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Velappan N, Ferrara F, D’Angelo S, Close D, Naranjo L, Bolding MR, Mozden SC, Troup CB, McCullough DK, Gomez A, Kedge M, Bradbury ARM. Direct selection of functional fluorescent-protein antibody fusions by yeast display. PLoS One 2023; 18:e0280930. [PMID: 36827414 PMCID: PMC9956592 DOI: 10.1371/journal.pone.0280930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 01/11/2023] [Indexed: 02/26/2023] Open
Abstract
Antibodies are important reagents for research, diagnostics, and therapeutics. Many examples of chimeric proteins combining the specific target recognition of antibodies with complementing functionalities such as fluorescence, toxicity or enzymatic activity have been described. However, antibodies selected solely on the basis of their binding specificities are not necessarily ideal candidates for the construction of chimeras. Here, we describe a high throughput method based on yeast display to directly select antibodies most suitable for conversion to fluorescent chimera. A library of scFv binders was converted to a fluorescent chimeric form, by cloning thermal green protein into the linker between VH and VL, and directly selecting for both binding and fluorescent functionality. This allowed us to directly identify antibodies functional in the single chain TGP format, that manifest higher protein expression, easier protein purification, and one-step binding assays.
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Affiliation(s)
- Nileena Velappan
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | | | - Sara D’Angelo
- Specifica Inc., Santa Fe, NM, United States of America
| | - Devin Close
- Arup Laboratories, Salt Lake City, UT, United States of America
| | | | - Madeline R. Bolding
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Sarah C. Mozden
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | | | - Donna K. McCullough
- Microbiology Department, University of Tennessee, Knoxville, TN, United States of America
| | - Analyssa Gomez
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Marijo Kedge
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
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Zheng B, Yang Y, Chen L, Wu M, Zhou S. B-Cell Receptor Repertoire Sequencing: Deeper Digging into the Mechanisms and Clinical Aspects of Immune-mediated Diseases. iScience 2022; 25:105002. [PMID: 36157582 PMCID: PMC9494237 DOI: 10.1016/j.isci.2022.105002] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
B cells play an essential role in adaptive immunity and are intimately correlated with pleiotropic immune-mediated diseases. Each B cell occupies a unique B cell receptor (BCR), and all BCRs throughout our body form “BCR repertoire.” With the development of sequencing technology and coupled bioinformatics, accumulating evidence indicates that BCR repertoire largely varies under physiological and pathological conditions. Therefore, comprehensive grasp of BCR repertoire will provide new insights into the pathogenesis of immune-mediated diseases and help exploit efficient diagnostic and treatment strategies. In this review, we start with an overview of BCR repertoire and related sequencing technologies and summarize their current applications in immune-mediated diseases. We also underscore the challenges of this emerging field and propose promising future directions in advancing BCR repertoire exploration.
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Affiliation(s)
- Bohao Zheng
- Wuxi School of Medicine, Jiangnan University, Wuxi, P. R. China
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, P. R. China
| | - Yuqing Yang
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, P. R. China
| | - Lin Chen
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, P. R. China
| | - Mengrui Wu
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, P. R. China
| | - Shengtao Zhou
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, P. R. China
- Corresponding author
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3
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Heydarchi B, Fong DS, Gao H, Salazar-Quiroz NA, Edwards JM, Gonelli CA, Grimley S, Aktepe TE, Mackenzie C, Wales WJ, van Gils MJ, Cupo A, Rouiller I, Gooley PR, Moore JP, Sanders RW, Montefiori D, Sethi A, Purcell DFJ. Broad and ultra-potent cross-clade neutralization of HIV-1 by a vaccine-induced CD4 binding site bovine antibody. Cell Rep Med 2022; 3:100635. [PMID: 35584627 PMCID: PMC9133467 DOI: 10.1016/j.xcrm.2022.100635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/27/2022] [Accepted: 04/22/2022] [Indexed: 11/30/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) vaccination of cows has elicited broadly neutralizing antibodies (bNAbs). In this study, monoclonal antibodies (mAbs) are isolated from a clade A (KNH1144 and BG505) vaccinated cow using a heterologous clade B antigen (AD8). CD4 binding site (CD4bs) bNAb (MEL-1872) is more potent than a majority of CD4bs bNAbs isolated so far. MEL-1872 mAb with CDRH3 of 57 amino acids shows more potency (geometric mean half-maximal inhibitory concentration [IC50]: 0.009 μg/mL; breadth: 66%) than VRC01 against clade B viruses (29-fold) and than CHO1-31 against tested clade A viruses (21-fold). It also shows more breadth and potency than NC-Cow1, the only other reported anti-HIV-1 bovine bNAb, which has 60% breadth with geometric mean IC50 of 0.090 μg/mL in this study. Using successive different stable-structured SOSIP trimers in bovines can elicit bNAbs focusing on epitopes ubiquitous across subtypes. Furthermore, the cross-clade selection strategy also results in ultra-potent bNAbs. Sequential vaccine with different SOSIP trimers could elicit bNAbs Cross-clade B-cell-sorting probe could select ultra-potent bNAbs Bovine CD4bs monoclonal antibody neutralizes HIV-1 isolates potently
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Affiliation(s)
- Behnaz Heydarchi
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Danielle S Fong
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Hongmei Gao
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Natalia A Salazar-Quiroz
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Jack M Edwards
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Christopher A Gonelli
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Samantha Grimley
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Turgut E Aktepe
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Charlene Mackenzie
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - William J Wales
- Dairy Production Sciences, Victorian Department of Jobs, Precincts and Resources, Ellinbank, VIC, Australia; Centre for Agricultural Innovation, School of Agriculture and Food, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Marit J van Gils
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105AZ Amsterdam, the Netherlands
| | - Albert Cupo
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Isabelle Rouiller
- Department of Biochemistry & Pharmacology, The University of Melbourne, Melbourne, VIC 3010, Australia; Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia; Australian Research Council Centre for Cryo-Electron Microscopy of Membrane Proteins, Parkville, VIC, Australia
| | - Paul R Gooley
- Department of Biochemistry & Pharmacology, The University of Melbourne, Melbourne, VIC 3010, Australia; Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - John P Moore
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Rogier W Sanders
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, 1105AZ Amsterdam, the Netherlands; Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - David Montefiori
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Ashish Sethi
- Department of Biochemistry & Pharmacology, The University of Melbourne, Melbourne, VIC 3010, Australia; Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Damian F J Purcell
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection Immunity, University of Melbourne, Melbourne, VIC 3000, Australia.
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4
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A single donor is sufficient to produce a highly functional in vitro antibody library. Commun Biol 2021; 4:350. [PMID: 33742103 PMCID: PMC7979914 DOI: 10.1038/s42003-021-01881-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/19/2021] [Indexed: 01/31/2023] Open
Abstract
Antibody complementarity determining region diversity has been considered to be the most important metric for the production of a functional antibody library. Generally, the greater the antibody library diversity, the greater the probability of selecting a diverse array of high affinity leads. According to this paradigm, the primary means of elevating library diversity has been by increasing the number of donors. In the present study we explored the possibility of creating an in vitro antibody library from a single healthy individual, showing that the number of lymphocytes, rather than the number of donors, is the key criterion in the production of a diverse and functional antibody library. We describe the construction of a high-quality phage display library comprising 5 × 109 human antibodies by applying an efficient B cell extraction protocol from a single donor and a targeted V-gene amplification strategy favoring specific antibody families for their improved developability profiles. Each step of the library generation process was followed and validated by next generation sequencing to monitor the library quality and diversity. The functionality of the library was tested using several therapeutically relevant targets for which a vast number of different antibodies with desired biophysical properties were obtained.
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Ferrara F, Teixeira AA, Naranjo L, Erasmus MF, D'Angelo S, Bradbury ARM. Exploiting next-generation sequencing in antibody selections - a simple PCR method to recover binders. MAbs 2021; 12:1701792. [PMID: 31829073 PMCID: PMC7009332 DOI: 10.1080/19420862.2019.1701792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Antibody discovery using invitro display technologies such as phage and/or yeast display has become acornerstone in many research and development projects, including the creation of new drugs for clinical use. Traditionally, after the selection phase, random clones are isolated for binding validation and Sanger sequencing. More recently, next-generation sequencing (NGS) technology has allowed deeper insight into the antibody population after aselection campaign, enabling the identification of many more specific binders. However, this approach only provides the DNA sequences of potential binders, the properties of which need to be fully elucidated by obtaining corresponding clones and expressing them for further validation. Here we present arapid novel method to harvest potential clones identified by NGS that uses asimple PCR and yeast recombination approach. The protocol was tested in selections against three different targets and was able to recover clones at an abundance level that would be impractical to identify using traditional methods.
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Affiliation(s)
| | - Andre A Teixeira
- Specifica Inc., Santa Fe, NM, USA.,Bioscience Division, New Mexico Consortium, Los Alamos, NM, USA
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Lehmann-Horn K, Irani SR, Wang S, Palanichamy A, Jahn S, Greenfield AL, Dandekar R, Lepennetier G, Michael S, Gelfand JM, Geschwind MD, Wilson MR, Zamvil SS, von Büdingen HC. Intrathecal B-cell activation in LGI1 antibody encephalitis. NEUROLOGY-NEUROIMMUNOLOGY & NEUROINFLAMMATION 2020; 7:7/2/e669. [PMID: 32029531 PMCID: PMC7051206 DOI: 10.1212/nxi.0000000000000669] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 12/23/2019] [Indexed: 01/17/2023]
Abstract
Objective To study intrathecal B-cell activity in leucine-rich, glioma-inactivated 1 (LGI1) antibody encephalitis. In patients with LGI1 antibodies, the lack of CSF lymphocytosis or oligoclonal bands and serum-predominant LGI1 antibodies suggests a peripherally initiated immune response. However, it is unknown whether B cells within the CNS contribute to the ongoing pathogenesis of LGI1 antibody encephalitis. Methods Paired CSF and peripheral blood (PB) mononuclear cells were collected from 6 patients with LGI1 antibody encephalitis and 2 patients with other neurologic diseases. Deep B-cell immune repertoire sequencing was performed on immunoglobulin heavy chain transcripts from CSF B cells and sorted PB B-cell subsets. In addition, LGI1 antibody levels were determined in CSF and PB. Results Serum LGI1 antibody titers were on average 127-fold higher than CSF LGI1 antibody titers. Yet, deep B-cell repertoire analysis demonstrated a restricted CSF repertoire with frequent extensive clusters of clonally related B cells connected to mature PB B cells. These clusters showed intensive mutational activity of CSF B cells, providing strong evidence for an independent CNS-based antigen-driven response in patients with LGI1 antibody encephalitis but not in controls. Conclusions Our results demonstrate that intrathecal immunoglobulin repertoire expansion is a feature of LGI1 antibody encephalitis and suggests a need for CNS-penetrant therapies.
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Affiliation(s)
- Klaus Lehmann-Horn
- From the Department of Neurology (K.L.-H., S.W., A.P., S.J., A.L.G., R.D., J.M.G., M.D.G., M.R.W., S.S.Z., H.-C.v.B.), UCSF Weill Institute for Neurosciences; Program in Immunology (K.L.-H., S.S.Z.), UCSF, San Francisco, CA; Department of Neurology (K.L.-H., G.L.), Klinikum rechts der Isar, Technische Universität München, Germany; and Oxford Autoimmune Neurology Group (S.R.I., S.M.), John Radcliffe Hospital, University of Oxford, UK.
| | - Sarosh R Irani
- From the Department of Neurology (K.L.-H., S.W., A.P., S.J., A.L.G., R.D., J.M.G., M.D.G., M.R.W., S.S.Z., H.-C.v.B.), UCSF Weill Institute for Neurosciences; Program in Immunology (K.L.-H., S.S.Z.), UCSF, San Francisco, CA; Department of Neurology (K.L.-H., G.L.), Klinikum rechts der Isar, Technische Universität München, Germany; and Oxford Autoimmune Neurology Group (S.R.I., S.M.), John Radcliffe Hospital, University of Oxford, UK
| | - Shengzhi Wang
- From the Department of Neurology (K.L.-H., S.W., A.P., S.J., A.L.G., R.D., J.M.G., M.D.G., M.R.W., S.S.Z., H.-C.v.B.), UCSF Weill Institute for Neurosciences; Program in Immunology (K.L.-H., S.S.Z.), UCSF, San Francisco, CA; Department of Neurology (K.L.-H., G.L.), Klinikum rechts der Isar, Technische Universität München, Germany; and Oxford Autoimmune Neurology Group (S.R.I., S.M.), John Radcliffe Hospital, University of Oxford, UK
| | - Arumugam Palanichamy
- From the Department of Neurology (K.L.-H., S.W., A.P., S.J., A.L.G., R.D., J.M.G., M.D.G., M.R.W., S.S.Z., H.-C.v.B.), UCSF Weill Institute for Neurosciences; Program in Immunology (K.L.-H., S.S.Z.), UCSF, San Francisco, CA; Department of Neurology (K.L.-H., G.L.), Klinikum rechts der Isar, Technische Universität München, Germany; and Oxford Autoimmune Neurology Group (S.R.I., S.M.), John Radcliffe Hospital, University of Oxford, UK
| | - Sarah Jahn
- From the Department of Neurology (K.L.-H., S.W., A.P., S.J., A.L.G., R.D., J.M.G., M.D.G., M.R.W., S.S.Z., H.-C.v.B.), UCSF Weill Institute for Neurosciences; Program in Immunology (K.L.-H., S.S.Z.), UCSF, San Francisco, CA; Department of Neurology (K.L.-H., G.L.), Klinikum rechts der Isar, Technische Universität München, Germany; and Oxford Autoimmune Neurology Group (S.R.I., S.M.), John Radcliffe Hospital, University of Oxford, UK
| | - Ariele L Greenfield
- From the Department of Neurology (K.L.-H., S.W., A.P., S.J., A.L.G., R.D., J.M.G., M.D.G., M.R.W., S.S.Z., H.-C.v.B.), UCSF Weill Institute for Neurosciences; Program in Immunology (K.L.-H., S.S.Z.), UCSF, San Francisco, CA; Department of Neurology (K.L.-H., G.L.), Klinikum rechts der Isar, Technische Universität München, Germany; and Oxford Autoimmune Neurology Group (S.R.I., S.M.), John Radcliffe Hospital, University of Oxford, UK
| | - Ravi Dandekar
- From the Department of Neurology (K.L.-H., S.W., A.P., S.J., A.L.G., R.D., J.M.G., M.D.G., M.R.W., S.S.Z., H.-C.v.B.), UCSF Weill Institute for Neurosciences; Program in Immunology (K.L.-H., S.S.Z.), UCSF, San Francisco, CA; Department of Neurology (K.L.-H., G.L.), Klinikum rechts der Isar, Technische Universität München, Germany; and Oxford Autoimmune Neurology Group (S.R.I., S.M.), John Radcliffe Hospital, University of Oxford, UK
| | - Gildas Lepennetier
- From the Department of Neurology (K.L.-H., S.W., A.P., S.J., A.L.G., R.D., J.M.G., M.D.G., M.R.W., S.S.Z., H.-C.v.B.), UCSF Weill Institute for Neurosciences; Program in Immunology (K.L.-H., S.S.Z.), UCSF, San Francisco, CA; Department of Neurology (K.L.-H., G.L.), Klinikum rechts der Isar, Technische Universität München, Germany; and Oxford Autoimmune Neurology Group (S.R.I., S.M.), John Radcliffe Hospital, University of Oxford, UK
| | - Sophia Michael
- From the Department of Neurology (K.L.-H., S.W., A.P., S.J., A.L.G., R.D., J.M.G., M.D.G., M.R.W., S.S.Z., H.-C.v.B.), UCSF Weill Institute for Neurosciences; Program in Immunology (K.L.-H., S.S.Z.), UCSF, San Francisco, CA; Department of Neurology (K.L.-H., G.L.), Klinikum rechts der Isar, Technische Universität München, Germany; and Oxford Autoimmune Neurology Group (S.R.I., S.M.), John Radcliffe Hospital, University of Oxford, UK
| | - Jeffrey M Gelfand
- From the Department of Neurology (K.L.-H., S.W., A.P., S.J., A.L.G., R.D., J.M.G., M.D.G., M.R.W., S.S.Z., H.-C.v.B.), UCSF Weill Institute for Neurosciences; Program in Immunology (K.L.-H., S.S.Z.), UCSF, San Francisco, CA; Department of Neurology (K.L.-H., G.L.), Klinikum rechts der Isar, Technische Universität München, Germany; and Oxford Autoimmune Neurology Group (S.R.I., S.M.), John Radcliffe Hospital, University of Oxford, UK
| | - Michael D Geschwind
- From the Department of Neurology (K.L.-H., S.W., A.P., S.J., A.L.G., R.D., J.M.G., M.D.G., M.R.W., S.S.Z., H.-C.v.B.), UCSF Weill Institute for Neurosciences; Program in Immunology (K.L.-H., S.S.Z.), UCSF, San Francisco, CA; Department of Neurology (K.L.-H., G.L.), Klinikum rechts der Isar, Technische Universität München, Germany; and Oxford Autoimmune Neurology Group (S.R.I., S.M.), John Radcliffe Hospital, University of Oxford, UK
| | - Michael R Wilson
- From the Department of Neurology (K.L.-H., S.W., A.P., S.J., A.L.G., R.D., J.M.G., M.D.G., M.R.W., S.S.Z., H.-C.v.B.), UCSF Weill Institute for Neurosciences; Program in Immunology (K.L.-H., S.S.Z.), UCSF, San Francisco, CA; Department of Neurology (K.L.-H., G.L.), Klinikum rechts der Isar, Technische Universität München, Germany; and Oxford Autoimmune Neurology Group (S.R.I., S.M.), John Radcliffe Hospital, University of Oxford, UK
| | - Scott S Zamvil
- From the Department of Neurology (K.L.-H., S.W., A.P., S.J., A.L.G., R.D., J.M.G., M.D.G., M.R.W., S.S.Z., H.-C.v.B.), UCSF Weill Institute for Neurosciences; Program in Immunology (K.L.-H., S.S.Z.), UCSF, San Francisco, CA; Department of Neurology (K.L.-H., G.L.), Klinikum rechts der Isar, Technische Universität München, Germany; and Oxford Autoimmune Neurology Group (S.R.I., S.M.), John Radcliffe Hospital, University of Oxford, UK
| | - H-Christian von Büdingen
- From the Department of Neurology (K.L.-H., S.W., A.P., S.J., A.L.G., R.D., J.M.G., M.D.G., M.R.W., S.S.Z., H.-C.v.B.), UCSF Weill Institute for Neurosciences; Program in Immunology (K.L.-H., S.S.Z.), UCSF, San Francisco, CA; Department of Neurology (K.L.-H., G.L.), Klinikum rechts der Isar, Technische Universität München, Germany; and Oxford Autoimmune Neurology Group (S.R.I., S.M.), John Radcliffe Hospital, University of Oxford, UK
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Martinez BI, Stabenfeldt SE. Current trends in biomarker discovery and analysis tools for traumatic brain injury. J Biol Eng 2019; 13:16. [PMID: 30828380 PMCID: PMC6381710 DOI: 10.1186/s13036-019-0145-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 02/06/2019] [Indexed: 12/13/2022] Open
Abstract
Traumatic brain injury (TBI) affects 1.7 million people in the United States each year, causing lifelong functional deficits in cognition and behavior. The complex pathophysiology of neural injury is a primary barrier to developing sensitive and specific diagnostic tools, which consequentially has a detrimental effect on treatment regimens. Biomarkers of other diseases (e.g. cancer) have provided critical insight into disease emergence and progression that lend to developing powerful clinical tools for intervention. Therefore, the biomarker discovery field has recently focused on TBI and made substantial advancements to characterize markers with promise of transforming TBI patient diagnostics and care. This review focuses on these key advances in neural injury biomarkers discovery, including novel approaches spanning from omics-based approaches to imaging and machine learning as well as the evolution of established techniques.
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Affiliation(s)
- Briana I. Martinez
- School of Life Sciences, Arizona State University, Tempe, AZ USA
- School of Biological and Health Systems Engineering, Ira A. Fulton School of Engineering, Arizona State University, PO Box 879709, Tempe, AZ 85287-9709 USA
| | - Sarah E. Stabenfeldt
- School of Biological and Health Systems Engineering, Ira A. Fulton School of Engineering, Arizona State University, PO Box 879709, Tempe, AZ 85287-9709 USA
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8
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Ramage W, Gaiotto T, Ball C, Risley P, Carnell GW, Temperton N, Cheung CY, Engelhardt OG, Hufton SE. Cross-Reactive and Lineage-Specific Single Domain Antibodies against Influenza B Hemagglutinin. Antibodies (Basel) 2019; 8:E14. [PMID: 31544820 PMCID: PMC6640691 DOI: 10.3390/antib8010014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 01/30/2019] [Accepted: 02/01/2019] [Indexed: 11/23/2022] Open
Abstract
Influenza B virus (IBV) circulates in the human population and causes considerable disease burden worldwide, each year. Current IBV vaccines can struggle to mount an effective cross-reactive immune response, as strains become mismatched, due to constant antigenic changes. Additional strategies which use monoclonal antibodies, with broad reactivity, are of considerable interest, both, as diagnostics and as immunotherapeutics. Alternatives to conventional monoclonal antibodies, such as single domain antibodies (NanobodiesTM) with well-documented advantages for applications in infectious disease, have been emerging. In this study we have isolated single domain antibodies (sdAbs), specific to IBV, using alpacas immunised with recombinant hemagglutinin (HA) from two representative viruses, B/Florida/04/2006 (B/Yamagata lineage) and B/Brisbane/60/2008 (B/Victoria lineage). Using phage display, we have isolated a panel of single domain antibodies (sdAbs), with both cross-reactive and lineage-specific binding. Several sdAbs recognise whole virus antigens, corresponding to influenza B strains included in vaccines spanning over 20 years, and were capable of neutralising IBV pseudotypes corresponding to prototype strains from both lineages. Lineage-specific sdAbs recognised the head domain, whereas, sdAbs identified as cross-reactive could be classified as either head binding or stem binding. Using yeast display, we were able to correlate lineage specificity with naturally occurring sequence divergence, at residue 122 in the highly variable 120 loop of the HA1 domain. The single domain antibodies described, might have applications in IBV diagnostics, vaccine potency testing and as immunotherapeutics.
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Affiliation(s)
- Walter Ramage
- Biotherapeutics Division, National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, UK.
| | - Tiziano Gaiotto
- Biotherapeutics Division, National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, UK.
| | - Christina Ball
- Biotherapeutics Division, National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, UK.
| | - Paul Risley
- Biotherapeutics Division, National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, UK.
| | - George W Carnell
- Infectious Diseases and Allergy Group, School of Pharmacy, University of Kent, Kent ME4 4TB, UK.
| | - Nigel Temperton
- Infectious Diseases and Allergy Group, School of Pharmacy, University of Kent, Kent ME4 4TB, UK.
| | - Chung Y Cheung
- Division of Virology, National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, UK.
| | - Othmar G Engelhardt
- Division of Virology, National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, UK.
| | - Simon E Hufton
- Biotherapeutics Division, National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3QG, UK.
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9
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Stutz CC, Georgieva JV, Shusta EV. Coupling Brain Perfusion Screens and Next Generation Sequencing to Identify Blood-Brain Barrier Binding Antibodies. AIChE J 2018; 64:4229-4236. [PMID: 30872841 DOI: 10.1002/aic.16360] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Antibodies that target the blood-brain barrier (BBB) in vivo are of particular interest for the treatment of neurological diseases. Here, we screened a phage display single-chain antibody (scFv) library by brain perfusion in an attempt to isolate scFv that target the rat BBB. After four rounds of screening, the resulting antibody pool remained highly complex and discrete clonal sampling did not identify any scFvs capable of binding to the rat BBB. Thus, the heavy chain CDR3 in the resulting pools was subjected to NGS, and the resulting data was used to identify 12 scFv clones that were of high abundance and/or enriched from round 3 to 4, signifying potential hits. Of these, two scFv, denoted scFv 4 and scFv 40, were identified that bound the rat BBB. Neither of these scFvs was identified by discrete sampling, motivating NGS as a tool to identify lead antibodies from complex in vivo screens.
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Affiliation(s)
- Charles C. Stutz
- Dept. of Chemical and Biological Engineering University of Wisconsin—Madison Madison WI 53706
| | - Julia V. Georgieva
- Dept. of Chemical and Biological Engineering University of Wisconsin—Madison Madison WI 53706
| | - Eric V. Shusta
- Dept. of Chemical and Biological Engineering University of Wisconsin—Madison Madison WI 53706
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10
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Abstract
The display of antibodies on the surface of Saccharomyces cerevisiae cells enables the high-throughput and precise selection of specific binders for the target antigen. The recent implementation of next-generation sequencing (NGS) to antibody display screening provides a complete picture of the entire selected polyclonal population. As such, NGS overcomes the limitations of random clones screening, but it comes with two main limitations: (1) depending upon the platform, the sequencing is usually restricted to the variable heavy chain domain complementary determining region 3 (HCDR3), or VH gene, and does not provide additional information on the rest of the antibody gene, including the VL; and (2) the sequence-identified clones are not physically available for validation. Here, we describe a rapid and effective protocol based on an inverse-PCR method to recover specific antibody clones based on their HCDR3 sequence from a yeast display selection output.
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11
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D'Angelo S, Staquicini FI, Ferrara F, Staquicini DI, Sharma G, Tarleton CA, Nguyen H, Naranjo LA, Sidman RL, Arap W, Bradbury AR, Pasqualini R. Selection of phage-displayed accessible recombinant targeted antibodies (SPARTA): methodology and applications. JCI Insight 2018; 3:98305. [PMID: 29720567 DOI: 10.1172/jci.insight.98305] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 04/05/2018] [Indexed: 11/17/2022] Open
Abstract
We developed a potentially novel and robust antibody discovery methodology, termed selection of phage-displayed accessible recombinant targeted antibodies (SPARTA). This combines an in vitro screening step of a naive human antibody library against known tumor targets, with in vivo selections based on tumor-homing capabilities of a preenriched antibody pool. This unique approach overcomes several rate-limiting challenges to generate human antibodies amenable to rapid translation into medical applications. As a proof of concept, we evaluated SPARTA on 2 well-established tumor cell surface targets, EphA5 and GRP78. We evaluated antibodies that showed tumor-targeting selectivity as a representative panel of antibody-drug conjugates (ADCs) and were highly efficacious. Our results validate a discovery platform to identify and validate monoclonal antibodies with favorable tumor-targeting attributes. This approach may also extend to other diseases with known cell surface targets and affected tissues easily isolated for in vivo selection.
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Affiliation(s)
| | - Fernanda I Staquicini
- Rutgers Cancer Institute of New Jersey at University Hospital and Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | | | - Daniela I Staquicini
- Rutgers Cancer Institute of New Jersey at University Hospital and Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Geetanjali Sharma
- University of New Mexico Comprehensive Cancer Center, University of New Mexico School of Medicine, Albuquerque, New Mexico, USA
| | - Christy A Tarleton
- University of New Mexico Comprehensive Cancer Center, University of New Mexico School of Medicine, Albuquerque, New Mexico, USA
| | - Huynh Nguyen
- University of New Mexico Comprehensive Cancer Center, University of New Mexico School of Medicine, Albuquerque, New Mexico, USA
| | | | - Richard L Sidman
- Department of Neurology, Harvard Medical School, Boston, Massachusetts, USA
| | - Wadih Arap
- Rutgers Cancer Institute of New Jersey at University Hospital and Division of Hematology/Oncology, Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | | | - Renata Pasqualini
- Rutgers Cancer Institute of New Jersey at University Hospital and Division of Cancer Biology, Department of Radiation Oncology, Rutgers New Jersey Medical School, Newark, New Jersey, USA
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12
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Abstract
Somatic assembly of T cell receptor and B cell receptor (BCR) genes produces a vast diversity of lymphocyte antigen recognition capacity. The advent of efficient high-throughput sequencing of lymphocyte antigen receptor genes has recently generated unprecedented opportunities for exploration of adaptive immune responses. With these opportunities have come significant challenges in understanding the analysis techniques that most accurately reflect underlying biological phenomena. In this regard, sample preparation and sequence analysis techniques, which have largely been borrowed and adapted from other fields, continue to evolve. Here, we review current methods and challenges of library preparation, sequencing and statistical analysis of lymphocyte receptor repertoire studies. We discuss the general steps in the process of immune repertoire generation including sample preparation, platforms available for sequencing, processing of sequencing data, measurable features of the immune repertoire, and the statistical tools that can be used for analysis and interpretation of the data. Because BCR analysis harbors additional complexities, such as immunoglobulin (Ig) (i.e., antibody) gene somatic hypermutation and class switch recombination, the emphasis of this review is on Ig/BCR sequence analysis.
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Affiliation(s)
- Neha Chaudhary
- Division of Rheumatology, Department of Medicine, Immunology and Allergy, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Duane R. Wesemann
- Division of Rheumatology, Department of Medicine, Immunology and Allergy, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
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13
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D'Angelo S, Ferrara F, Naranjo L, Erasmus MF, Hraber P, Bradbury ARM. Many Routes to an Antibody Heavy-Chain CDR3: Necessary, Yet Insufficient, for Specific Binding. Front Immunol 2018; 9:395. [PMID: 29568296 PMCID: PMC5852061 DOI: 10.3389/fimmu.2018.00395] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 02/13/2018] [Indexed: 12/11/2022] Open
Abstract
Because of its great potential for diversity, the immunoglobulin heavy-chain complementarity-determining region 3 (HCDR3) is taken as an antibody molecule’s most important component in conferring binding activity and specificity. For this reason, HCDR3s have been used as unique identifiers to investigate adaptive immune responses in vivo and to characterize in vitro selection outputs where display systems were employed. Here, we show that many different HCDR3s can be identified within a target-specific antibody population after in vitro selection. For each identified HCDR3, a number of different antibodies bearing differences elsewhere can be found. In such selected populations, all antibodies with the same HCDR3 recognize the target, albeit at different affinities. In contrast, within unselected populations, the majority of antibodies with the same HCDR3 sequence do not bind the target. In one HCDR3 examined in depth, all target-specific antibodies were derived from the same VDJ rearrangement, while non-binding antibodies with the same HCDR3 were derived from many different V and D gene rearrangements. Careful examination of previously published in vivo datasets reveals that HCDR3s shared between, and within, different individuals can also originate from rearrangements of different V and D genes, with up to 26 different rearrangements yielding the same identical HCDR3 sequence. On the basis of these observations, we conclude that the same HCDR3 can be generated by many different rearrangements, but that specific target binding is an outcome of unique rearrangements and VL pairing: the HCDR3 is necessary, albeit insufficient, for specific antibody binding.
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Affiliation(s)
| | | | | | | | - Peter Hraber
- Los Alamos National Laboratory, Los Alamos, NM, United States
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14
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Rouet R, Jackson KJL, Langley DB, Christ D. Next-Generation Sequencing of Antibody Display Repertoires. Front Immunol 2018; 9:118. [PMID: 29472918 PMCID: PMC5810246 DOI: 10.3389/fimmu.2018.00118] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 01/15/2018] [Indexed: 01/09/2023] Open
Abstract
In vitro selection technology has transformed the development of therapeutic monoclonal antibodies. Using methods such as phage, ribosome, and yeast display, high affinity binders can be selected from diverse repertoires. Here, we review strategies for the next-generation sequencing (NGS) of phage- and other antibody-display libraries, as well as NGS platforms and analysis tools. Moreover, we discuss recent examples relating to the use of NGS to assess library diversity, clonal enrichment, and affinity maturation.
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Affiliation(s)
- Romain Rouet
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | | | - David B Langley
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Daniel Christ
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,Faculty of Medicine, St Vincent's Clinical School, The University of New South Wales, Sydney, NSW, Australia
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15
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Prohaska TA, Que X, Diehl CJ, Hendrikx S, Chang MW, Jepsen K, Glass CK, Benner C, Witztum JL. Massively Parallel Sequencing of Peritoneal and Splenic B Cell Repertoires Highlights Unique Properties of B-1 Cell Antibodies. THE JOURNAL OF IMMUNOLOGY 2018; 200:1702-1717. [PMID: 29378911 PMCID: PMC5821571 DOI: 10.4049/jimmunol.1700568] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 01/03/2018] [Indexed: 12/26/2022]
Abstract
B-1 cells are a unique subset of B cells that are positively selected for expressing autoreactive BCRs. We isolated RNA from peritoneal (B-1a, B-1b, B-2) and splenic (B-1a, marginal zone, follicular) B cells from C57BL/6 mice and used 5'-RACE to amplify the IgH V region using massively parallel sequencing. By analyzing 379,000 functional transcripts, we demonstrate that B-1a cells use a distinct and restricted repertoire. All B-1 cell subsets, especially peritoneal B-1a cells, had a high proportion of sequences without N additions, suggesting predominantly prenatal development. Their transcripts differed markedly and uniquely contained VH11 and VH12 genes, which were rearranged only with a restricted selection of D and J genes, unlike other V genes. Compared to peritoneal B-1a, the peritoneal B-1b repertoire was larger, had little overlap with B-1a, and most sequences contained N additions. Similarly, the splenic B-1a repertoire differed from peritoneal B-1a sequences, having more unique sequences and more frequent N additions, suggesting influx of B-1a cells into the spleen from nonperitoneal sites. Two CDR3s, previously described as Abs to bromelain-treated RBCs, comprised 43% of peritoneal B-1a sequences. We show that a single-chain variable fragment designed after the most prevalent B-1a sequence bound oxidation-specific epitopes such as the phosphocholine of oxidized phospholipids. In summary, we provide the IgH V region library of six murine B cell subsets, including, to our knowledge for the first time, a comparison between B-1a and B-1b cells, and we highlight qualities of B-1 cell Abs that indicate unique selection processes.
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Affiliation(s)
- Thomas A Prohaska
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Xuchu Que
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Cody J Diehl
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Sabrina Hendrikx
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Max W Chang
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093; and
| | - Christopher K Glass
- Department of Medicine, University of California San Diego, La Jolla, CA 92093.,Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093
| | - Christopher Benner
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Joseph L Witztum
- Department of Medicine, University of California San Diego, La Jolla, CA 92093;
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16
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Abstract
Next-generation sequencing is making it possible to study the antibody repertoire of an organism in unprecedented detail, and, by so doing, to characterize its behavior in the response to infection and in pathological conditions such as autoimmunity and cancer. The polymorphic nature of the repertoire poses unique challenges that rule out the use of many commonly used NGS methods and require tradeoffs to be made when considering experimental design.We outline the main contexts in which antibody repertoire analysis has been used, and summarize the key tools that are available. The humoral immune response to vaccination has been a particular focus of repertoire analyses, and we review the key conclusions and methods used in these studies.
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Affiliation(s)
- William D Lees
- Department of Biological Sciences and Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London, WC1E 7HX, UK
| | - Adrian J Shepherd
- Department of Biological Sciences and Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London, WC1E 7HX, UK.
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17
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Farfán-Arribas DJ, Liu S, Wang S, Lu S. The dynamics of immunoglobulin V-gene usage and clonotype expansion in mice after prime and boost immunizations as analyzed by NGS. Hum Vaccin Immunother 2017; 13:2987-2995. [PMID: 29049006 PMCID: PMC5718813 DOI: 10.1080/21645515.2017.1379638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the current study, an improved NGS approach was developed to study the B-cell repertoire evolution in a simple mouse immunization model including only two DNA immunizations. The combination of 5′RACE and Ion Torrent long reads enabled unbiased immunoglobulin repertoire analysis even from small amounts of peripheral mouse blood. The B-cell population expanded by the vaccine displayed a relatively strong clonality. Upon priming with the first vaccine dose, we observed a consistent pattern of V-segment gene and CDR3 usage (public specificities). Interestingly, this pattern diversified with the second dose of immunization —it was relatively different in individual mice in spite of having received the same vaccine regimen (private specificities). Nevertheless, there were several instances in which the same public V-segment genes and CDR3s that were expanded after the first dose were further amplified after the second immunization. Taken together, it appears that the major clonotypes expanded by vaccination were originally a homogeneous subset that later diversified after a second dose leading to diverse “private” clonal compositions in different mice. These results established a new platform valuable to perform longitudinal analyses of the Ig germline gene usage and clonotype evolution throughout an immunization regimen in a commonly used animal model.
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Affiliation(s)
- Diego J Farfán-Arribas
- a Department of Medicine , University of Massachusetts Medical School , Worcester , MA , USA
| | - Shuying Liu
- a Department of Medicine , University of Massachusetts Medical School , Worcester , MA , USA
| | - Shixia Wang
- a Department of Medicine , University of Massachusetts Medical School , Worcester , MA , USA
| | - Shan Lu
- a Department of Medicine , University of Massachusetts Medical School , Worcester , MA , USA
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18
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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.
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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
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19
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Christley S, Levin MK, Toby IT, Fonner JM, Monson NL, Rounds WH, Rubelt F, Scarborough W, Scheuermann RH, Cowell LG. VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data. BMC Bioinformatics 2017; 18:448. [PMID: 29020925 PMCID: PMC5637252 DOI: 10.1186/s12859-017-1853-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 10/02/2017] [Indexed: 12/20/2022] Open
Abstract
Background Pre-processing of high-throughput sequencing data for immune repertoire profiling is essential to insure high quality input for downstream analysis. VDJPipe is a flexible, high-performance tool that can perform multiple pre-processing tasks with just a single pass over the data files. Results Processing tasks provided by VDJPipe include base composition statistics calculation, read quality statistics calculation, quality filtering, homopolymer filtering, length and nucleotide filtering, paired-read merging, barcode demultiplexing, 5′ and 3′ PCR primer matching, and duplicate reads collapsing. VDJPipe utilizes a pipeline approach whereby multiple processing steps are performed in a sequential workflow, with the output of each step passed as input to the next step automatically. The workflow is flexible enough to handle the complex barcoding schemes used in many immunosequencing experiments. Because VDJPipe is designed for computational efficiency, we evaluated this by comparing execution times with those of pRESTO, a widely-used pre-processing tool for immune repertoire sequencing data. We found that VDJPipe requires <10% of the run time required by pRESTO. Conclusions VDJPipe is a high-performance tool that is optimized for pre-processing large immune repertoire sequencing data sets.
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Affiliation(s)
- Scott Christley
- Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | | | - Inimary T Toby
- Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - John M Fonner
- Texas Advanced Computing Center, Austin, TX, 78758-4497, USA
| | - Nancy L Monson
- Department of Neurology and Neurotherapeutics, UT Southwestern Medical Center, Dallas, TX, 75390, USA.,Department of Immunology, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - William H Rounds
- Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Florian Rubelt
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | | | - Richard H Scheuermann
- J. Craig Venter Institute, La Jolla, CA, 92037, USA.,Department of Pathology, University of California, San Diego, CA, 92093, USA.,La Jolla Institute for Allergy & Immunology, La Jolla, CA, 92037, USA
| | - Lindsay G Cowell
- Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
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20
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Jain T, Boland T, Lilov A, Burnina I, Brown M, Xu Y, Vásquez M. Prediction of delayed retention of antibodies in hydrophobic interaction chromatography from sequence using machine learning. Bioinformatics 2017; 33:3758-3766. [DOI: 10.1093/bioinformatics/btx519] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 08/11/2017] [Indexed: 12/16/2022] Open
Affiliation(s)
- Tushar Jain
- Computational Biology, Adimab, Palo Alto, CA, USA
| | - Todd Boland
- Computational Biology, Adimab, Palo Alto, CA, USA
| | | | | | | | - Yingda Xu
- Protein Analytics, Adimab, Lebanon, NH, USA
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21
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A Haystack Heuristic for Autoimmune Disease Biomarker Discovery Using Next-Gen Immune Repertoire Sequencing Data. Sci Rep 2017; 7:5338. [PMID: 28706301 PMCID: PMC5509648 DOI: 10.1038/s41598-017-04439-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 05/16/2017] [Indexed: 01/03/2023] Open
Abstract
Large-scale DNA sequencing of immunological repertoires offers an opportunity for the discovery of novel biomarkers for autoimmune disease. Available bioinformatics techniques however, are not adequately suited for elucidating possible biomarker candidates from within large immunosequencing datasets due to unsatisfactory scalability and sensitivity. Here, we present the Haystack Heuristic, an algorithm customized to computationally extract disease-associated motifs from next-generation-sequenced repertoires by contrasting disease and healthy subjects. This technique employs a local-search graph-theory approach to discover novel motifs in patient data. We apply the Haystack Heuristic to nine million B-cell receptor sequences obtained from nearly 100 individuals in order to elucidate a new motif that is significantly associated with multiple sclerosis. Our results demonstrate the effectiveness of the Haystack Heuristic in computing possible biomarker candidates from high throughput sequencing data and could be generalized to other datasets.
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22
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Production of individualized V gene databases reveals high levels of immunoglobulin genetic diversity. Nat Commun 2016; 7:13642. [PMID: 27995928 PMCID: PMC5187446 DOI: 10.1038/ncomms13642] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 10/21/2016] [Indexed: 12/19/2022] Open
Abstract
Comprehensive knowledge of immunoglobulin genetics is required to advance our understanding of B cell biology. Validated immunoglobulin variable (V) gene databases are close to completion only for human and mouse. We present a novel computational approach, IgDiscover, that identifies germline V genes from expressed repertoires to a specificity of 100%. IgDiscover uses a cluster identification process to produce candidate sequences that, once filtered, results in individualized germline V gene databases. IgDiscover was tested in multiple species, validated by genomic cloning and cross library comparisons and produces comprehensive gene databases even where limited genomic sequence is available. IgDiscover analysis of the allelic content of the Indian and Chinese-origin rhesus macaques reveals high levels of immunoglobulin gene diversity in this species. Further, we describe a novel human IGHV3-21 allele and confirm significant gene differences between Balb/c and C57BL6 mouse strains, demonstrating the power of IgDiscover as a germline V gene discovery tool. Current databases of V genes for antibody repertoire have limitations. Here Corcoran et al. develop a computational approach named IgDiscover that can identify germline V gene sequences from expressed antibody repertoires to high specificity and completeness.
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23
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Lehmann-Horn K, Wang SZ, Sagan SA, Zamvil SS, von Büdingen HC. B cell repertoire expansion occurs in meningeal ectopic lymphoid tissue. JCI Insight 2016; 1:e87234. [PMID: 27942581 DOI: 10.1172/jci.insight.87234] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Ectopic lymphoid tissues (ELT) can be found in multiple sclerosis (MS) and other organ-specific inflammatory conditions. Whether ELT in the meninges of central nervous system (CNS) autoimmune disease exhibit local germinal center (GC) activity remains unknown. In an experimental autoimmune encephalomyelitis model of CNS autoimmunity, we found activation-induced cytidine deaminase, a GC-defining enzyme, in meningeal ELT (mELT) densely populated by B and T cells. To determine GC activity in mELT, we excised meningeal lymphoid aggregates using laser capture microscopy and evaluated B cell repertoires in mELT and secondary lymphoid organs by next-generation immune repertoire sequencing. We found immunoglobulin heavy chain variable region sequences that were unique to mELT and had accumulated functionally relevant somatic mutations, together indicating localized antigen-driven affinity maturation. Our results suggest that B cells in mELT actively participate in CNS autoimmunity, which may be relevant to mELT in MS and ELT in other chronic inflammatory conditions.
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24
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Yao VJ, D'Angelo S, Butler KS, Theron C, Smith TL, Marchiò S, Gelovani JG, Sidman RL, Dobroff AS, Brinker CJ, Bradbury ARM, Arap W, Pasqualini R. Ligand-targeted theranostic nanomedicines against cancer. J Control Release 2016; 240:267-286. [PMID: 26772878 PMCID: PMC5444905 DOI: 10.1016/j.jconrel.2016.01.002] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 12/17/2015] [Accepted: 01/02/2016] [Indexed: 02/06/2023]
Abstract
Nanomedicines have significant potential for cancer treatment. Although the majority of nanomedicines currently tested in clinical trials utilize simple, biocompatible liposome-based nanocarriers, their widespread use is limited by non-specificity and low target site concentration and thus, do not provide a substantial clinical advantage over conventional, systemic chemotherapy. In the past 20years, we have identified specific receptors expressed on the surfaces of tumor endothelial and perivascular cells, tumor cells, the extracellular matrix and stromal cells using combinatorial peptide libraries displayed on bacteriophage. These studies corroborate the notion that unique receptor proteins such as IL-11Rα, GRP78, EphA5, among others, are differentially overexpressed in tumors and present opportunities to deliver tumor-specific therapeutic drugs. By using peptides that bind to tumor-specific cell-surface receptors, therapeutic agents such as apoptotic peptides, suicide genes, imaging dyes or chemotherapeutics can be precisely and systemically delivered to reduce tumor growth in vivo, without harming healthy cells. Given the clinical applicability of peptide-based therapeutics, targeted delivery of nanocarriers loaded with therapeutic cargos seems plausible. We propose a modular design of a functionalized protocell in which a tumor-targeting moiety, such as a peptide or recombinant human antibody single chain variable fragment (scFv), is conjugated to a lipid bilayer surrounding a silica-based nanocarrier core containing a protected therapeutic cargo. The functionalized protocell can be tailored to a specific cancer subtype and treatment regimen by exchanging the tumor-targeting moiety and/or therapeutic cargo or used in combination to create unique, theranostic agents. In this review, we summarize the identification of tumor-specific receptors through combinatorial phage display technology and the use of antibody display selection to identify recombinant human scFvs against these tumor-specific receptors. We compare the characteristics of different types of simple and complex nanocarriers, and discuss potential types of therapeutic cargos and conjugation strategies. The modular design of functionalized protocells may improve the efficacy and safety of nanomedicines for future cancer therapy.
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Affiliation(s)
- Virginia J Yao
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131; Division of Molecular Medicine, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM 87131
| | - Sara D'Angelo
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131; Division of Molecular Medicine, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM 87131
| | - Kimberly S Butler
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM 87131
| | - Christophe Theron
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM 87131
| | - Tracey L Smith
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131; Division of Molecular Medicine, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM 87131
| | - Serena Marchiò
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131; Division of Molecular Medicine, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM 87131; Department of Oncology, University of Turin, Candiolo, 10060, Italy
| | - Juri G Gelovani
- Department of Biomedical Engineering, College of Engineering and School of Medicine, Wayne State University, Detroit, MI 48201
| | - Richard L Sidman
- Department of Neurology, Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, MA 02215
| | - Andrey S Dobroff
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131; Division of Molecular Medicine, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM 87131
| | - C Jeffrey Brinker
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM 87131; Center for Micro-Engineered Materials, University of New Mexico, Albuquerque, NM 87131; Cancer Research and Treatment Center, Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, University of New Mexico, Albuquerque, NM 87131; Self-Assembled Materials Department, Sandia National Laboratories, Albuquerque, NM 87185
| | - Andrew R M Bradbury
- Bioscience Division, Los Alamos National Laboratories, Los Alamos, NM, 87545
| | - Wadih Arap
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131; Division of Hematology/Oncology, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM 87131.
| | - Renata Pasqualini
- University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131; Division of Molecular Medicine, Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM 87131.
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Toby IT, Levin MK, Salinas EA, Christley S, Bhattacharya S, Breden F, Buntzman A, Corrie B, Fonner J, Gupta NT, Hershberg U, Marthandan N, Rosenfeld A, Rounds W, Rubelt F, Scarborough W, Scott JK, Uduman M, Vander Heiden JA, Scheuermann RH, Monson N, Kleinstein SH, Cowell LG. VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements. BMC Bioinformatics 2016; 17:333. [PMID: 27766961 PMCID: PMC5073965 DOI: 10.1186/s12859-016-1214-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Background The genes that produce antibodies and the immune receptors expressed on lymphocytes are not germline encoded; rather, they are somatically generated in each developing lymphocyte by a process called V(D)J recombination, which assembles specific, independent gene segments into mature composite genes. The full set of composite genes in an individual at a single point in time is referred to as the immune repertoire. V(D)J recombination is the distinguishing feature of adaptive immunity and enables effective immune responses against an essentially infinite array of antigens. Characterization of immune repertoires is critical in both basic research and clinical contexts. Recent technological advances in repertoire profiling via high-throughput sequencing have resulted in an explosion of research activity in the field. This has been accompanied by a proliferation of software tools for analysis of repertoire sequencing data. Despite the widespread use of immune repertoire profiling and analysis software, there is currently no standardized format for output files from V(D)J analysis. Researchers utilize software such as IgBLAST and IMGT/High V-QUEST to perform V(D)J analysis and infer the structure of germline rearrangements. However, each of these software tools produces results in a different file format, and can annotate the same result using different labels. These differences make it challenging for users to perform additional downstream analyses. Results To help address this problem, we propose a standardized file format for representing V(D)J analysis results. The proposed format, VDJML, provides a common standardized format for different V(D)J analysis applications to facilitate downstream processing of the results in an application-agnostic manner. The VDJML file format specification is accompanied by a support library, written in C++ and Python, for reading and writing the VDJML file format. Conclusions The VDJML suite will allow users to streamline their V(D)J analysis and facilitate the sharing of scientific knowledge within the community. The VDJML suite and documentation are available from https://vdjserver.org/vdjml/. We welcome participation from the community in developing the file format standard, as well as code contributions.
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Affiliation(s)
- Inimary T Toby
- Department of Clinical Sciences, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9066, USA
| | - Mikhail K Levin
- Bank of America Corporate Center, 100 North Tryon Street, Charlotte, NC, 28202, USA
| | | | - Scott Christley
- Department of Clinical Sciences, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9066, USA
| | - Sanchita Bhattacharya
- Institute for Computational Health Sciences, University of California San Francisco, Mission Hall, 550 16th Street, 4th Floor, Box 0110, San Francisco, CA, 94158, USA
| | - Felix Breden
- Department of Biological Sciences and The IRMACS Centre, Simon Fraser University, 8888 University Drive, Burnaby, V5A 1S6, British Columbia, Canada
| | - Adam Buntzman
- Department of Immunobiology, University of Arizona School of Medicine, 1656 E. Mabel Street, P.O. Box 245221, Tucson, AZ, 85724-5221, USA
| | - Brian Corrie
- New Zealand eScience Infrastructure, University of Auckland, Level 10, 49 Symonds Street, Auckland, New Zealand
| | - John Fonner
- Texas Advanced Computing Center, Research Office Complex 1.101, J.J. Pickle Research Campus, Building 196, 10100 Burnet Road (R8700), Austin, TX, 78758-4497, USA
| | - Namita T Gupta
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, 300 George Street, Suite 505, New Haven, CT, 06511, USA
| | - Uri Hershberg
- School of Biomedical Engineering, Science and Health Systems and Department of Microbiology and Immunology, College of Medicine, Drexel University, 3141 Chestnut Street, Philadelphia, PA, 19104, USA
| | - Nishanth Marthandan
- The IRMACS Centre (ASB 10905), Simon Fraser University, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Aaron Rosenfeld
- School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, PA, 19104, USA
| | - William Rounds
- Department of Neurology and Neurotherapeutics, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9036, USA
| | - Florian Rubelt
- Stanford University School of Medicine, 279 Campus Drive, Stanford, CA, 94305-5101, USA
| | - Walter Scarborough
- Texas Advanced Computing Center, Research Office Complex 1.101, J.J. Pickle Research Campus, Building 196, 10100 Burnet Road (R8700), Austin, TX, 78758-4497, USA
| | - Jamie K Scott
- Department of Molecular Biology and Biochemistry and Faculty of Health Sciences, Simon Fraser University, Blusson Hall, Room 11300, 8888 University Drive, Burnaby, BC, V5A 1S6, Canada
| | - Mohamed Uduman
- Department of Pathology, Yale School of Medicine, 300 George Street, Suite 505, New Haven, CT, 06511, USA
| | - Jason A Vander Heiden
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, 300 George Street, Suite 505, New Haven, CT, 06511, USA
| | - Richard H Scheuermann
- J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA.,Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.,Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Nancy Monson
- Department of Neurology and Neurotherapeutics, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9036, USA
| | - Steven H Kleinstein
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, 300 George Street, Suite 505, New Haven, CT, 06511, USA.,Department of Pathology, Yale School of Medicine, 300 George Street, Suite 505, New Haven, CT, 06511, USA.,Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Lindsay G Cowell
- Department of Clinical Sciences, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9066, USA.
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Huston JS. The burgeoning antibody landscape. Protein Eng Des Sel 2016; 29:399-401. [DOI: 10.1093/protein/gzw044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Indexed: 12/12/2022] Open
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Phipps ML, Lillo AM, Shou Y, Schmidt EN, Paavola CD, Naranjo L, Bemdich S, Swanson BI, Bradbury ARM, Martinez JS. Beyond Helper Phage: Using "Helper Cells" to Select Peptide Affinity Ligands. PLoS One 2016; 11:e0160940. [PMID: 27626637 PMCID: PMC5023105 DOI: 10.1371/journal.pone.0160940] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 07/27/2016] [Indexed: 12/16/2022] Open
Abstract
Peptides are important affinity ligands for microscopy, biosensing, and targeted delivery. However, because they can have low affinity for their targets, their selection from large naïve libraries can be challenging. When selecting peptidic ligands from display libraries, it is important to: 1) ensure efficient display; 2) maximize the ability to select high affinity ligands; and 3) minimize the effect of the display context on binding. The “helper cell” packaging system has been described as a tool to produce filamentous phage particles based on phagemid constructs with varying display levels, while remaining free of helper phage contamination. Here we report on the first use of this system for peptide display, including the systematic characterization and optimization of helper cells, their inefficient use in antibody display and their use in creating and selecting from a set of phage display peptide libraries. Our libraries were analyzed with unprecedented precision by standard or deep sequencing, and shown to be superior in quality than commercial gold standards. Using our helper cell libraries, we have obtained ligands recognizing Yersinia pestis surface antigen F1V and L-glutamine-binding periplasmic protein QBP. In the latter case, unlike any of the peptide library selections described so far, we used a combination of phage and yeast display to select intriguing peptide ligands. Based on the success of our selections we believe that peptide libraries obtained with helper cells are not only suitable, but preferable to traditional phage display libraries for selection of peptidic ligands.
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Affiliation(s)
- M. Lisa Phipps
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
| | - Antoinetta M. Lillo
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
| | - Yulin Shou
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
| | - Emily N. Schmidt
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
| | - Chad D. Paavola
- Space Biosciences Division, National Aeronautics and Space Administration Ames Research Center, Moffett Field, CA 94035, United States of America
| | - Leslie Naranjo
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
| | - Sara Bemdich
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
| | - Basil I. Swanson
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
| | - Andrew R. M. Bradbury
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
| | - Jennifer S. Martinez
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
- Institute for Materials Science, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
- * E-mail:
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28
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Glanville J, D'Angelo S, Khan TA, Reddy ST, Naranjo L, Ferrara F, Bradbury ARM. Deep sequencing in library selection projects: what insight does it bring? Curr Opin Struct Biol 2016; 33:146-60. [PMID: 26451649 DOI: 10.1016/j.sbi.2015.09.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 08/19/2015] [Accepted: 09/17/2015] [Indexed: 11/17/2022]
Abstract
High throughput sequencing is poised to change all aspects of the way antibodies and other binders are discovered and engineered. Millions of available sequence reads provide an unprecedented sampling depth able to guide the design and construction of effective, high quality naïve libraries containing tens of billions of unique molecules. Furthermore, during selections, high throughput sequencing enables quantitative tracing of enriched clones and position-specific guidance to amino acid variation under positive selection during antibody engineering. Successful application of the technologies relies on specific PCR reagent design, correct sequencing platform selection, and effective use of computational tools and statistical measures to remove error, identify antibodies, estimate diversity, and extract signatures of selection from the clone down to individual structural positions. Here we review these considerations and discuss some of the remaining challenges to the widespread adoption of the technology.
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Affiliation(s)
- J Glanville
- Program in Computational and Systems Immunology, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - S D'Angelo
- University of New Mexico Comprehensive Cancer Center, and Division of Molecular Medicine, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - T A Khan
- ETH Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland
| | - S T Reddy
- ETH Zurich, Department of Biosystems Science and Engineering, Basel, Switzerland
| | - L Naranjo
- Bioscience division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - F Ferrara
- University of New Mexico Comprehensive Cancer Center, and Division of Molecular Medicine, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - A R M Bradbury
- Bioscience division, Los Alamos National Laboratory, Los Alamos, NM, USA.
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29
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Frost SDW, Murrell B, Hossain ASMM, Silverman GJ, Pond SLK. Assigning and visualizing germline genes in antibody repertoires. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0240. [PMID: 26194754 PMCID: PMC4528417 DOI: 10.1098/rstb.2014.0240] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Identifying the germline genes involved in immunoglobulin rearrangements is an essential first step in the analysis of antibody repertoires. Based on our prior work in analysing diverse recombinant viruses, we present IgSCUEAL (Immunoglobulin Subtype Classification Using Evolutionary ALgorithms), a phylogenetic approach to assign V and J regions of immunoglobulin sequences to their corresponding germline alleles, with D regions assigned using a simple pairwise alignment algorithm. We also develop an interactive web application for viewing the results, allowing the user to explore the frequency distribution of sequence assignments and CDR3 region length statistics, which is useful for summarizing repertoires, as well as a detailed viewer of rearrangements and region alignments for individual query sequences. We demonstrate the accuracy and utility of our method compared with sequence similarity-based approaches and other non-phylogenetic model-based approaches, using both simulated data and a set of evaluation datasets of human immunoglobulin heavy chain sequences. IgSCUEAL demonstrates the highest accuracy of V and J assignment amongst existing approaches, even when the reassorted sequence is highly mutated, and can successfully cluster sequences on the basis of shared V/J germline alleles.
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Affiliation(s)
- Simon D W Frost
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, Cambridgeshire CB3 0ES, UK
| | - Ben Murrell
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - A S Md Mukarram Hossain
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, Cambridgeshire CB3 0ES, UK
| | - Gregg J Silverman
- Department of Medicine, New York University School of Medicine, New York, NY 10016, USA Department of Pathology, New York University School of Medicine, New York, NY 10016, USA
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30
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Cortina-Ceballos B, Godoy-Lozano EE, Sámano-Sánchez H, Aguilar-Salgado A, Velasco-Herrera MDC, Vargas-Chávez C, Velázquez-Ramírez D, Romero G, Moreno J, Téllez-Sosa J, Martínez-Barnetche J. Reconstructing and mining the B cell repertoire with ImmunediveRsity. MAbs 2016; 7:516-24. [PMID: 25875140 PMCID: PMC4622655 DOI: 10.1080/19420862.2015.1026502] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The B cell antigen receptor repertoire is highly diverse and constantly modified by clonal selection. High-throughput DNA sequencing (HTS) of the lymphocyte repertoire (Rep-Seq) represents a promising technology to explore such diversity ex-vivo and assist in the identification of antigen-specific antibodies based on molecular signatures of clonal selection. Therefore, integrative tools for repertoire reconstruction and analysis from antibody sequences are needed. We developed ImmunediveRity, a stand-alone pipeline primarily based in R programming for the integral analysis of B cell repertoire data generated by HTS. The pipeline integrates GNU software and in house scripts to perform quality filtering, sequencing noise correction and repertoire reconstruction based on V, D and J segment assignment, clonal origin and unique heavy chain identification. Post-analysis scripts generate a wealth of repertoire metrics that in conjunction with a rich graphical output facilitates sample comparison and repertoire mining. Its performance was tested with raw and curated human and mouse 454-Roche sequencing benchmarks providing good approximations of repertoire structure. Furthermore, ImmunediveRsity was used to mine the B cell repertoire of immunized mice with a model antigen, allowing the identification of previously validated antigen-specific antibodies, and revealing different and unexpected clonal diversity patterns in the post-immunization IgM and IgG compartments. Although ImmunediveRsity is similar to other recently developed tools, it offers significant advantages that facilitate repertoire analysis and repertoire mining. ImmunediveRsity is open source and free for academic purposes and it runs on 64 bit GNU/Linux and MacOS. Available at: https://bitbucket.org/ImmunediveRsity/immunediversity/
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Affiliation(s)
- Bernardo Cortina-Ceballos
- a Centro de Investigación Sobre Enfermedades Infecciosas; Instituto Nacional de Salud Pública (CISEI-INSP); Cuernavaca , Morelos , México
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31
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Shugay M, Bagaev DV, Turchaninova MA, Bolotin DA, Britanova OV, Putintseva EV, Pogorelyy MV, Nazarov VI, Zvyagin IV, Kirgizova VI, Kirgizov KI, Skorobogatova EV, Chudakov DM. VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires. PLoS Comput Biol 2015; 11:e1004503. [PMID: 26606115 PMCID: PMC4659587 DOI: 10.1371/journal.pcbi.1004503] [Citation(s) in RCA: 396] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 08/13/2015] [Indexed: 12/11/2022] Open
Abstract
Despite the growing number of immune repertoire sequencing studies, the field still lacks software for analysis and comprehension of this high-dimensional data. Here we report VDJtools, a complementary software suite that solves a wide range of T cell receptor (TCR) repertoires post-analysis tasks, provides a detailed tabular output and publication-ready graphics, and is built on top of a flexible API. Using TCR datasets for a large cohort of unrelated healthy donors, twins, and multiple sclerosis patients we demonstrate that VDJtools greatly facilitates the analysis and leads to sound biological conclusions. VDJtools software and documentation are available at https://github.com/mikessh/vdjtools.
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Affiliation(s)
- Mikhail Shugay
- Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitriy V. Bagaev
- Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia
| | - Maria A. Turchaninova
- Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitriy A. Bolotin
- Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Olga V. Britanova
- Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Ekaterina V. Putintseva
- Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | | | - Vadim I. Nazarov
- Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia
- National Research University Higher School of Economics, Moscow, Russia
| | - Ivan V. Zvyagin
- Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | | | | | | | - Dmitriy M. Chudakov
- Shemyakin-Ovchinnikov Institute of bioorganic chemistry RAS, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- * E-mail:
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32
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Longitudinal analysis of the peripheral B cell repertoire reveals unique effects of immunization with a new influenza virus strain. Genome Med 2015; 7:124. [PMID: 26608341 PMCID: PMC4658769 DOI: 10.1186/s13073-015-0239-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 11/06/2015] [Indexed: 01/12/2023] Open
Abstract
Background Despite the potential to produce antibodies that can neutralize different virus (heterotypic neutralization), there is no knowledge of why vaccination against influenza induces protection predominantly against the utilized viral strains (homotypic response). Identification of structural patterns of the B cell repertoire associated to heterotypic neutralization may contribute to identify relevant epitopes for a universal vaccine against influenza. Methods Blood samples were collected from volunteers immunized with 2008/2009 trivalent inactivated vaccine (TIV), pandemic H1N1 (pdmH1N1) monovalent inactivated vaccine (MIV) and the 2014/2015 TIV. Neutralization was assessed by hemagglutination and microneutralization test. IgG VH amplicons derived from peripheral blood RNA from pre-immune and 7 days post vaccination were subjected to 454-Roche sequencing. Full reconstruction of the sampled repertoires was done with ImmunediveRsity. Results The TIV induced a predominantly homotypic neutralizing serologic response, while the 09 MIV induced a heterotypic neutralizing seroconversion in 17 % of the individuals. Both the 08/09 and the 14/15 TIV were associated with a reduction in clonotypic diversity, whereas 09 MIV was the opposite. Moreover, TIV and MIV induced distinctive patterns of IGHV segment use that are consistent with B cell selection by conserved antigenic determinants shared by the pre-pandemic and the pandemic strains. However, low somatic hypermutation rates in IgG after 09 MIV immunization, but not after 08/09 and 14/15 TIV immunization were observed. Furthermore, no evidence of the original antigenic sin was found in the same individuals after vaccination with the three vaccines. Conclusions Immunization with a new influenza virus strain (2009 pdmH1N1) induced unique effects in the peripheral B cell repertoire clonal structure, a stereotyped response involving distinctive IGHV segment use and low somatic hypermutation levels. These parameters were contrastingly different to those observed in response to pre-pandemic and post-pandemic vaccination, and may be the result of clonal selection of common antigenic determinants, as well as germinal center-independent responses that wane as the pandemic strain becomes seasonal. Our findings may contribute in the understanding of the structural and cellular basis required to develop a universal influenza vaccine. Electronic supplementary material The online version of this article (doi:10.1186/s13073-015-0239-y) contains supplementary material, which is available to authorized users.
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Ferrara F, D'Angelo S, Gaiotto T, Naranjo L, Tian H, Gräslund S, Dobrovetsky E, Hraber P, Lund-Johansen F, Saragozza S, Sblattero D, Kiss C, Bradbury ARM. Recombinant renewable polyclonal antibodies. MAbs 2015; 7:32-41. [PMID: 25530082 DOI: 10.4161/19420862.2015.989047] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Only a small fraction of the antibodies in a traditional polyclonal antibody mixture recognize the target of interest, frequently resulting in undesirable polyreactivity. Here, we show that high-quality recombinant polyclonals, in which hundreds of different antibodies are all directed toward a target of interest, can be easily generated in vitro by combining phage and yeast display. We show that, unlike traditional polyclonals, which are limited resources, recombinant polyclonal antibodies can be amplified over one hundred million-fold without losing representation or functionality. Our protocol was tested on 9 different targets to demonstrate how the strategy allows the selective amplification of antibodies directed toward desirable target specific epitopes, such as those found in one protein but not a closely related one, and the elimination of antibodies recognizing common epitopes, without significant loss of diversity. These recombinant renewable polyclonal antibodies are usable in different assays, and can be generated in high throughput. This approach could potentially be used to develop highly specific recombinant renewable antibodies against all human gene products.
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34
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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.
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Affiliation(s)
- Owen Kavanagh
- Institute for Global Food Security (IGFS), School of Biological Sciences, Queen's University Belfast, Belfast, Northern Ireland, UK,
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35
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Abstract
Antibody drugs have become an increasingly significant component of the therapeutic landscape. Their success has been driven by some of their unique properties, in particular their very high specificity and selectivity, in contrast to the off-target liabilities of small molecules (SMs). Antibodies can bring additional functionality to the table with their ability to interact with the immune system, and this can be further manipulated with advances in antibody engineering. This review summarizes what antibody therapeutics have achieved to date and what opportunities and challenges lie ahead. The target landscape for large molecules (LMs) versus SMs and some of the challenges for antibody drug development are discussed. Effective penetration of membrane barriers and intracellular targeting is one challenge, particularly across the highly resistant blood-brain barrier. The expanding pipeline of antibody-drug conjugates offers the potential to combine SM and LM modalities in a variety of creative ways, and antibodies also offer exciting potential to build bi- and multispecific molecules. The ability to pursue more challenging targets can also be further exploited but highlights the need for earlier screening in functional cell-based assays. I discuss how this might be addressed given the practical constraints imposed by high-throughput screening sample type and process differences in antibody primary screening.
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Affiliation(s)
- Alison J. Smith
- Department of Antibody Discovery and Protein Engineering, MedImmune Ltd, Cambridge, UK
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36
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D'Angelo S, Kumar S, Naranjo L, Ferrara F, Kiss C, Bradbury ARM. From deep sequencing to actual clones. Protein Eng Des Sel 2014; 27:301-7. [PMID: 25183780 DOI: 10.1093/protein/gzu032] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The application of deep sequencing to in vitro display technologies has been invaluable for the straightforward analysis of enriched clones. After sequencing in vitro selected populations, clones are binned into identical or similar groups and ordered by abundance, allowing identification of those that are most enriched. However, the greatest strength of deep sequencing is also its greatest weakness: clones are easily identified by their DNA sequences, but are not physically available for testing without a laborious multistep process involving several rounds of polymerization chain reaction (PCR), assembly and cloning. Here, using the isolation of antibody genes from a phage and yeast display selection as an example, we show the power of a rapid and simple inverse PCR-based method to easily isolate clones identified by deep sequencing. Once primers have been received, clone isolation can be carried out in a single day, rather than two days. Furthermore the reduced number of PCRs required will reduce PCR mutations correspondingly. We have observed a 100% success rate in amplifying clones with an abundance as low as 0.5% in a polyclonal population. This approach allows us to obtain full-length clones even when an incomplete sequence is available, and greatly simplifies the subcloning process. Moreover, rarer, but functional clones missed by traditional screening can be easily isolated using this method, and the approach can be extended to any selected library (scFv, cDNA, libraries based on scaffold proteins) where a unique sequence signature for the desired clones of interest is available.
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Affiliation(s)
| | - Sandeep Kumar
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA Present address: Compugen USA, Inc., San Francisco, CA 94080, USA
| | - Leslie Naranjo
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | | | - Csaba Kiss
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
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Jha RK, Kern TL, Fox DT, M Strauss CE. Engineering an Acinetobacter regulon for biosensing and high-throughput enzyme screening in E. coli via flow cytometry. Nucleic Acids Res 2014; 42:8150-60. [PMID: 24861620 PMCID: PMC4081070 DOI: 10.1093/nar/gku444] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
We created a single cell sorting system to screen for enzyme activity in Escherichia coli producing 3,4 dihydroxy benzoate (34DHB). To do so, we engineered a transcription factor regulon controlling the expression of green fluorescent protein (GFP) for induction by 34DHB. An autoregulated transcription factor, pcaU, was borrowed from Acinetobacter sp ADP1 to E. coli and its promoter region adapted for activity in E. Coli. The engineered pcaU regulon was inducible at >5 μM exogenous 34DHB, making it a sensitive biosensor for this industrially significant nylon precursor. Addition of a second plasmid provided IPTG inducible expression of dehydroshikimate dehydratase enzyme (AsbF), which converts endogenous dehydroshikimate to 34DHB. This system produced GFP fluorescence in an IPTG dose-dependent manner, and was easily detected in single cell on flow cytometer despite a moderate catalytic efficiency of AsbF. Using fluorescence-activated cell sorting (FACS), individual cells carrying the active AsbF could be isolated even when diluted into a decoy population of cells carrying a mutant (inactivated) AsbF variant at one part in a million. The same biosensor was also effective for further optimization of itself. FACS on E. coli carrying randomized loci in the promoter showed several variants with enhanced response to 34DHB.
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Affiliation(s)
- Ramesh K Jha
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Theresa L Kern
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - David T Fox
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Charlie E M Strauss
- Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545
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Close DW, Ferrara F, Dichosa AEK, Kumar S, Daughton AR, Daligault HE, Reitenga KG, Velappan N, Sanchez TC, Iyer S, Kiss C, Han CS, Bradbury ARM. Using phage display selected antibodies to dissect microbiomes for complete de novo genome sequencing of low abundance microbes. BMC Microbiol 2013; 13:270. [PMID: 24279426 PMCID: PMC3907030 DOI: 10.1186/1471-2180-13-270] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Accepted: 11/21/2013] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Single cell genomics has revolutionized microbial sequencing, but complete coverage of genomes in complex microbiomes is imperfect due to enormous variation in organismal abundance and amplification bias. Empirical methods that complement rapidly improving bioinformatic tools will improve characterization of microbiomes and facilitate better genome coverage for low abundance microbes. METHODS We describe a new approach to sequencing individual species from microbiomes that combines antibody phage display against intact bacteria with fluorescence activated cell sorting (FACS). Single chain (scFv) antibodies are selected using phage display against a bacteria or microbial community, resulting in species-specific antibodies that can be used in FACS for relative quantification of an organism in a community, as well as enrichment or depletion prior to genome sequencing. RESULTS We selected antibodies against Lactobacillus acidophilus and demonstrate a FACS-based approach for identification and enrichment of the organism from both laboratory-cultured and commercially derived bacterial mixtures. The ability to selectively enrich for L. acidophilus when it is present at a very low abundance (<0.2%) leads to complete (>99.8%) de novo genome coverage whereas the standard single-cell sequencing approach is incomplete (<68%). We show that specific antibodies can be selected against L. acidophilus when the monoculture is used as antigen as well as when a community of 10 closely related species is used demonstrating that in principal antibodies can be generated against individual organisms within microbial communities. CONCLUSIONS The approach presented here demonstrates that phage-selected antibodies against bacteria enable identification, enrichment of rare species, and depletion of abundant organisms making it tractable to virtually any microbe or microbial community. Combining antibody specificity with FACS provides a new approach for characterizing and manipulating microbial communities prior to genome sequencing.
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Affiliation(s)
- Devin W Close
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
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