Ellebrecht
- Department of Dermatology, 1008 BRB, 421 Curie Boulevard, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eric M Mukherjee
- Department of Dermatology, 1008 BRB, 421 Curie Boulevard, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hsin-Yao Tang
- Proteomics Facility, Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA
| | - Chenyan Lin
- Department of Dermatology, 1008 BRB, 421 Curie Boulevard, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Huijie Yuan
- Department of Dermatology, 1008 BRB, 421 Curie Boulevard, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Meng Pan
- Department of Dermatology, 1008 BRB, 421 Curie Boulevard, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jana Langenhan
- Institute of Experimental Immunology, Euroimmun, Seekamp 31, 23560 Lübeck, Germany
| | - Lars Komorowski
- Institute of Experimental Immunology, Euroimmun, Seekamp 31, 23560 Lübeck, Germany
| | - Don L Siegel
- Department of Pathology and Laboratory Medicine, 510 Stellar-Chance Laboratories, 422 Curie Boulevard, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Aimee S Payne
- Department of Dermatology, 1008 BRB, 421 Curie Boulevard, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John R Stanley
- Department of Dermatology, 1008 BRB, 421 Curie Boulevard, University of Pennsylvania, Philadelphia, PA 19104, USA.
| |
Collapse
|
55
|
Parola C, Neumeier D, Reddy ST. Integrating high-throughput screening and sequencing for monoclonal antibody discovery and engineering. Immunology 2017; 153:31-41. [PMID: 28898398 DOI: 10.1111/imm.12838] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 09/06/2017] [Accepted: 09/06/2017] [Indexed: 12/14/2022] Open
Abstract
Monoclonal antibody discovery and engineering is a field that has traditionally been dominated by high-throughput screening platforms (e.g. hybridomas and surface display). In recent years the emergence of high-throughput sequencing has made it possible to obtain large-scale information on antibody repertoire diversity. Additionally, it has now become more routine to perform high-throughput sequencing on antibody repertoires to also directly discover antibodies. In this review, we provide an overview of the progress in this field to date and show how high-throughput screening and sequencing are converging to deliver powerful new workflows for monoclonal antibody discovery and engineering.
Collapse
Affiliation(s)
- Cristina Parola
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,Life Science Zurich Graduate School, Systems Biology, ETH Zurich, University of Zurich, Zurich, Switzerland
| | - Daniel Neumeier
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| |
Collapse
|
56
|
Shlemov A, Bankevich S, Bzikadze A, Turchaninova MA, Safonova Y, Pevzner PA. Reconstructing Antibody Repertoires from Error-Prone Immunosequencing Reads. THE JOURNAL OF IMMUNOLOGY 2017; 199:3369-3380. [PMID: 28978691 DOI: 10.4049/jimmunol.1700485] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 08/24/2017] [Indexed: 12/16/2022]
Abstract
Transforming error-prone immunosequencing datasets into Ab repertoires is a fundamental problem in immunogenomics, and a prerequisite for studies of immune responses. Although various repertoire reconstruction algorithms were released in the last 3 y, it remains unclear how to benchmark them and how to assess the accuracy of the reconstructed repertoires. We describe an accurate IgReC algorithm for constructing Ab repertoires from high-throughput immunosequencing datasets and a new framework for assessing the quality of reconstructed repertoires. Surprisingly, Ab repertoires constructed by IgReC from barcoded immunosequencing datasets in the blind mode (without using information about unique molecular identifiers) improved upon the repertoires constructed by the state-of-the-art tools that use barcoding. This finding suggests that IgReC may alleviate the need to generate repertoires using the barcoding technology (the workhorse of current immunogenomics efforts) because our computational approach to error correction of immunosequencing data is nearly as powerful as the experimental approach based on barcoding.
Collapse
Affiliation(s)
- Alexander Shlemov
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg University, St. Petersburg, Russia 199034
| | - Sergey Bankevich
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg University, St. Petersburg, Russia 199034
| | - Andrey Bzikadze
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg University, St. Petersburg, Russia 199034
| | - Maria A Turchaninova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia 117997
| | - Yana Safonova
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg University, St. Petersburg, Russia 199034; .,Information Theory and Applications Center, University of California, San Diego, La Jolla, CA 92093; and
| | - Pavel A Pevzner
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg University, St. Petersburg, Russia 199034.,Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093
| |
Collapse
|
57
|
The road to a more effective influenza vaccine: Up to date studies and future prospects. Vaccine 2017; 35:5388-5395. [PMID: 28866292 DOI: 10.1016/j.vaccine.2017.08.034] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 08/01/2017] [Accepted: 08/04/2017] [Indexed: 12/15/2022]
Abstract
Influenza virus causes an acute respiratory infection in humans. Frequent point mutations in the influenza genome and occasional exchange of genetic segments between virus strains help the virus evade the pre-existing immunity, resulting in epidemics and pandemics. Although vaccination is the most effective intervention, mismatches between circulating viruses and vaccine strains reduce vaccine efficacy. Furthermore, current injectable vaccines induce IgG antibodies in serum (which limit progression of influenza symptoms) but not secretory IgA antibodies in the respiratory mucosa (which prevent virus infection efficiently). Therefore, numerous studies have attempted to improve influenza vaccines. The discovery of broadly neutralizing antibodies has progressed research into antigen design. Studies designed to improve vaccine efficacy by changing the vaccine administration route have also been conducted. A thorough understanding of the mechanisms underlying the action of various vaccines is essential if we are to develop a universal influenza vaccine. Therefore, evaluating the quality and quantity of antibodies induced by vaccines, which determine vaccine efficacy, is critical. However, at present vaccine evaluation relies on hemagglutination inhibition tests, which only measure the quantity of antibody produced. Antibody repertoires comprise a set of antibodies with specific genetic or molecular features that correspond to their functions. Genetically and functionally similar antibodies may be produced by multiple individuals exposed to an identical stimulus. Therefore, it may be possible to evaluate and compare multiple vaccine strategies in terms of the quality and quantity of an antibody response induced by a vaccine by examining antibody repertoires. Recent studies have used single cell expression and high-throughput immunoglobulin sequencing to provide a detailed picture of antibody responses. These novel methods may be critical for detailed characterization of antibody repertoires induced by various vaccination strategies.
Collapse
|
58
|
Lucar O, Su B, Potard V, Samri A, Autran B, Moog C, Debré P, Vieillard V. Neutralizing Antibodies Against a Specific Human Immunodeficiency Virus gp41 Epitope are Associated With Long-term Non-progressor Status. EBioMedicine 2017; 22:122-132. [PMID: 28712768 PMCID: PMC5552210 DOI: 10.1016/j.ebiom.2017.07.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 07/07/2017] [Accepted: 07/07/2017] [Indexed: 02/07/2023] Open
Abstract
Antibodies (Abs) play a central role in human immunodeficiency virus (HIV) protection due to their multiple functional inhibitory activities. W614A-3S Abs recognize a specific form of a highly conserved motif of the gp41 envelope protein and can elicit viral neutralization to protect CD4+ T cells. Here, we describe in detail the neutralizing profile of W614A-3S Abs in untreated long-term non-progressor (LTNP) HIV-infected patients. W614A-3S Abs were detected in 23.5% (16/68) of untreated LTNP patients compared with <5% (5/104) of HIV-1 progressor patients. The W614A-3S Abs had efficient neutralizing activity that inhibited transmitted founder primary viruses and exhibited Fc-mediated inhibitory functions at low concentrations in primary monocyte-derived macrophages. The neutralizing capacity of W614A-3S Abs was inversely correlated with viral load (r=-0.9013; p<0.0001), viral DNA (r=-0.7696; p=0.0005) and was associated the preservation of high CD4+ T-cell counts and T-cell responses. This study demonstrates that W614A-3S neutralizing Abs may confer a crucial advantage to LTNP patients. These results provide insights for both pathophysiological research and the development of vaccine strategies.
Collapse
Affiliation(s)
- Olivier Lucar
- Sorbonne Universités, UPMC Univ Paris 06, INSERM U1135, CNRS ERL8255, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Bin Su
- U1109 INSERM, FMTS, Université de Strasbourg, Strasbourg, France; Center for Infectious Diseases, Beijing You'an Hospital, Capital Medical University, Beijing 100069, China
| | - Valérie Potard
- Sorbonne Universités, UPMC Univ Paris 06, UMR-S 1136, Paris, France
| | - Assia Samri
- Sorbonne Universités, UPMC Univ Paris 06, INSERM U1135, CNRS ERL8255, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Brigitte Autran
- Sorbonne Universités, UPMC Univ Paris 06, INSERM U1135, CNRS ERL8255, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Christiane Moog
- U1109 INSERM, FMTS, Université de Strasbourg, Strasbourg, France
| | - Patrice Debré
- Sorbonne Universités, UPMC Univ Paris 06, INSERM U1135, CNRS ERL8255, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Vincent Vieillard
- Sorbonne Universités, UPMC Univ Paris 06, INSERM U1135, CNRS ERL8255, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Paris, France.
| |
Collapse
|
59
|
Antibody therapies for the prevention and treatment of viral infections. NPJ Vaccines 2017; 2:19. [PMID: 29263875 PMCID: PMC5627241 DOI: 10.1038/s41541-017-0019-3] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 05/08/2017] [Accepted: 05/16/2017] [Indexed: 12/18/2022] Open
Abstract
Antibodies are an important component in host immune responses to viral pathogens. Because of their unique maturation process, antibodies can evolve to be highly specific to viral antigens. Physicians and researchers have been relying on such high specificity in their quest to understand host–viral interaction and viral pathogenesis mechanisms and to find potential cures for viral infection and disease. With more than 60 recombinant monoclonal antibodies developed for human use in the last 20 years, monoclonal antibodies are now considered a viable therapeutic modality for infectious disease targets, including newly emerging viral pathogens such as Ebola representing heightened public health concerns, as well as pathogens that have long been known, such as human cytomegalovirus. Here, we summarize some recent advances in identification and characterization of monoclonal antibodies suitable as drug candidates for clinical evaluation, and review some promising candidates in the development pipeline.
Collapse
|
60
|
Díez P, Ibarrola N, Dégano RM, Lécrevisse Q, Rodriguez-Caballero A, Criado I, Nieto WG, Góngora R, González M, Almeida J, Orfao A, Fuentes M. A systematic approach for peptide characterization of B-cell receptor in chronic lymphocytic leukemia cells. Oncotarget 2017; 8:42836-42846. [PMID: 28467808 PMCID: PMC5522109 DOI: 10.18632/oncotarget.17076] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 03/22/2017] [Indexed: 01/09/2023] Open
Abstract
A wide variety of immunoglobulins (Ig) is produced by the immune system thanks to different mechanisms (V(D)J recombination, somatic hypermutation, and antigen selection). The profiling of Ig sequences (at both DNA and peptide levels) are of great relevance to developing targeted vaccines or treatments for specific diseases or infections. Thus, genomics and proteomics techniques (such as Next-Generation Sequencing (NGS) and mass spectrometry (MS)) have notably increased the knowledge in Ig sequencing and serum Ig peptide profiling in a high-throughput manner. However, the peptide characterization of membrane-bound Ig (e.g., B-cell receptors, BCR) is still a challenge mainly due to the poor recovery of mentioned Ig.Herein, we have evaluated three different sample processing methods for peptide sequencing of BCR belonging to chronic lymphocytic leukemia (CLL) B cells identifying up to 426 different peptide sequences (MS/MS data are available via ProteomeXchange with identifier PXD004466). Moreover, as a consequence of the results here obtained, recommended guidelines have been described for BCR-sequencing of B-CLL samples by MS approaches.For this purpose, an in-house algorithm has been designed and developed to compare the MS/MS results with those obtained by molecular biology in order to integrate both proteomics and genomics results and establish the steps to follow when sequencing membrane-bound Ig by MS/MS.
Collapse
MESH Headings
- Aged
- Aged, 80 and over
- Amino Acid Sequence
- Female
- Genomics/methods
- High-Throughput Nucleotide Sequencing
- Humans
- Immunoglobulin Heavy Chains/chemistry
- Immunoglobulin Heavy Chains/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/immunology
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Male
- Middle Aged
- Peptide Fragments/chemistry
- Peptide Fragments/genetics
- Proteomics/methods
- Receptors, Antigen, B-Cell/chemistry
- Receptors, Antigen, B-Cell/genetics
- Receptors, Antigen, B-Cell/metabolism
- Tandem Mass Spectrometry
- Workflow
Collapse
Affiliation(s)
- Paula Díez
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Nieves Ibarrola
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Rosa M. Dégano
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Quentin Lécrevisse
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Arancha Rodriguez-Caballero
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Ignacio Criado
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Wendy G. Nieto
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Rafael Góngora
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Marcos González
- Hematology Service, Institute of Biomedical Research of Salamanca, University Hospital of Salamanca, Cancer Research and Institute of Molecular Biology and Cellular Oncology, 37007 Salamanca, Spain
| | - Julia Almeida
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Alberto Orfao
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), 37007 Salamanca, Spain
| |
Collapse
|
61
|
Cotham VC, Horton AP, Lee J, Georgiou G, Brodbelt JS. Middle-Down 193-nm Ultraviolet Photodissociation for Unambiguous Antibody Identification and its Implications for Immunoproteomic Analysis. Anal Chem 2017; 89:6498-6504. [PMID: 28517930 DOI: 10.1021/acs.analchem.7b00564] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mass spectrometry (MS) has emerged as a powerful tool within the growing field of immunoproteomics, which aims to understand antibody-mediated immunity at the molecular-level based on the direct determination of serological antibody repertoire. To date, these methods have relied on the use of high-resolution bottom-up proteomic strategies that require effective sampling and characterization of low abundance peptides derived from the antigen-binding domains of polyclonal antibody mixtures. Herein, we describe a method that uses restricted Lys-C enzymatic digestion to increase the average mass of proteolytic IgG peptides (≥4.5 kDa) and produce peptides which uniquely derive from single antibody species. This enhances the capacity to discriminate between very similar antibodies present within polyclonal mixtures. Furthermore, our use of 193-nm ultraviolet photodissociation (UVPD) improves spectral coverage of the antibody sequence relative to conventional collision- and electron-based fragmentation methods. We apply these methods to both a monoclonal and an antibody mixture. By identifying from a database search of approximately 15 000 antibody sequences those which compose the mixture, we demonstrate the analytical potential of middle-down UVPD for MS-based serological repertoire analysis.
Collapse
Affiliation(s)
- Victoria C Cotham
- Department of Chemistry, ‡Center for Systems and Synthetic Biology, §Department of Biomedical Engineering, ∥Department of Chemical Engineering, ⊥Institute for Cellular and Molecular Biology, #Department of Molecular Biosciences, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Andrew P Horton
- Department of Chemistry, ‡Center for Systems and Synthetic Biology, §Department of Biomedical Engineering, ∥Department of Chemical Engineering, ⊥Institute for Cellular and Molecular Biology, #Department of Molecular Biosciences, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Jiwon Lee
- Department of Chemistry, ‡Center for Systems and Synthetic Biology, §Department of Biomedical Engineering, ∥Department of Chemical Engineering, ⊥Institute for Cellular and Molecular Biology, #Department of Molecular Biosciences, The University of Texas at Austin , Austin, Texas 78712, United States
| | - George Georgiou
- Department of Chemistry, ‡Center for Systems and Synthetic Biology, §Department of Biomedical Engineering, ∥Department of Chemical Engineering, ⊥Institute for Cellular and Molecular Biology, #Department of Molecular Biosciences, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, ‡Center for Systems and Synthetic Biology, §Department of Biomedical Engineering, ∥Department of Chemical Engineering, ⊥Institute for Cellular and Molecular Biology, #Department of Molecular Biosciences, The University of Texas at Austin , Austin, Texas 78712, United States
| |
Collapse
|
62
|
Ruggles KV, Krug K, Wang X, Clauser KR, Wang J, Payne SH, Fenyö D, Zhang B, Mani DR. Methods, Tools and Current Perspectives in Proteogenomics. Mol Cell Proteomics 2017; 16:959-981. [PMID: 28456751 DOI: 10.1074/mcp.mr117.000024] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Indexed: 12/20/2022] Open
Abstract
With combined technological advancements in high-throughput next-generation sequencing and deep mass spectrometry-based proteomics, proteogenomics, i.e. the integrative analysis of proteomic and genomic data, has emerged as a new research field. Early efforts in the field were focused on improving protein identification using sample-specific genomic and transcriptomic sequencing data. More recently, integrative analysis of quantitative measurements from genomic and proteomic studies have identified novel insights into gene expression regulation, cell signaling, and disease. Many methods and tools have been developed or adapted to enable an array of integrative proteogenomic approaches and in this article, we systematically classify published methods and tools into four major categories, (1) Sequence-centric proteogenomics; (2) Analysis of proteogenomic relationships; (3) Integrative modeling of proteogenomic data; and (4) Data sharing and visualization. We provide a comprehensive review of methods and available tools in each category and highlight their typical applications.
Collapse
Affiliation(s)
- Kelly V Ruggles
- From the ‡Department of Medicine, New York University School of Medicine, New York, New York 10016
| | - Karsten Krug
- §The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Xiaojing Wang
- ¶Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030.,‖Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - Karl R Clauser
- §The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Jing Wang
- ¶Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030.,‖Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - Samuel H Payne
- **Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354
| | - David Fenyö
- ‡‡Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016; .,§§Institute for Systems Genetics, New York University School of Medicine, New York, New York 10016
| | - Bing Zhang
- ¶Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030; .,‖Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - D R Mani
- §The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142;
| |
Collapse
|
63
|
Weber J, Peng H, Rader C. From rabbit antibody repertoires to rabbit monoclonal antibodies. Exp Mol Med 2017; 49:e305. [PMID: 28336958 PMCID: PMC5382564 DOI: 10.1038/emm.2017.23] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 12/22/2016] [Indexed: 12/11/2022] Open
Abstract
In this review, we explain why and how rabbit monoclonal antibodies have become outstanding reagents for laboratory research and increasingly for diagnostic and therapeutic applications. Starting with the unique ontogeny of rabbit B cells that affords highly distinctive antibody repertoires rich in in vivo pruned binders of high diversity, affinity and specificity, we describe the generation of rabbit monoclonal antibodies by hybridoma technology, phage display and alternative methods, along with an account of successful humanization strategies.
Collapse
Affiliation(s)
- Justus Weber
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Haiyong Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Christoph Rader
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| |
Collapse
|
64
|
Banerjee S, Shi H, Banasik M, Moon H, Lees W, Qin Y, Harley A, Shepherd A, Cho MW. Evaluation of a novel multi-immunogen vaccine strategy for targeting 4E10/10E8 neutralizing epitopes on HIV-1 gp41 membrane proximal external region. Virology 2017; 505:113-126. [PMID: 28237764 DOI: 10.1016/j.virol.2017.02.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Revised: 02/13/2017] [Accepted: 02/15/2017] [Indexed: 02/01/2023]
Abstract
The membrane proximal external region (MPER) of HIV-1 gp41 is targeted by broadly neutralizing antibodies (bnAbs) 4E10 and 10E8. In this proof-of-concept study, we evaluated a novel multi-immunogen vaccine strategy referred to as Incremental, Phased Antigenic Stimulation for Rapid Antibody Maturation (IPAS-RAM) to induce 4E10/10E8-like bnAbs. Rabbits were immunized sequentially, but in a phased manner, with three immunogens that are progressively more native (gp41-28×3, gp41-54CT, and rVV-gp160DH12). Although nAbs were not induced, epitope-mapping analyses indicated that IPAS-RAM vaccination was better able to target antibodies towards the 4E10/10E8 epitopes than homologous prime-boost immunization using gp41-28×3 alone. MPER-specific rabbit monoclonal antibodies were generated, including 9F6. Although it lacked neutralizing activity, the target epitope profile of 9F6 closely resembled those of 4E10 and 10E8 (671NWFDITNWLWYIK683). B-cell repertoire analyses suggested the importance of co-immunizations for maturation of 9F6, which warrants further evaluation of our IPAS-RAM vaccine strategy using an improved priming immunogen.
Collapse
Affiliation(s)
- Saikat Banerjee
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, United States
| | - Heliang Shi
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, United States
| | - Marisa Banasik
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, United States
| | - Hojin Moon
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, United States
| | - William Lees
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, UK
| | - Yali Qin
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, United States
| | - Andrew Harley
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, United States
| | - Adrian Shepherd
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, UK
| | - Michael W Cho
- Department of Biomedical Sciences, Iowa State University, Ames, IA 50011, United States.
| |
Collapse
|
65
|
Zhang YF, Ho M. Humanization of rabbit monoclonal antibodies via grafting combined Kabat/IMGT/Paratome complementarity-determining regions: Rationale and examples. MAbs 2017; 9:419-429. [PMID: 28165915 DOI: 10.1080/19420862.2017.1289302] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Rabbit monoclonal antibodies (RabMAbs) can recognize diverse epitopes, including those poorly immunogenic in mice and humans. However, there have been only a few reports on RabMAb humanization, an important antibody engineering step usually done before clinical applications are investigated. To pursue a general method for humanization of RabMAbs, we analyzed the complex structures of 5 RabMAbs with their antigens currently available in the Protein Data Bank, and identified antigen-contacting residues on the rabbit Fv within the 6 Angstrom distance to its antigen. We also analyzed the supporting residues for antigen-contacting residues on the same heavy or light chain. We identified "HV4" and "LV4" in rabbit Fvs, non-complementarity-determining region (CDR) loops that are structurally close to the antigen and located in framework 3 of the heavy chain and light chain, respectively. Based on our structural and sequence analysis, we designed a humanization strategy by grafting the combined Kabat/IMGT/Paratome CDRs, which cover most antigen-contacting residues, into a human germline framework sequence. Using this strategy, we humanized 4 RabMAbs that recognize poorly immunogenic epitopes in the cancer target mesothelin. Three of the 4 humanized rabbit Fvs have similar or improved functional binding affinity for mesothelin-expressing cells. Interestingly, 4 immunotoxins composed of the humanized scFvs fused to a clinically used fragment of Pseudomonas exotoxin (PE38) showed stronger cytotoxicity against tumor cells than the immunotoxins derived from their original rabbit scFvs. Our data suggest that grafting the combined Kabat/IMGT/Paratome CDRs to a stable human germline framework can be a general approach to humanize RabMAbs.
Collapse
Affiliation(s)
- Yi-Fan Zhang
- a Laboratory of Molecular Biology , National Cancer Institute , Bethesda , MD , USA
| | - Mitchell Ho
- a Laboratory of Molecular Biology , National Cancer Institute , Bethesda , MD , USA
| |
Collapse
|
66
|
Drabek D, Janssens R, de Boer E, Rademaker R, Kloess J, Skehel J, Grosveld F. Expression Cloning and Production of Human Heavy-Chain-Only Antibodies from Murine Transgenic Plasma Cells. Front Immunol 2016; 7:619. [PMID: 28066429 PMCID: PMC5165034 DOI: 10.3389/fimmu.2016.00619] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 12/06/2016] [Indexed: 12/02/2022] Open
Abstract
Several technologies have been developed to isolate human antibodies against different target antigens as a source of potential therapeutics, including hybridoma technology, phage and yeast display systems. For conventional antibodies, this involves either random pairing of VH and variable light (VL) domains in combinatorial display libraries or isolation of cognate pairs of VH and VL domains from human B cells or from transgenic mice carrying human immunoglobulin loci followed by single-cell sorting, single-cell RT-PCR, and bulk cloning of isolated natural VH–VL pairs. Heavy-chain-only antibodies (HCAbs) that naturally occur in camelids require only heavy immunoglobulin chain cloning. Here, we present an automatable novel, high-throughput technology for rapid direct cloning and production of fully human HCAbs from sorted population of transgenic mouse plasma cells carrying a human HCAb locus. Utility of the technique is demonstrated by isolation of diverse sets of sequence unique, soluble, high-affinity influenza A strain X-31 hemagglutinin-specific HCAbs.
Collapse
Affiliation(s)
- Dubravka Drabek
- Department of Cell Biology, Erasmus MC , Rotterdam , Netherlands
| | - Rick Janssens
- Department of Cell Biology, Erasmus MC , Rotterdam , Netherlands
| | - Ernie de Boer
- Department of Cell Biology, Erasmus MC , Rotterdam , Netherlands
| | | | | | - John Skehel
- WHO Influenza Centre, Frances Crick Institute , London , UK
| | - Frank Grosveld
- Department of Cell Biology, Erasmus MC, Rotterdam, Netherlands; Harbour Antibodies BV, Rotterdam, Netherlands
| |
Collapse
|
67
|
Chen Z, Ren X, Yang J, Dong J, Xue Y, Sun L, Zhu Y, Jin Q. An elaborate landscape of the human antibody repertoire against enterovirus 71 infection is revealed by phage display screening and deep sequencing. MAbs 2016; 9:342-349. [PMID: 27929745 DOI: 10.1080/19420862.2016.1267086] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Enterovirus 71 (EV71) causes outbreaks of hand, foot and mouth disease (HFMD), primarily in the Asia-Pacific area, that are often associated with complications of severe to fatal neurological symptoms. There are currently no anti-viral therapies or vaccines available for the treatment of EV71 infection. Illustrating human antibody responses neutralizing EV71 infection could potentially provide valuable information for the development of effective therapies and vaccines. Here, we constructed a comprehensive phage display library based on peripheral blood of eight EV71-infected donors and identified 27 EV71-specific human antibodies, of which four have neutralizing activity in in vitro experiments. Deep sequencing analysis of the antibody heavy chains at the transcript level of another three independent EV71-infected donors and three controls demonstrates that heavy chains of the EV71-specific antibodies are conserved among EV71-infected individuals but absent in controls, suggesting convergent evolution of human antibodies against EV71.
Collapse
Affiliation(s)
- Zhe Chen
- a MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing , China
| | - Xianwen Ren
- a MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing , China
| | - Jian Yang
- a MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing , China
| | - Jie Dong
- a MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing , China
| | - Ying Xue
- a MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing , China
| | - Lilian Sun
- a MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing , China
| | - Yafang Zhu
- a MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing , China
| | - Qi Jin
- a MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing , China
| |
Collapse
|
68
|
Zhang W, Wang IM, Wang C, Lin L, Chai X, Wu J, Bett AJ, Dhanasekaran G, Casimiro DR, Liu X. IMPre: An Accurate and Efficient Software for Prediction of T- and B-Cell Receptor Germline Genes and Alleles from Rearranged Repertoire Data. Front Immunol 2016; 7:457. [PMID: 27867380 PMCID: PMC5095119 DOI: 10.3389/fimmu.2016.00457] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 10/12/2016] [Indexed: 12/29/2022] Open
Abstract
Large-scale study of the properties of T-cell receptor (TCR) and B-cell receptor (BCR) repertoires through next-generation sequencing is providing excellent insights into the understanding of adaptive immune responses. Variable(Diversity)Joining [V(D)J] germline genes and alleles must be characterized in detail to facilitate repertoire analyses. However, most species do not have well-characterized TCR/BCR germline genes because of their high homology. Also, more germline alleles are required for humans and other species, which limits the capacity for studying immune repertoires. Herein, we developed "Immune Germline Prediction" (IMPre), a tool for predicting germline V/J genes and alleles using deep-sequencing data derived from TCR/BCR repertoires. We developed a new algorithm, "Seed_Clust," for clustering, produced a multiway tree for assembly and optimized the sequence according to the characteristics of rearrangement. We trained IMPre on human samples of T-cell receptor beta (TRB) and immunoglobulin heavy chain and then tested it on additional human samples. Accuracy of 97.7, 100, 92.9, and 100% was obtained for TRBV, TRBJ, IGHV, and IGHJ, respectively. Analyses of subsampling performance for these samples showed IMPre to be robust using different data quantities. Subsequently, IMPre was tested on samples from rhesus monkeys and human long sequences: the highly accurate results demonstrated IMPre to be stable with animal and multiple data types. With rapid accumulation of high-throughput sequence data for TCR and BCR repertoires, IMPre can be applied broadly for obtaining novel genes and a large number of novel alleles. IMPre is available at https://github.com/zhangwei2015/IMPre.
Collapse
Affiliation(s)
- Wei Zhang
- Beijing Genomics Institute (BGI-Shenzhen) , Shenzhen , China
| | - I-Ming Wang
- Merck Research Laboratories , West Point, PA , USA
| | - Changxi Wang
- Beijing Genomics Institute (BGI-Shenzhen) , Shenzhen , China
| | - Liya Lin
- Beijing Genomics Institute (BGI-Shenzhen) , Shenzhen , China
| | - Xianghua Chai
- Beijing Genomics Institute (BGI-Shenzhen) , Shenzhen , China
| | - Jinghua Wu
- Beijing Genomics Institute (BGI-Shenzhen) , Shenzhen , China
| | | | | | | | - Xiao Liu
- Beijing Genomics Institute (BGI-Shenzhen) , Shenzhen , China
| |
Collapse
|
69
|
Guthals A, Gan Y, Murray L, Chen Y, Stinson J, Nakamura G, Lill JR, Sandoval W, Bandeira N. De Novo MS/MS Sequencing of Native Human Antibodies. J Proteome Res 2016; 16:45-54. [PMID: 27779884 DOI: 10.1021/acs.jproteome.6b00608] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One direct route for the discovery of therapeutic human monoclonal antibodies (mAbs) involves the isolation of peripheral B cells from survivors/sero-positive individuals after exposure to an infectious reagent or disease etiology, followed by single-cell sequencing or hybridoma generation. Peripheral B cells, however, are not always easy to obtain and represent only a small percentage of the total B-cell population across all bodily tissues. Although it has been demonstrated that tandem mass spectrometry (MS/MS) techniques can interrogate the full polyclonal antibody (pAb) response to an antigen in vivo, all current approaches identify MS/MS spectra against databases derived from genetic sequencing of B cells from the same patient. In this proof-of-concept study, we demonstrate the feasibility of a novel MS/MS antibody discovery approach in which only serum antibodies are required without the need for sequencing of genetic material. Peripheral pAbs from a cytomegalovirus-exposed individual were purified by glycoprotein B antigen affinity and de novo sequenced from MS/MS data. Purely MS-derived mAbs were then manufactured in mammalian cells to validate potency via antigen-binding ELISA. Interestingly, we found that these mAbs accounted for 1 to 2% of total donor IgG but were not detected in parallel sequencing of memory B cells from the same patient.
Collapse
Affiliation(s)
- Adrian Guthals
- Mapp Biopharmaceutical, Inc. , 6160 Lusk Boulevard #C105, San Diego, California 92121, United States
| | - Yutian Gan
- Department of Proteomics & Biological Resources, Genentech, Inc. , South San Francisco, California 94080, United States
| | - Laura Murray
- Department of Protein Chemistry, Genentech, Inc. , South San Francisco, California 94080, United States
| | - Yongmei Chen
- Department of Antibody Engineering, Genentech, Inc. , South San Francisco, California 94080, United States
| | - Jeremy Stinson
- Department of Molecular Biology, Genentech, Inc. , South San Francisco, California 94080, United States
| | - Gerald Nakamura
- Department of Antibody Engineering, Genentech, Inc. , South San Francisco, California 94080, United States
| | - Jennie R Lill
- Department of Proteomics & Biological Resources, Genentech, Inc. , South San Francisco, California 94080, United States
| | - Wendy Sandoval
- Department of Proteomics & Biological Resources, Genentech, Inc. , South San Francisco, California 94080, United States
| | - Nuno Bandeira
- Department of Computer Science and Engineering, University of California, San Diego , 9500 Gilman Drive, Mail Code 0404, La Jolla, California 92093, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego , 9500 Gilman Drive, Mail Code 0657, La Jolla, California 92093, United States
| |
Collapse
|
70
|
Zucchelli S, Patrucco L, Persichetti F, Gustincich S, Cotella D. Engineering Translation in Mammalian Cell Factories to Increase Protein Yield: The Unexpected Use of Long Non-Coding SINEUP RNAs. Comput Struct Biotechnol J 2016; 14:404-410. [PMID: 27872686 PMCID: PMC5107644 DOI: 10.1016/j.csbj.2016.10.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 10/21/2016] [Accepted: 10/24/2016] [Indexed: 12/26/2022] Open
Abstract
Mammalian cells are an indispensable tool for the production of recombinant proteins in contexts where function depends on post-translational modifications. Among them, Chinese Hamster Ovary (CHO) cells are the primary factories for the production of therapeutic proteins, including monoclonal antibodies (MAbs). To improve expression and stability, several methodologies have been adopted, including methods based on media formulation, selective pressure and cell- or vector engineering. This review presents current approaches aimed at improving mammalian cell factories that are based on the enhancement of translation. Among well-established techniques (codon optimization and improvement of mRNA secondary structure), we describe SINEUPs, a family of antisense long non-coding RNAs that are able to increase translation of partially overlapping protein-coding mRNAs. By exploiting their modular structure, SINEUP molecules can be designed to target virtually any mRNA of interest, and thus to increase the production of secreted proteins. Thus, synthetic SINEUPs represent a new versatile tool to improve the production of secreted proteins in biomanufacturing processes.
Collapse
Affiliation(s)
- Silvia Zucchelli
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy; Area of Neuroscience, SISSA, Trieste, Italy
| | - Laura Patrucco
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| | | | - Stefano Gustincich
- Area of Neuroscience, SISSA, Trieste, Italy; Department of Neuroscience and Brain Technologies, Italian Institute of Technology (IIT), Genova, Italy
| | - Diego Cotella
- Department of Health Sciences, Università del Piemonte Orientale, Novara, Italy
| |
Collapse
|
71
|
Deconstructing the Antiviral Neutralizing-Antibody Response: Implications for Vaccine Development and Immunity. Microbiol Mol Biol Rev 2016; 80:989-1010. [PMID: 27784796 DOI: 10.1128/mmbr.00024-15] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The antibody response plays a key role in protection against viral infections. While antiviral antibodies may reduce the viral burden via several mechanisms, the ability to directly inhibit (neutralize) infection of cells has been extensively studied. Eliciting a neutralizing-antibody response is a goal of many vaccine development programs and commonly correlates with protection from disease. Considerable insights into the mechanisms of neutralization have been gained from studies of monoclonal antibodies, yet the individual contributions and dynamics of the repertoire of circulating antibody specificities elicited by infection and vaccination are poorly understood on the functional and molecular levels. Neutralizing antibodies with the most protective functionalities may be a rare component of a polyclonal, pathogen-specific antibody response, further complicating efforts to identify the elements of a protective immune response. This review discusses advances in deconstructing polyclonal antibody responses to flavivirus infection or vaccination. Our discussions draw comparisons to HIV-1, a virus with a distinct structure and replication cycle for which the antibody response has been extensively investigated. Progress toward deconstructing and understanding the components of polyclonal antibody responses identifies new targets and challenges for vaccination strategies.
Collapse
|
72
|
Friedensohn S, Khan TA, Reddy ST. Advanced Methodologies in High-Throughput Sequencing of Immune Repertoires. Trends Biotechnol 2016; 35:203-214. [PMID: 28341036 DOI: 10.1016/j.tibtech.2016.09.010] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 09/19/2016] [Accepted: 09/30/2016] [Indexed: 11/19/2022]
Abstract
In recent years, major efforts have been made to develop sophisticated experimental and bioinformatic workflows for sequencing adaptive immune repertoires. The immunological insight gained has been applied to fields as varied as lymphocyte biology, immunodiagnostics, vaccines, cancer immunotherapy, and antibody engineering. In this review, we provide a detailed overview of these advanced methodologies, focusing specifically on strategies to reduce sequencing errors and bias and to achieve high-throughput pairing of variable regions (e.g., heavy-light or alpha-beta chains). In addition, we highlight recent technologies for single-cell transcriptome sequencing that can be integrated with immune repertoires. Finally, we provide a perspective on advanced immune repertoire sequencing and its ability to impact basic immunology, biopharmaceutical drug discovery and development, and cancer immunotherapy.
Collapse
Affiliation(s)
- Simon Friedensohn
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Tarik A Khan
- Pharmaceutical Development & Supplies Biologics Europe, F. Hoffman-La Roche Ltd, Basel, Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
| |
Collapse
|
73
|
Wang JJ, Al Kindi MA, Colella AD, Dykes L, Jackson MW, Chataway TK, Reed JH, Gordon TP. IgV peptide mapping of native Ro60 autoantibody proteomes in primary Sjögren's syndrome reveals molecular markers of Ro/La diversification. Clin Immunol 2016; 173:57-63. [PMID: 27609500 DOI: 10.1016/j.clim.2016.09.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 08/18/2016] [Accepted: 09/01/2016] [Indexed: 01/25/2023]
Abstract
We have used high-resolution mass spectrometry to sequence precipitating anti-Ro60 proteomes from sera of patients with primary Sjögren's syndrome and compare immunoglobulin variable-region (IgV) peptide signatures in Ro/La autoantibody subsets. Anti-Ro60 were purified by elution from native Ro60-coated ELISA plates and subjected to combined de novo amino acid sequencing and database matching. Monospecific anti-Ro60 Igs comprised dominant public and minor private sets of IgG1 kappa and lambda restricted heavy and light chains. Specific IgV amino acid substitutions stratified anti-Ro60 from anti-Ro60/La responses, providing a molecular fingerprint of Ro60/La determinant spreading and suggesting that different forms of Ro60 antigen drive these responses. Sequencing of linked anti-Ro52 proteomes from individual patients and comparison with their anti-Ro60 partners revealed sharing of a dominant IGHV3-23/IGKV3-20 paired clonotype but with divergent IgV mutational signatures. In summary, anti-Ro60 IgV peptide mapping provides insights into Ro/La autoantibody diversification and reveals serum-based molecular markers of humoral Ro60 autoimmunity.
Collapse
Affiliation(s)
- Jing J Wang
- Department of Immunology, Flinders Medical Centre and Flinders University, SA Pathology, Bedford Park 5042, South Australia, Australia
| | - Mahmood A Al Kindi
- Department of Immunology, Flinders Medical Centre and Flinders University, SA Pathology, Bedford Park 5042, South Australia, Australia; Department of Microbiology and Immunology, Sultan Qaboos University Hospital, Muscat 123, Oman
| | - Alex D Colella
- Department of Immunology, Flinders Medical Centre and Flinders University, SA Pathology, Bedford Park 5042, South Australia, Australia; Flinders Proteomics Facility, Flinders University, Bedford Park 5042, South Australia, Australia
| | - Lukah Dykes
- Flinders Proteomics Facility, Flinders University, Bedford Park 5042, South Australia, Australia
| | - Michael W Jackson
- Department of Immunology, Flinders Medical Centre and Flinders University, SA Pathology, Bedford Park 5042, South Australia, Australia
| | - Tim K Chataway
- Flinders Proteomics Facility, Flinders University, Bedford Park 5042, South Australia, Australia
| | - Joanne H Reed
- Garvan Institute of Medical Research, Immunology Division, Immunogenomics Laboratory, 384 Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Tom P Gordon
- Department of Immunology, Flinders Medical Centre and Flinders University, SA Pathology, Bedford Park 5042, South Australia, Australia.
| |
Collapse
|
74
|
Han Y, Li H, Guan Y, Huang J. Immune repertoire: A potential biomarker and therapeutic for hepatocellular carcinoma. Cancer Lett 2016; 379:206-12. [DOI: 10.1016/j.canlet.2015.06.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 06/29/2015] [Accepted: 06/30/2015] [Indexed: 12/27/2022]
|
75
|
Antibodies elicited by the first non-viral prophylactic cancer vaccine show tumor-specificity and immunotherapeutic potential. Sci Rep 2016; 6:31740. [PMID: 27545199 PMCID: PMC4992835 DOI: 10.1038/srep31740] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 07/25/2016] [Indexed: 01/30/2023] Open
Abstract
MUC1 is a shared tumor antigen expressed on >80% of human cancers. We completed the first prophylactic cancer vaccine clinical trial based on a non-viral antigen, MUC1, in healthy individuals at-risk for colon cancer. This trial provided a unique source of potentially effective and safe immunotherapeutic drugs, fully-human antibodies affinity-matured in a healthy host to a tumor antigen. We purified, cloned, and characterized 13 IgGs specific for several tumor-associated MUC1 epitopes with a wide range of binding affinities. These antibodies bind hypoglycosylated MUC1 on human cancer cell lines and tumor tissues but show no reactivity against fully-glycosylated MUC1 on normal cells and tissues. We found that several antibodies activate complement-mediated cytotoxicity and that T cells carrying chimeric antigen receptors with the antibody variable regions kill MUC1(+) target cells, express activation markers, and produce interferon gamma. Fully-human and tumor-specific, these antibodies are candidates for further testing and development as immunotherapeutic drugs.
Collapse
|
76
|
Ogishi M, Yotsuyanagi H, Moriya K, Koike K. Delineation of autoantibody repertoire through differential proteogenomics in hepatitis C virus-induced cryoglobulinemia. Sci Rep 2016; 6:29532. [PMID: 27403724 PMCID: PMC4941579 DOI: 10.1038/srep29532] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/17/2016] [Indexed: 12/21/2022] Open
Abstract
Antibodies cross-reactive to pathogens and autoantigens are considered pivotal in both infection control and accompanying autoimmunity. However, the pathogenic roles of autoantibodies largely remain elusive without a priori knowledge of disease-specific autoantigens. Here, through a novel quantitative proteogenomics approach, we demonstrated a successful identification of immunoglobulin variable heavy chain (VH) sequences highly enriched in pathological immune complex from clinical specimens obtained from a patient with hepatitis C virus-induced cryoglobulinemia (HCV-CG). Reconstructed single-domain antibodies were reactive to both HCV antigens and potentially liver-derived human proteins. Moreover, over the course of antiviral therapy, a substantial "de-evolution" of a distinct sub-repertoire was discovered, to which proteomically identified cryoprecipitation-prone autoantibodies belonged. This sub-repertoire was characterized by IGHJ6*03-derived, long, hydrophobic complementarity determining region (CDR-H3). This study provides a proof-of-concept of de novo mining of autoantibodies and corresponding autoantigen candidates in a disease-specific context in human, thus facilitating future reverse-translational research for the discovery of novel biomarkers and the development of antigen-specific immunotherapy against various autoantibody-related disorders.
Collapse
Affiliation(s)
- Masato Ogishi
- Department of Infectious Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Yotsuyanagi
- Department of Infectious Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kyoji Moriya
- Department of Infectious Control and Prevention, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kazuhiko Koike
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
77
|
Chang YH, Kuan HC, Hsieh TC, Ma KH, Yang CH, Hsu WB, Tsai SF, Chao A, Liu HH. Network Signatures of IgG Immune Repertoires in Hepatitis B Associated Chronic Infection and Vaccination Responses. Sci Rep 2016; 6:26556. [PMID: 27222149 PMCID: PMC4879636 DOI: 10.1038/srep26556] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 05/05/2016] [Indexed: 12/20/2022] Open
Abstract
The repertoire of IgG antibody responses to infection and vaccination varies depending on the characteristics of the immunogen and the ability of the host to mount a protective immune response. Chronic hepatitis B virus (HBV) infections are marked by persistent infection and immune tolerance to vaccination. This disease offers a unique opportunity to discover key repertoire signatures during infection and in response to vaccination. Complementarity determining region 3 of an antibody heavy chain (CDR-H3) has a major impact on the antigenic specificity of an antibody. We used next-generation sequencing to characterize the CDR-H3 sequences in paired siblings of 4 families in which only one member of each pair had chronic HBV infection. Blood samples were obtained before and 2 weeks after HBV vaccination. The analysis revealed a huge network of sequence-related CDR-H3 clones found almost exclusively among carriers. In contrast, vaccination induced significant increases of CDR-H3 cluster diversities among siblings without hepatitis B. Several vaccination-associated clone clusters were identified. Similar findings of vaccination-associated clone networks were observed in healthy adults receiving HBV boosters. These strategies can be used to identify signatures of other infectious diseases and accelerate discoveries of antibody sequences with important biomedical implications.
Collapse
Affiliation(s)
- Ya-Hui Chang
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan 35053, Taiwan
| | | | - T C Hsieh
- Institute of Statistics, National Tsing Hua University, Hsin-Chu 30043, Taiwan
| | - K H Ma
- Institute of Statistics, National Tsing Hua University, Hsin-Chu 30043, Taiwan
| | - Chung-Hsiang Yang
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan 35053, Taiwan
| | - Wei-Bin Hsu
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan 35053, Taiwan
| | - Shih-Feng Tsai
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan 35053, Taiwan
| | - Anne Chao
- Institute of Statistics, National Tsing Hua University, Hsin-Chu 30043, Taiwan
| | - Hong-Hsing Liu
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan 35053, Taiwan.,Pediatrics, En Chu Kong Hospital, Sanxia 23702, Taiwan
| |
Collapse
|
78
|
Plomp R, Bondt A, de Haan N, Rombouts Y, Wuhrer M. Recent Advances in Clinical Glycoproteomics of Immunoglobulins (Igs). Mol Cell Proteomics 2016; 15:2217-28. [PMID: 27009965 PMCID: PMC4937499 DOI: 10.1074/mcp.o116.058503] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Indexed: 11/06/2022] Open
Abstract
Antibody glycosylation analysis has seen methodological progress resulting in new findings with regard to antibody glycan structure and function in recent years. For example, antigen-specific IgG glycosylation analysis is now applicable for clinical samples because of the increased sensitivity of measurements, and this has led to new insights in the relationship between IgG glycosylation and various diseases. Furthermore, many new methods have been developed for the purification and analysis of IgG Fc glycopeptides, notably multiple reaction monitoring for high-throughput quantitative glycosylation analysis. In addition, new protocols for IgG Fab glycosylation analysis were established revealing autoimmune disease-associated changes. Functional analysis has shown that glycosylation of IgA and IgE is involved in transport across the intestinal epithelium and receptor binding, respectively.
Collapse
Affiliation(s)
- Rosina Plomp
- From the ‡Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, The Netherlands
| | - Albert Bondt
- From the ‡Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, The Netherlands; §Leiden University Medical Center, Department of Rheumatology, Leiden, The Netherlands
| | - Noortje de Haan
- From the ‡Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, The Netherlands
| | - Yoann Rombouts
- ¶Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, France
| | - Manfred Wuhrer
- From the ‡Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, The Netherlands;
| |
Collapse
|
79
|
Liu J, Li R, Liu K, Li L, Zai X, Chi X, Fu L, Xu J, Chen W. Identification of antigen-specific human monoclonal antibodies using high-throughput sequencing of the antibody repertoire. Biochem Biophys Res Commun 2016; 473:23-28. [PMID: 26979754 DOI: 10.1016/j.bbrc.2016.03.038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 03/08/2016] [Indexed: 12/26/2022]
Abstract
High-throughput sequencing of the antibody repertoire provides a large number of antibody variable region sequences that can be used to generate human monoclonal antibodies. However, current screening methods for identifying antigen-specific antibodies are inefficient. In the present study, we developed an antibody clone screening strategy based on clone dynamics and relative frequency, and used it to identify antigen-specific human monoclonal antibodies. Enzyme-linked immunosorbent assay showed that at least 52% of putative positive immunoglobulin heavy chains composed antigen-specific antibodies. Combining information on dynamics and relative frequency improved identification of positive clones and elimination of negative clones. and increase the credibility of putative positive clones. Therefore the screening strategy could simplify the subsequent experimental screening and may facilitate the generation of antigen-specific antibodies.
Collapse
Affiliation(s)
- Ju Liu
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing 100071, China
| | - Ruihua Li
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing 100071, China
| | - Kun Liu
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing 100071, China
| | - Liangliang Li
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing 100071, China
| | - Xiaodong Zai
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing 100071, China
| | - Xiangyang Chi
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing 100071, China
| | - Ling Fu
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing 100071, China
| | - Junjie Xu
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing 100071, China.
| | - Wei Chen
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing 100071, China.
| |
Collapse
|
80
|
Khan TA, Friedensohn S, de Vries ARG, Straszewski J, Ruscheweyh HJ, Reddy ST. Accurate and predictive antibody repertoire profiling by molecular amplification fingerprinting. SCIENCE ADVANCES 2016; 2:e1501371. [PMID: 26998518 PMCID: PMC4795664 DOI: 10.1126/sciadv.1501371] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 01/17/2016] [Indexed: 05/31/2023]
Abstract
High-throughput antibody repertoire sequencing (Ig-seq) provides quantitative molecular information on humoral immunity. However, Ig-seq is compromised by biases and errors introduced during library preparation and sequencing. By using synthetic antibody spike-in genes, we determined that primer bias from multiplex polymerase chain reaction (PCR) library preparation resulted in antibody frequencies with only 42 to 62% accuracy. Additionally, Ig-seq errors resulted in antibody diversity measurements being overestimated by up to 5000-fold. To rectify this, we developed molecular amplification fingerprinting (MAF), which uses unique molecular identifier (UID) tagging before and during multiplex PCR amplification, which enabled tagging of transcripts while accounting for PCR efficiency. Combined with a bioinformatic pipeline, MAF bias correction led to measurements of antibody frequencies with up to 99% accuracy. We also used MAF to correct PCR and sequencing errors, resulting in enhanced accuracy of full-length antibody diversity measurements, achieving 98 to 100% error correction. Using murine MAF-corrected data, we established a quantitative metric of recent clonal expansion-the intraclonal diversity index-which measures the number of unique transcripts associated with an antibody clone. We used this intraclonal diversity index along with antibody frequencies and somatic hypermutation to build a logistic regression model for prediction of the immunological status of clones. The model was able to predict clonal status with high confidence but only when using MAF error and bias corrected Ig-seq data. Improved accuracy by MAF provides the potential to greatly advance Ig-seq and its utility in immunology and biotechnology.
Collapse
Affiliation(s)
- Tarik A. Khan
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Simon Friedensohn
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | | | - Jakub Straszewski
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- Scientific IT Services, ETH Zurich, 4058 Basel, Switzerland
| | - Hans-Joachim Ruscheweyh
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- Scientific IT Services, ETH Zurich, 4058 Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Sai T. Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| |
Collapse
|
81
|
Al Kindi MA, Colella AD, Chataway TK, Jackson MW, Wang JJ, Gordon TP. Secreted autoantibody repertoires in Sjögren's syndrome and systemic lupus erythematosus: A proteomic approach. Autoimmun Rev 2016; 15:405-10. [PMID: 26804757 DOI: 10.1016/j.autrev.2016.01.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 01/13/2016] [Indexed: 12/18/2022]
Abstract
The structures of epitopes bound by autoantibodies against RNA-protein complexes have been well-defined over several decades, but little is known of the clonality, immunoglobulin (Ig) variable (V) gene usage and mutational status of the autoantibodies themselves at the level of the secreted (serum) proteome. A novel proteomic workflow is presented based on affinity purification of specific Igs from serum, high-resolution two-dimensional gel electrophoresis, and de novo and database-driven sequencing of V-region proteins by mass spectrometry. Analysis of anti-Ro52/Ro60/La proteomes in primary Sjögren's syndrome (SS) and anti-Sm and anti-ribosomal P proteomes in systemic lupus erythematosus (SLE) has revealed that these antibody responses are dominated by restricted sets of public (shared) clonotypes, consistent with common pathways of production across unrelated individuals. The discovery of shared sets of specific V-region peptides can be exploited for diagnostic biomarkers in targeted mass spectrometry platforms and for tracking and removal of pathogenic clones.
Collapse
Affiliation(s)
- Mahmood A Al Kindi
- Department of Immunology, Flinders Medical Centre and Flinders University, SA Pathology, Bedford Park, 5042, South Australia, Australia
| | - Alex D Colella
- Department of Immunology, Flinders Medical Centre and Flinders University, SA Pathology, Bedford Park, 5042, South Australia, Australia; Flinders Proteomic Facility, Flinders University, Australia
| | - Tim K Chataway
- Flinders Proteomic Facility, Flinders University, Australia
| | - Michael W Jackson
- Department of Immunology, Flinders Medical Centre and Flinders University, SA Pathology, Bedford Park, 5042, South Australia, Australia
| | - Jing J Wang
- Department of Immunology, Flinders Medical Centre and Flinders University, SA Pathology, Bedford Park, 5042, South Australia, Australia.
| | - Tom P Gordon
- Department of Immunology, Flinders Medical Centre and Flinders University, SA Pathology, Bedford Park, 5042, South Australia, Australia.
| |
Collapse
|
82
|
Yaari G, Kleinstein SH. Practical guidelines for B-cell receptor repertoire sequencing analysis. Genome Med 2015; 7:121. [PMID: 26589402 PMCID: PMC4654805 DOI: 10.1186/s13073-015-0243-2] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
High-throughput sequencing of B-cell immunoglobulin repertoires is increasingly being applied to gain insights into the adaptive immune response in healthy individuals and in those with a wide range of diseases. Recent applications include the study of autoimmunity, infection, allergy, cancer and aging. As sequencing technologies continue to improve, these repertoire sequencing experiments are producing ever larger datasets, with tens- to hundreds-of-millions of sequences. These data require specialized bioinformatics pipelines to be analyzed effectively. Numerous methods and tools have been developed to handle different steps of the analysis, and integrated software suites have recently been made available. However, the field has yet to converge on a standard pipeline for data processing and analysis. Common file formats for data sharing are also lacking. Here we provide a set of practical guidelines for B-cell receptor repertoire sequencing analysis, starting from raw sequencing reads and proceeding through pre-processing, determination of population structure, and analysis of repertoire properties. These include methods for unique molecular identifiers and sequencing error correction, V(D)J assignment and detection of novel alleles, clonal assignment, lineage tree construction, somatic hypermutation modeling, selection analysis, and analysis of stereotyped or convergent responses. The guidelines presented here highlight the major steps involved in the analysis of B-cell repertoire sequencing data, along with recommendations on how to avoid common pitfalls.
Collapse
Affiliation(s)
- Gur Yaari
- Bioengineering Program, Faculty of Engineering, Bar-Ilan University, 5290002, Ramat Gan, Israel.
| | - Steven H Kleinstein
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06511, USA. .,Departments of Pathology and Immunobiology, Yale University School of Medicine, New Haven, CT, 06520, USA.
| |
Collapse
|
83
|
Kuwata T, Uchida A, Takano E, Kitayama Y, Takeuchi T. Molecularly Imprinted Polymer Arrays as Synthetic Protein Chips Prepared by Transcription-type Molecular Imprinting by Use of Protein-Immobilized Dots as Stamps. Anal Chem 2015; 87:11784-91. [DOI: 10.1021/acs.analchem.5b03134] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Takahiro Kuwata
- Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Akane Uchida
- Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Eri Takano
- Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Yukiya Kitayama
- Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Toshifumi Takeuchi
- Graduate School of Engineering, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| |
Collapse
|
84
|
Safonova Y, Bonissone S, Kurpilyansky E, Starostina E, Lapidus A, Stinson J, DePalatis L, Sandoval W, Lill J, Pevzner PA. IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis. Bioinformatics 2015; 31:i53-61. [PMID: 26072509 PMCID: PMC4542777 DOI: 10.1093/bioinformatics/btv238] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
UNLABELLED The analysis of concentrations of circulating antibodies in serum (antibody repertoire) is a fundamental, yet poorly studied, problem in immunoinformatics. The two current approaches to the analysis of antibody repertoires [next generation sequencing (NGS) and mass spectrometry (MS)] present difficult computational challenges since antibodies are not directly encoded in the germline but are extensively diversified by somatic recombination and hypermutations. Therefore, the protein database required for the interpretation of spectra from circulating antibodies is custom for each individual. Although such a database can be constructed via NGS, the reads generated by NGS are error-prone and even a single nucleotide error precludes identification of a peptide by the standard proteomics tools. Here, we present the IgRepertoireConstructor algorithm that performs error-correction of immunosequencing reads and uses mass spectra to validate the constructed antibody repertoires. AVAILABILITY AND IMPLEMENTATION IgRepertoireConstructor is open source and freely available as a C++ and Python program running on all Unix-compatible platforms. The source code is available from http://bioinf.spbau.ru/igtools. CONTACT ppevzner@ucsd.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Yana Safonova
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Stefano Bonissone
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Eugene Kurpilyansky
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Ekaterina Starostina
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Alla Lapidus
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Jeremy Stinson
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Laura DePalatis
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Wendy Sandoval
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Jennie Lill
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Pavel A Pevzner
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| |
Collapse
|
85
|
Bioinformatic and Statistical Analysis of Adaptive Immune Repertoires. Trends Immunol 2015; 36:738-749. [DOI: 10.1016/j.it.2015.09.006] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 09/15/2015] [Accepted: 09/15/2015] [Indexed: 01/16/2023]
|
86
|
Ohlin M, Söderberg-Nauclér C. Human antibody technology and the development of antibodies against cytomegalovirus. Mol Immunol 2015; 67:153-70. [DOI: 10.1016/j.molimm.2015.02.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 02/13/2015] [Accepted: 02/15/2015] [Indexed: 02/08/2023]
|
87
|
Halliley JL, Tipton CM, Liesveld J, Rosenberg AF, Darce J, Gregoretti IV, Popova L, Kaminiski D, Fucile CF, Albizua I, Kyu S, Chiang KY, Bradley KT, Burack R, Slifka M, Hammarlund E, Wu H, Zhao L, Walsh EE, Falsey AR, Randall TD, Cheung WC, Sanz I, Lee FEH. Long-Lived Plasma Cells Are Contained within the CD19(-)CD38(hi)CD138(+) Subset in Human Bone Marrow. Immunity 2015; 43:132-45. [PMID: 26187412 DOI: 10.1016/j.immuni.2015.06.016] [Citation(s) in RCA: 346] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Revised: 01/16/2015] [Accepted: 04/28/2015] [Indexed: 01/09/2023]
Abstract
Antibody responses to viral infections are sustained for decades by long-lived plasma cells (LLPCs). However, LLPCs have yet to be characterized in humans. Here we used CD19, CD38, and CD138 to identify four PC subsets in human bone marrow (BM). We found that the CD19(-)CD38(hi)CD138(+) subset was morphologically distinct, differentially expressed PC-associated genes, and exclusively contained PCs specific for viral antigens to which the subjects had not been exposed for more than 40 years. Protein sequences of measles- and mumps-specific circulating antibodies were encoded for by CD19(-)CD38(hi)CD138(+) PCs in the BM. Finally, we found that CD19(-)CD38(hi)CD138(+) PCs had a distinct RNA transcriptome signature and human immunoglobulin heavy chain (VH) repertoire that was relatively uncoupled from other BM PC subsets and probably represents the B cell response's "historical record" of antigenic exposure. Thus, our studies define human LLPCs and provide a mechanism for the life-long maintenance of anti-viral antibodies in the serum.
Collapse
Affiliation(s)
- Jessica L Halliley
- Divisions of Pulmonary, Allergy, & Critical Care Medicine, Emory University, Atlanta, GA 30322, USA; Pulmonary & Critical Care Medicine, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Christopher M Tipton
- Division of Rheumatology, Emory University, Atlanta, GA 30322, USA; Lowance Center for Human Immunology in the Departments of Medicine and Pediatrics, Emory University, Atlanta, GA 30322, USA
| | - Jane Liesveld
- Divisions of Hematology/Oncology/James P. Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Alexander F Rosenberg
- Division of Allergy, Immunology, and Rheumatology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Jaime Darce
- Cell Signaling Technology, Inc., Danvers, MA 01923, USA
| | | | - Lana Popova
- Cell Signaling Technology, Inc., Danvers, MA 01923, USA
| | - Denise Kaminiski
- Division of Allergy, Immunology, and Rheumatology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Christopher F Fucile
- Division of Allergy, Immunology, and Rheumatology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Igor Albizua
- Divisions of Pulmonary, Allergy, & Critical Care Medicine, Emory University, Atlanta, GA 30322, USA
| | - Shuya Kyu
- Divisions of Pulmonary, Allergy, & Critical Care Medicine, Emory University, Atlanta, GA 30322, USA
| | - Kuang-Yueh Chiang
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Emory University, Atlanta, GA 30322, USA
| | - Kyle T Bradley
- Department of Pathology & Laboratory Medicine, Emory University, Atlanta, GA 30322, USA
| | - Richard Burack
- Department of Pathology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Mark Slifka
- Oregon Health & Sciences University, Beaverton, OR 97006, USA
| | | | - Hao Wu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA
| | - Liping Zhao
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA
| | - Edward E Walsh
- Division of Infectious Diseases, University of Rochester Medical Center & Rochester General Hospital, Rochester, NY 14621, USA
| | - Ann R Falsey
- Division of Infectious Diseases, University of Rochester Medical Center & Rochester General Hospital, Rochester, NY 14621, USA
| | - Troy D Randall
- Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | | | - Iñaki Sanz
- Division of Rheumatology, Emory University, Atlanta, GA 30322, USA; Lowance Center for Human Immunology in the Departments of Medicine and Pediatrics, Emory University, Atlanta, GA 30322, USA
| | - F Eun-Hyung Lee
- Divisions of Pulmonary, Allergy, & Critical Care Medicine, Emory University, Atlanta, GA 30322, USA; Lowance Center for Human Immunology in the Departments of Medicine and Pediatrics, Emory University, Atlanta, GA 30322, USA.
| |
Collapse
|
88
|
Wine Y, Horton AP, Ippolito GC, Georgiou G. Serology in the 21st century: the molecular-level analysis of the serum antibody repertoire. Curr Opin Immunol 2015; 35:89-97. [PMID: 26172290 DOI: 10.1016/j.coi.2015.06.009] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 06/22/2015] [Accepted: 06/22/2015] [Indexed: 12/11/2022]
Abstract
The ensemble of antibodies found in serum and secretions represents the key adaptive component of B-cell mediated humoral immunity. The antibody repertoire is shaped by the historical record of exposure to exogenous factors such as pathogens and vaccines, as well as by endogenous host-intrinsic factors such as genetics, self-antigens, and age. Thanks to very recent technology advancements it is now becoming possible to identify and quantify the individual antibodies comprising the serological repertoire. In parallel, the advent of high throughput methods for antigen and immunosignature discovery opens up unprecedented opportunities to transform our understanding of numerous key questions in adaptive humoral immunity, including the nature and dynamics of serological memory, the role of polyspecific antibodies in health and disease and how protective responses to infections or vaccine challenge arise. Additionally, these technologies also hold great promise for therapeutic antibody and biomarker discovery in a variety of settings.
Collapse
Affiliation(s)
- Yariv Wine
- Department of Molecular Microbiology and Biotechnology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Andrew P Horton
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA
| | - Gregory C Ippolito
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - George Georgiou
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA; Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA; Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA; Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX, USA.
| |
Collapse
|
89
|
Diversity, cellular origin and autoreactivity of antibody-secreting cell population expansions in acute systemic lupus erythematosus. Nat Immunol 2015; 16:755-65. [PMID: 26006014 PMCID: PMC4512288 DOI: 10.1038/ni.3175] [Citation(s) in RCA: 373] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 04/13/2015] [Indexed: 12/17/2022]
Abstract
Acute SLE courses with antibody-secreting cells (ASC) surges whose origin, diversity, and contribution to serum autoantibodies remain unknown. Deep sequencing, autoantibody proteome and single-cell analysis demonstrated highly diversified ASC punctuated by VH4-34 clones that produce dominant serum autoantibodies. A fraction of ASC clones contained unmutated autoantibodies, a finding consistent with differentiation outside the germinal centers. A substantial ASC segment derived from a distinct subset of newly activated naïve cells of significant clonality that persist in the circulation for several months. Thus, selection of SLE autoreactivities occurred during polyclonal activation with prolonged recruitment of recently activated naïve B cells. These findings shed light into SLE pathogenesis, help explain the benefit of anti-B cell agents and facilitate the design of future therapies.
Collapse
|
90
|
Greer SM, Parker WR, Brodbelt JS. Impact of Protease on Ultraviolet Photodissociation Mass Spectrometry for Bottom-up Proteomics. J Proteome Res 2015; 14:2626-32. [DOI: 10.1021/acs.jproteome.5b00165] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sylvester M. Greer
- Department of Chemistry, University of Texas at Austin, 105
East 24th Street, Austin, Texas 78712, United States
| | - W. Ryan Parker
- Department of Chemistry, University of Texas at Austin, 105
East 24th Street, Austin, Texas 78712, United States
| | - Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, 105
East 24th Street, Austin, Texas 78712, United States
| |
Collapse
|
91
|
Korbakis D, Brinc D, Schiza C, Soosaipillai A, Jarvi K, Drabovich AP, Diamandis EP. Immunocapture-Selected Reaction Monitoring Screening Facilitates the Development of ELISA for the Measurement of Native TEX101 in Biological Fluids. Mol Cell Proteomics 2015; 14:1517-26. [PMID: 25813379 DOI: 10.1074/mcp.m114.047571] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Indexed: 11/06/2022] Open
Abstract
Monoclonal antibodies that bind the native conformation of proteins are indispensable reagents for the development of immunoassays, production of therapeutic antibodies and delineating protein interaction networks by affinity purification-mass spectrometry. Antibodies generated against short peptides, protein fragments, or even full length recombinant proteins may not bind the native protein form in biological fluids, thus limiting their utility. Here, we report the application of immunocapture coupled with selected reaction monitoring measurements (immunocapture-SRM), in the rapid screening of hybridoma culture supernatants for monoclonal antibodies that bind the native protein conformation. We produced mouse monoclonal antibodies, which detect in human serum or seminal plasma the native form of the human testis-expressed sequence 101 (TEX101) protein-a recently proposed biomarker of male infertility. Pairing of two monoclonal antibodies against unique TEX101 epitopes led to the development of an ELISA for the measurement of TEX101 in seminal plasma (limit of detection: 20 pg/ml) and serum (limit of detection: 40 pg/ml). Measurements of matched seminal plasma samples, obtained from men pre- and post-vasectomy, confirmed the absolute diagnostic specificity and sensitivity of TEX101 for noninvasive identification of physical obstructions in the male reproductive tract. Measurement of male and female serum samples revealed undetectable levels of TEX101 in the systemic circulation of healthy individuals. Immunocapture-SRM screening may facilitate development of monoclonal antibodies and immunoassays against native forms of challenging protein targets.
Collapse
Affiliation(s)
- Dimitrios Korbakis
- From the ‡Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; §Department of Clinical Biochemistry, University Health Network, Toronto, Canada
| | - Davor Brinc
- ¶Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada
| | - Christina Schiza
- From the ‡Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; ¶Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada
| | | | - Keith Jarvi
- ‖Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada; **Department of Surgery, Division of Urology, Mount Sinai Hospital, University of Toronto, Canada
| | - Andrei P Drabovich
- From the ‡Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; §Department of Clinical Biochemistry, University Health Network, Toronto, Canada;
| | - Eleftherios P Diamandis
- From the ‡Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; §Department of Clinical Biochemistry, University Health Network, Toronto, Canada; ¶Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada; ‖Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada;
| |
Collapse
|
92
|
Kavanagh O, Elliott CT, Campbell K. Progress in the development of immunoanalytical methods incorporating recombinant antibodies to small molecular weight biotoxins. Anal Bioanal Chem 2015; 407:2749-70. [PMID: 25716465 DOI: 10.1007/s00216-015-8502-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Revised: 01/15/2015] [Accepted: 01/19/2015] [Indexed: 01/08/2023]
Abstract
Rapid immunoanalytical screening of food and environmental samples for small molecular weight (hapten) biotoxin contaminations requires the production of antibody reagents that possess the requisite sensitivity and specificity. To date animal-derived polyclonal (pAb) and monoclonal (mAb) antibodies have provided the binding element of the majority of these assays but recombinant antibodies (rAb) isolated from in vitro combinatorial phage display libraries are an exciting alternative due to (1) circumventing the need for experimental animals, (2) speed of production in commonly used in vitro expression systems and (3) subsequent molecular enhancement of binder performance. Short chain variable fragments (scFv) have been the most commonly employed rAb reagents for hapten biotoxin detection over the last two decades but antibody binding fragments (Fab) and single domain antibodies (sdAb) are increasing in popularity due to increased expression efficiency of functional binders and superior resistance to solvents. rAb-based immunochromatographic assays and surface plasmon resonance (SPR) biosensors have been reported to detect sub-regulatory levels of fungal (mycotoxins), marine (phycotoxins) and aquatic biotoxins in a wide range of food and environmental matrices, however this technology has yet to surpass the performances of the equivalent mAb- and pAb-based formats. As such the full potential of rAb technology in hapten biotoxin detection has yet to be achieved, but in time the inherent advantages of engineered rAb are set to provide the next generation of ultra-high performing binder reagents for the rapid and specific detection of hapten biotoxins.
Collapse
Affiliation(s)
- Owen Kavanagh
- Institute for Global Food Security (IGFS), School of Biological Sciences, Queen's University Belfast, Belfast, Northern Ireland, UK,
| | | | | |
Collapse
|
93
|
Kumar A, Baycin-Hizal D, Shiloach J, Bowen MA, Betenbaugh MJ. Coupling enrichment methods with proteomics for understanding and treating disease. Proteomics Clin Appl 2015; 9:33-47. [PMID: 25523641 DOI: 10.1002/prca.201400097] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 11/12/2014] [Accepted: 12/15/2014] [Indexed: 12/17/2022]
Abstract
Owing to recent advances in proteomics analytical methods and bioinformatics capabilities there is a growing trend toward using these capabilities for the development of drugs to treat human disease, including target and drug evaluation, understanding mechanisms of drug action, and biomarker discovery. Currently, the genetic sequences of many major organisms are available, which have helped greatly in characterizing proteomes in model animal systems and humans. Through proteomics, global profiles of different disease states can be characterized (e.g. changes in types and relative levels as well as changes in PTMs such as glycosylation or phosphorylation). Although intracellular proteomics can provide a broad overview of physiology of cells and tissues, it has been difficult to quantify the low abundance proteins which can be important for understanding the diseased states and treatment progression. For this reason, there is increasing interest in coupling comparative proteomics methods with subcellular fractionation and enrichment techniques for membranes, nucleus, phosphoproteome, glycoproteome as well as low abundance serum proteins. In this review, we will provide examples of where the utilization of different proteomics-coupled enrichment techniques has aided target and biomarker discovery, understanding the drug targeting mechanism, and mAb discovery. Taken together, these improvements will help to provide a better understanding of the pathophysiology of various diseases including cancer, autoimmunity, inflammation, cardiovascular disease, and neurological conditions, and in the design and development of better medicines for treating these afflictions.
Collapse
Affiliation(s)
- Amit Kumar
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA; Antibody Discovery and Protein Engineering, MedImmune LLC, One MedImmune Way, Gaithersburg, MD, USA; Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | | | | | | |
Collapse
|
94
|
Calis JJA, Rosenberg BR. Characterizing immune repertoires by high throughput sequencing: strategies and applications. Trends Immunol 2014; 35:581-590. [PMID: 25306219 PMCID: PMC4390416 DOI: 10.1016/j.it.2014.09.004] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 09/05/2014] [Accepted: 09/09/2014] [Indexed: 01/09/2023]
Abstract
As the key cellular effectors of adaptive immunity, T and B lymphocytes utilize specialized receptors to recognize, respond to, and neutralize a diverse array of extrinsic threats. These receptors (immunoglobulins in B lymphocytes, T cell receptors in T lymphocytes) are incredibly variable, the products of specialized genetic diversification mechanisms that generate complex lymphocyte repertoires with extensive collections of antigen specificities. Recent advances in high throughput sequencing (HTS) technologies have transformed our ability to examine antigen receptor repertoires at single nucleotide, and more recently, single cell, resolution. Here we review current approaches to examining antigen receptor repertoires by HTS, and discuss inherent biological and technical challenges. We further describe emerging applications of this powerful methodology for exploring the adaptive immune system.
Collapse
Affiliation(s)
| | - Brad R Rosenberg
- The Rockefeller University, New York, NY, USA; John C. Whitehead Presidential Fellows Program, The Rockefeller University, New York, NY, USA.
| |
Collapse
|
95
|
Tan YC, Kongpachith S, Blum LK, Ju CH, Lahey LJ, Lu DR, Cai X, Wagner CA, Lindstrom TM, Sokolove J, Robinson WH. Barcode-enabled sequencing of plasmablast antibody repertoires in rheumatoid arthritis. Arthritis Rheumatol 2014; 66:2706-15. [PMID: 24965753 DOI: 10.1002/art.38754] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 06/17/2014] [Indexed: 12/29/2022]
Abstract
OBJECTIVE A hallmark of rheumatoid arthritis (RA) is the production of autoantibodies, including anti-citrullinated protein antibodies (ACPAs). Nevertheless, the specific targets of these autoantibodies remain incompletely defined. During an immune response, B cells specific for the inciting antigen(s) are activated and differentiate into plasmablasts, which are released into the blood. We undertook this study to sequence the plasmablast antibody repertoire to define the targets of the active immune response in RA. METHODS We developed a novel DNA barcoding method to sequence the cognate heavy- and light-chain pairs of antibodies expressed by individual blood plasmablasts in RA. The method uses a universal 5' adapter that enables full-length sequencing of the antibodies' variable regions and recombinant expression of the paired antibody chains. The sequence data sets were bioinformatically analyzed to generate phylogenetic trees that identify clonal families of antibodies sharing heavy- and light-chain VJ sequences. Representative antibodies were expressed, and their binding properties were characterized using anti-cyclic citrullinated peptide 2 (anti-CCP-2) enzyme-linked immunosorbent assay (ELISA) and antigen microarrays. RESULTS We used our sequencing method to generate phylogenetic trees representing the antibody repertoires of peripheral blood plasmablasts from 4 individuals with anti-CCP+ RA, and recombinantly expressed 14 antibodies that were either "singleton" antibodies or representative of clonal antibody families. Anti-CCP-2 ELISA identified 4 ACPAs, and antigen microarray analysis identified ACPAs that differentially targeted epitopes on α-enolase, citrullinated fibrinogen, and citrullinated histone H2B. CONCLUSION Our data provide evidence that autoantibodies targeting α-enolase, citrullinated fibrinogen, and citrullinated histone H2B are produced by the ongoing activated B cell response in, and thus may contribute to the pathogenesis of, RA.
Collapse
Affiliation(s)
- Yann-Chong Tan
- Stanford University, Stanford, California, and VA Palo Alto Health Care System, Palo Alto, California
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
96
|
Lavinder JJ, Horton AP, Georgiou G, Ippolito GC. Next-generation sequencing and protein mass spectrometry for the comprehensive analysis of human cellular and serum antibody repertoires. Curr Opin Chem Biol 2014; 24:112-20. [PMID: 25461729 DOI: 10.1016/j.cbpa.2014.11.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 11/08/2014] [Accepted: 11/10/2014] [Indexed: 12/19/2022]
Abstract
Recent developments of high-throughput technologies are enabling the molecular-level analysis and bioinformatic mining of antibody-mediated (humoral) immunity in humans at an unprecedented level. These approaches explore either the sequence space of B-cell receptor repertoires using next-generation deep sequencing (BCR-seq), or the amino acid identities of antibody in blood using protein mass spectrometry (Ig-seq), or both. Generalizable principles about the molecular composition of the protective humoral immune response are being defined, and as such, the field could supersede traditional methods for the development of diagnostics, vaccines, and antibody therapeutics. Three key challenges remain and have driven recent advances: (1) incorporation of innovative techniques for paired BCR-seq to ascertain the complete antibody variable-domain VH:VL clonotype, (2) integration of proteomic Ig-seq with BCR-seq to reveal how the serum antibody repertoire compares with the antibody repertoire encoded by circulating B cells, and (3) a demand to link antibody sequence data to functional meaning (binding and protection).
Collapse
Affiliation(s)
- Jason J Lavinder
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712-1062, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712-1062, USA
| | - Andrew P Horton
- Center for Systems & Synthetic Biology, University of Texas at Austin, Austin, TX 78712-1062, USA; Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712-1062, USA
| | - George Georgiou
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712-1062, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712-1062, USA; Center for Systems & Synthetic Biology, University of Texas at Austin, Austin, TX 78712-1062, USA; Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712-1062, USA; Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712-1062, USA
| | - Gregory C Ippolito
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712-1062, USA.
| |
Collapse
|
97
|
Yang S, Jia Y, Liu X, Winters C, Wang X, Zhang Y, Devor EJ, Hovey AM, Reyes HD, Xiao X, Xu Y, Dai D, Meng X, Thiel KW, Domann FE, Leslie KK. Systematic dissection of the mechanisms underlying progesterone receptor downregulation in endometrial cancer. Oncotarget 2014; 5:9783-97. [PMID: 25229191 PMCID: PMC4259437 DOI: 10.18632/oncotarget.2392] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 08/23/2014] [Indexed: 12/21/2022] Open
Abstract
UNLABELLED Progesterone, acting through its receptor, PR (progesterone receptor), is the natural inhibitor of uterine endometrial carcinogenesis by inducing differentiation. PR is downregulated in more advanced cases of endometrial cancer, thereby limiting the effectiveness of hormonal therapy. Our objective was to understand and reverse the mechanisms underlying loss of PR expression in order to improve therapeutic outcomes. Using endometrial cancer cell lines and data from The Cancer Genome Atlas, our findings demonstrate that PR expression is downregulated at four distinct levels. In well-differentiated cancers, ligand-induced receptor activation and downregulation are intact. miRNAs mediate fine tuning of PR levels. As differentiation is lost, PR silencing is primarily at the epigenetic level. Initially, recruitment of the polycomb repressor complex 2 to the PR promoter suppresses transcription. Subsequently, DNA methylation prevents PR expression. Appropriate epigenetic modulators reverse these mechanisms. These data provide a rationale for combining epigenetic modulators with progestins as a therapeutic strategy for endometrial cancer. SIGNIFICANCE Traditional hormonal therapy for women with endometrial cancer can be molecularly enhanced by combining progestins with epigenetic modulators, thereby increasing progesterone receptor expression and significantly improving treatment efficacy.
Collapse
Affiliation(s)
- Shujie Yang
- Department of Obstetrics and Gynecology, University of Iowa, IA, 52242, USA
- Carver College of Medicine and Holden Comprehensive Cancer Center, University of Iowa, IA, 52242, USA
| | - Yichen Jia
- Department of Obstetrics and Gynecology, University of Iowa, IA, 52242, USA
| | - Xiaoyue Liu
- Department of Obstetrics and Gynecology, University of Iowa, IA, 52242, USA
| | | | - Xinjun Wang
- Department of Obstetrics and Gynecology, University of Iowa, IA, 52242, USA
| | - Yuping Zhang
- Department of Obstetrics and Gynecology, University of Iowa, IA, 52242, USA
| | - Eric J. Devor
- Department of Obstetrics and Gynecology, University of Iowa, IA, 52242, USA
| | - Adriann M. Hovey
- Department of Obstetrics and Gynecology, University of Iowa, IA, 52242, USA
| | - Henry D. Reyes
- Department of Obstetrics and Gynecology, University of Iowa, IA, 52242, USA
| | - Xue Xiao
- Department of Obstetrics and Gynecology, University of Iowa, IA, 52242, USA
| | - Yang Xu
- The Interdisciplinary Graduate Program in Informatics, University of Iowa, IA, 52242, USA
| | - Donghai Dai
- Department of Obstetrics and Gynecology, University of Iowa, IA, 52242, USA
| | - Xiangbing Meng
- Department of Obstetrics and Gynecology, University of Iowa, IA, 52242, USA
- Carver College of Medicine and Holden Comprehensive Cancer Center, University of Iowa, IA, 52242, USA
| | - Kristina W. Thiel
- Department of Obstetrics and Gynecology, University of Iowa, IA, 52242, USA
| | - Frederick E. Domann
- Free Radical and Radiation Biology Program, Department of Radiation Oncology, University of Iowa, IA, 52242, USA
- Carver College of Medicine and Holden Comprehensive Cancer Center, University of Iowa, IA, 52242, USA
| | - Kimberly K. Leslie
- Department of Obstetrics and Gynecology, University of Iowa, IA, 52242, USA
- Carver College of Medicine and Holden Comprehensive Cancer Center, University of Iowa, IA, 52242, USA
| |
Collapse
|
98
|
Greiff V, Menzel U, Haessler U, Cook SC, Friedensohn S, Khan TA, Pogson M, Hellmann I, Reddy ST. Quantitative assessment of the robustness of next-generation sequencing of antibody variable gene repertoires from immunized mice. BMC Immunol 2014; 15:40. [PMID: 25318652 PMCID: PMC4233042 DOI: 10.1186/s12865-014-0040-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 09/15/2014] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) of antibody variable regions has emerged as a powerful tool in systems immunology by providing quantitative molecular information on polyclonal humoral immune responses. Reproducible and robust information on antibody repertoires is valuable for basic and applied immunology studies: thus, it is essential to establish the reliability of antibody NGS data. RESULTS We isolated RNA from antibody-secreting cells (ASCs) from either 1 mouse or a pool of 9 immunized mice in order to simulate both normal and high diversity populations. Next, we prepared three technical replicates of antibody libraries by RT-PCR from each diversity scenario, which were sequenced using the Illumina MiSeq platform resulting in >106 250 bp paired-end reads per replicate. We then assessed the robustness of antibody repertoire data based on clonal identification defined by amino acid sequence of either full-length VDJ region or the complementarity determining region 3 (CDR3). Leveraging modeling approaches adapted from mathematical ecology, we found that in either diversity scenario both CDR3 and VDJ detection nears completeness indicating deep coverage of ASC repertoires. Additionally, we defined reliability thresholds for accurate quantification and ranking of CDR3s and VDJs. Importantly, we show that both factors-(i) replicate sequencing and (ii) sequencing depth-are crucial for robust CDR3 and VDJ detection and ranking. CONCLUSIONS In summary, we established widely applicable experimental and computational guidelines for robust antibody NGS and analysis, which will help advance systems immunology studies related to the quantitative profiling of antibody responses following infection and vaccination.
Collapse
Affiliation(s)
- Victor Greiff
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Ulrike Menzel
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Ulrike Haessler
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Skylar C Cook
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Simon Friedensohn
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Tarik A Khan
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Mark Pogson
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Ina Hellmann
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| |
Collapse
|
99
|
Exploiting the proteomics revolution in biotechnology: from disease and antibody targets to optimizing bioprocess development. Curr Opin Biotechnol 2014; 30:80-6. [PMID: 24997444 DOI: 10.1016/j.copbio.2014.06.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 06/02/2014] [Accepted: 06/08/2014] [Indexed: 11/24/2022]
Abstract
Recent advancements in proteomics have enabled the generation of high-quality data sets useful for applications ranging from target and monoclonal antibody (mAB) discovery to bioprocess optimization. Comparative proteomics approaches have recently been used to identify novel disease targets in oncology and other disease conditions. Proteomics has also been applied as a new avenue for mAb discovery. Finally, CHO and Escherichia coli cells represent the dominant production hosts for biopharmaceutical development, yet the physiology of these cells types has yet to be fully established. Proteomics approaches can provide new insights into these cell types, aiding in recombinant protein production, cell growth regulation, and medium formulation. Optimization of sample preparations and protein database developments are enhancing the quantity and accuracy of proteomic results. In these ways, innovations in proteomics are enriching biotechnology and bioprocessing research across a wide spectrum of applications.
Collapse
|
100
|
Poston CN, Higgs RE, You J, Gelfanova V, Hale JE, Knierman MD, Siegel R, Gutierrez JA. A quantitative tool to distinguish isobaric leucine and isoleucine residues for mass spectrometry-based de novo monoclonal antibody sequencing. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1228-1236. [PMID: 24845350 DOI: 10.1007/s13361-014-0892-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 03/05/2014] [Accepted: 03/10/2014] [Indexed: 06/03/2023]
Abstract
De novo sequencing by mass spectrometry (MS) allows for the determination of the complete amino acid (AA) sequence of a given protein based on the mass difference of detected ions from MS/MS fragmentation spectra. The technique relies on obtaining specific masses that can be attributed to characteristic theoretical masses of AAs. A major limitation of de novo sequencing by MS is the inability to distinguish between the isobaric residues leucine (Leu) and isoleucine (Ile). Incorrect identification of Ile as Leu or vice versa often results in loss of activity in recombinant antibodies. This functional ambiguity is commonly resolved with costly and time-consuming AA mutation and peptide sequencing experiments. Here, we describe a set of orthogonal biochemical protocols, which experimentally determine the identity of Ile or Leu residues in monoclonal antibodies (mAb) based on the selectivity that leucine aminopeptidase shows for n-terminal Leu residues and the cleavage preference for Leu by chymotrypsin. The resulting observations are combined with germline frequencies and incorporated into a logistic regression model, called Predictor for Xle Sites (PXleS) to provide a statistical likelihood for the identity of Leu at an ambiguous site. We demonstrate that PXleS can generate a probability for an Xle site in mAbs with 96% accuracy. The implementation of PXleS precludes the expression of several possible sequences and, therefore, reduces the overall time and resources required to go from spectra generation to a biologically active sequence for a mAb when an Ile or Leu residue is in question.
Collapse
Affiliation(s)
- Chloe N Poston
- Lilly Research Laboratories, Lilly Corporate Center, Indianapolis, IN, 46285, USA
| | | | | | | | | | | | | | | |
Collapse
|