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Lê Quý K, Chernigovskaya M, Stensland M, Singh S, Leem J, Revale S, Yadin DA, Nice FL, Povall C, Minns DH, Galson JD, Nyman TA, Snapkow I, Greiff V. Benchmarking and integrating human B-cell receptor genomic and antibody proteomic profiling. NPJ Syst Biol Appl 2024; 10:73. [PMID: 38997321 PMCID: PMC11245537 DOI: 10.1038/s41540-024-00402-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 07/01/2024] [Indexed: 07/14/2024] Open
Abstract
Immunoglobulins (Ig), which exist either as B-cell receptors (BCR) on the surface of B cells or as antibodies when secreted, play a key role in the recognition and response to antigenic threats. The capability to jointly characterize the BCR and antibody repertoire is crucial for understanding human adaptive immunity. From peripheral blood, bulk BCR sequencing (bulkBCR-seq) currently provides the highest sampling depth, single-cell BCR sequencing (scBCR-seq) allows for paired chain characterization, and antibody peptide sequencing by tandem mass spectrometry (Ab-seq) provides information on the composition of secreted antibodies in the serum. Yet, it has not been benchmarked to what extent the datasets generated by these three technologies overlap and complement each other. To address this question, we isolated peripheral blood B cells from healthy human donors and sequenced BCRs at bulk and single-cell levels, in addition to utilizing publicly available sequencing data. Integrated analysis was performed on these datasets, resolved by replicates and across individuals. Simultaneously, serum antibodies were isolated, digested with multiple proteases, and analyzed with Ab-seq. Systems immunology analysis showed high concordance in repertoire features between bulk and scBCR-seq within individuals, especially when replicates were utilized. In addition, Ab-seq identified clonotype-specific peptides using both bulk and scBCR-seq library references, demonstrating the feasibility of combining scBCR-seq and Ab-seq for reconstructing paired-chain Ig sequences from the serum antibody repertoire. Collectively, our work serves as a proof-of-principle for combining bulk sequencing, single-cell sequencing, and mass spectrometry as complementary methods towards capturing humoral immunity in its entirety.
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Grants
- The Leona M. and Harry B. Helmsley Charitable Trust (#2019PG-T1D011, to VG), UiO World-Leading Research Community (to VG), UiO: LifeScience Convergence Environment Immunolingo (to VG), EU Horizon 2020 iReceptorplus (#825821) (to VG), a Norwegian Cancer Society Grant (#215817, to VG), Research Council of Norway projects (#300740, (#311341, #331890 to VG), a Research Council of Norway IKTPLUSS project (#311341, to VG). This project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement No 101007799 (Inno4Vac). This Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation programme and EFPIA (to VG).
- Mass spectrometry-based proteomic analyses were performed by the Proteomics Core Facility, Department of Immunology, University of Oslo/Oslo University Hospital, which is supported by the Core Facilities program of the South-Eastern Norway Regional Health Authority. This core facility is also a member of the National Network of Advanced Proteomics Infrastructure (NAPI), which is funded by the Research Council of Norway INFRASTRUKTUR-program (project number: 295910).
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Affiliation(s)
- Khang Lê Quý
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Maria Chernigovskaya
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Maria Stensland
- Proteomics Core Facility, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Sachin Singh
- Proteomics Core Facility, University of Oslo and Oslo University Hospital, Oslo, Norway
| | | | | | | | | | | | | | | | - Tuula A Nyman
- Proteomics Core Facility, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Igor Snapkow
- Department of Chemical Toxicology, Norwegian Institute of Public Health, Oslo, Norway
| | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway.
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2
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Monoclonal antibody therapeutics for infectious diseases: Beyond normal human immunoglobulin. Pharmacol Ther 2022; 240:108233. [PMID: 35738431 PMCID: PMC9212443 DOI: 10.1016/j.pharmthera.2022.108233] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 05/30/2022] [Accepted: 06/16/2022] [Indexed: 12/15/2022]
Abstract
Antibody therapy is effective for treating infectious diseases. Due to the coronavirus disease 2019 (COVID-19) pandemic and the rise of drug-resistant bacteria, rapid development of neutralizing monoclonal antibodies (mAbs) to treat infectious diseases is urgently needed. Using a therapeutic human mAb with the lowest immunogenicity is recommended, because chimera and humanized mAbs are occasionally immunogenic. In order to directly obtain naïve human mAbs, there are three methods: phage display, B cell receptor (BCR) cDNA sequencing of a single cell, and antibody-encoding gene and amino acid sequencing of immortalized cells using memory B cells, which are isolated from human peripheral blood mononuclear cells of healthy, vaccinated, infected, or recovered individuals. After screening against the antigen and performing neutralization assays, a human neutralizing mAb is constructed from the antibody-encoding DNA sequences of these memory B cells. This review describes examples of obtaining human neutralizing mAbs against various infectious diseases using these methods. However, a few of these mAbs have been approved for therapy. Therefore, antigen characterization and evaluation of neutralization activity in vitro and in vivo are indispensable for the development of therapeutic mAbs. These results will accelerate the development of antibody drug as therapeutic agents.
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3
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Ionov S, Lee J. An Immunoproteomic Survey of the Antibody Landscape: Insights and Opportunities Revealed by Serological Repertoire Profiling. Front Immunol 2022; 13:832533. [PMID: 35178051 PMCID: PMC8843944 DOI: 10.3389/fimmu.2022.832533] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/14/2022] [Indexed: 12/12/2022] Open
Abstract
Immunoproteomics has emerged as a versatile tool for analyzing the antibody repertoire in various disease contexts. Until recently, characterization of antibody molecules in biological fluids was limited to bulk serology, which identifies clinically relevant features of polyclonal antibody responses. The past decade, however, has seen the rise of mass-spectrometry-enabled proteomics methods that have allowed profiling of the antibody response at the molecular level, with the disease-specific serological repertoire elucidated in unprecedented detail. In this review, we present an up-to-date survey of insights into the disease-specific immunological repertoire by examining how quantitative proteomics-based approaches have shed light on the humoral immune response to infection and vaccination in pathogenic illnesses, the molecular basis of autoimmune disease, and the tumor-specific repertoire in cancer. We address limitations of this technology with a focus on emerging potential solutions and discuss the promise of high-resolution immunoproteomics in therapeutic discovery and novel vaccine design.
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Affiliation(s)
| | - Jiwon Lee
- Thayer School of Engineering, Dartmouth College, Hanover, NH, United States
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4
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Matsuzaki Y, Aoki W, Miyazaki T, Aburaya S, Ohtani Y, Kajiwara K, Koike N, Minakuchi H, Miura N, Kadonosono T, Ueda M. Peptide barcoding for one-pot evaluation of sequence-function relationships of nanobodies. Sci Rep 2021; 11:21516. [PMID: 34728738 PMCID: PMC8563947 DOI: 10.1038/s41598-021-01019-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 10/21/2021] [Indexed: 11/17/2022] Open
Abstract
Optimisation of protein binders relies on laborious screening processes. Investigation of sequence–function relationships of protein binders is particularly slow, since mutants are purified and evaluated individually. Here we developed peptide barcoding, a high-throughput approach for accurate investigation of sequence–function relationships of hundreds of protein binders at once. Our approach is based on combining the generation of a mutagenised nanobody library fused with unique peptide barcodes, the formation of nanobody–antigen complexes at different ratios, their fine fractionation by size-exclusion chromatography and quantification of peptide barcodes by targeted proteomics. Applying peptide barcoding to an anti-GFP nanobody as a model, we successfully identified residues important for the binding affinity of anti-GFP nanobody at once. Peptide barcoding discriminated subtle changes in KD at the order of nM to sub-nM. Therefore, peptide barcoding is a powerful tool for engineering protein binders, enabling reliable one-pot evaluation of sequence–function relationships.
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Affiliation(s)
- Yusei Matsuzaki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Wataru Aoki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan. .,Kyoto Integrated Science and Technology Bio-Analysis Center, Simogyo-ku, Kyoto, 600-8813, Japan. .,JST, CREST, Chiyoda-ku, Tokyo, 102-0076, Japan. .,JST, COI-NEXT, Chiyoda-ku, Tokyo, 102-0076, Japan. .,JST, FOREST, Chiyoda-ku, Tokyo, 102-0076, Japan.
| | - Takumi Miyazaki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Shunsuke Aburaya
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Yuta Ohtani
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Kaho Kajiwara
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Naoki Koike
- TechnoPro, Inc. TechnoPro R&D, Company, Tokyo, 106-6135, Japan
| | | | - Natsuko Miura
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Naka-ku, Sakai, 599-8531, Japan
| | - Tetsuya Kadonosono
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama, 226-8501, Japan
| | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan.,Kyoto Integrated Science and Technology Bio-Analysis Center, Simogyo-ku, Kyoto, 600-8813, Japan.,JST, CREST, Chiyoda-ku, Tokyo, 102-0076, Japan.,JST, COI-NEXT, Chiyoda-ku, Tokyo, 102-0076, Japan
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5
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Progress and challenges in mass spectrometry-based analysis of antibody repertoires. Trends Biotechnol 2021; 40:463-481. [PMID: 34535228 DOI: 10.1016/j.tibtech.2021.08.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 12/22/2022]
Abstract
Humoral immunity is divided into the cellular B cell and protein-level antibody responses. High-throughput sequencing has advanced our understanding of both these fundamental aspects of B cell immunology as well as aspects pertaining to vaccine and therapeutics biotechnology. Although the protein-level serum and mucosal antibody repertoire make major contributions to humoral protection, the sequence composition and dynamics of antibody repertoires remain underexplored. This limits insight into important immunological and biotechnological parameters such as the number of antigen-specific antibodies, which are for example, relevant for pathogen neutralization, microbiota regulation, severity of autoimmunity, and therapeutic efficacy. High-resolution mass spectrometry (MS) has allowed initial insights into the antibody repertoire. We outline current challenges in MS-based sequence analysis of antibody repertoires and propose strategies for their resolution.
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6
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Gilchuk P, Guthals A, Bonissone SR, Shaw JB, Ilinykh PA, Huang K, Bombardi RG, Liang J, Grinyo A, Davidson E, Chen EC, Gunn BM, Alter G, Saphire EO, Doranz BJ, Bukreyev A, Zeitlin L, Castellana N, Crowe JE. Proteo-Genomic Analysis Identifies Two Major Sites of Vulnerability on Ebolavirus Glycoprotein for Neutralizing Antibodies in Convalescent Human Plasma. Front Immunol 2021; 12:706757. [PMID: 34335620 PMCID: PMC8322977 DOI: 10.3389/fimmu.2021.706757] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 06/28/2021] [Indexed: 11/21/2022] Open
Abstract
Three clinically relevant ebolaviruses - Ebola (EBOV), Bundibugyo (BDBV), and Sudan (SUDV) viruses, are responsible for severe disease and occasional deadly outbreaks in Africa. The largest Ebola virus disease (EVD) epidemic to date in 2013-2016 in West Africa highlighted the urgent need for countermeasures, leading to the development and FDA approval of the Ebola virus vaccine rVSV-ZEBOV (Ervebo®) in 2020 and two monoclonal antibody (mAb)-based therapeutics (Inmazeb® [atoltivimab, maftivimab, and odesivimab-ebgn] and Ebanga® (ansuvimab-zykl) in 2020. The humoral response plays an indispensable role in ebolavirus immunity, based on studies of mAbs isolated from the antibody genes in peripheral blood circulating ebolavirus-specific human memory B cells. However, antibodies in the body are not secreted by circulating memory B cells in the blood but rather principally by plasma cells in the bone marrow. Little is known about the protective polyclonal antibody responses in convalescent plasma. Here we exploited both single-cell antibody gene sequencing and proteomic sequencing approaches to assess the composition of the ebolavirus glycoprotein (GP)-reactive antibody repertoire in the plasma of an EVD survivor. We first identified 1,512 GP-specific mAb variable gene sequences from single cells in the memory B cell compartment. Using mass spectrometric analysis of the corresponding GP-specific plasma IgG, we found that only a portion of the large B cell antibody repertoire was represented in the plasma. Molecular and functional analysis of proteomics-identified mAbs revealed recognition of epitopes in three major antigenic sites - the GP head domain, the glycan cap, and the base region, with a high prevalence of neutralizing and protective mAb specificities that targeted the base and glycan cap regions on the GP. Polyclonal plasma antibodies from the survivor reacted broadly to EBOV, BDBV, and SUDV GP, while reactivity of the potently neutralizing mAbs we identified was limited mostly to the homologous EBOV GP. Together these results reveal a restricted diversity of neutralizing humoral response in which mAbs targeting two antigenic sites on GP - glycan cap and base - play a principal role in plasma-antibody-mediated protective immunity against EVD.
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Affiliation(s)
- Pavlo Gilchuk
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Adrian Guthals
- Mapp Biopharmaceutical, Inc. San Diego, CA, United States
| | - Stefano R. Bonissone
- Abterra Biosciences (formerly Digital Proteomics LLC), San Diego, CA, United States
| | - Jared B. Shaw
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Philipp A. Ilinykh
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
- Galveston National Laboratory, Galveston, TX, United States
| | - Kai Huang
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
- Galveston National Laboratory, Galveston, TX, United States
| | - Robin G. Bombardi
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Jenny Liang
- Integral Molecular, Inc., Philadelphia, PA, United States
| | - Ariadna Grinyo
- Integral Molecular, Inc., Philadelphia, PA, United States
| | - Edgar Davidson
- Integral Molecular, Inc., Philadelphia, PA, United States
| | - Elaine C. Chen
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Bronwyn M. Gunn
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, United States
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, United States
| | - Erica Ollmann Saphire
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
| | | | - Alexander Bukreyev
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
- Galveston National Laboratory, Galveston, TX, United States
- Department of Microbiology & Immunology, University of Texas Medical Branch, Galveston, TX, United States
| | - Larry Zeitlin
- Mapp Biopharmaceutical, Inc. San Diego, CA, United States
| | - Natalie Castellana
- Abterra Biosciences (formerly Digital Proteomics LLC), San Diego, CA, United States
| | - James E. Crowe
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, United States
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7
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Xiang Y, Sang Z, Bitton L, Xu J, Liu Y, Schneidman-Duhovny D, Shi Y. Integrative proteomics identifies thousands of distinct, multi-epitope, and high-affinity nanobodies. Cell Syst 2021; 12:220-234.e9. [PMID: 33592195 PMCID: PMC7979497 DOI: 10.1016/j.cels.2021.01.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 10/13/2020] [Accepted: 01/20/2021] [Indexed: 12/15/2022]
Abstract
The antibody immune response is essential for the survival of mammals. However, we still lack a systematic understanding of the antibody repertoire. Here, we developed a proteomic strategy to survey, at an unprecedented scale, the landscape of antigen-engaged, circulating camelid heavy-chain antibodies, whose minimal binding fragments are called VHH antibodies or nanobodies. The sensitivity and robustness of this approach were validated with three antigens spanning orders of magnitude in immune responses; thousands of distinct, high-affinity nanobody families were reliably identified and quantified. Using high-throughput structural modeling, cross-linking mass spectrometry, mutagenesis, and deep learning, we mapped and analyzed the epitopes of >100,000 antigen-nanobody complexes. Our results revealed a surprising diversity of ultrahigh-affinity camelid nanobodies for specific antigen binding on various dominant epitope clusters. Nanobodies utilize both shape and charge complementarity to enable highly selective antigen binding. Interestingly, we found that nanobody-antigen binding can mimic conserved intracellular protein-protein interactions. A record of this paper's Transparent Peer Review process is included in the Supplemental information.
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Affiliation(s)
- Yufei Xiang
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zhe Sang
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA; University of Pittsburgh, Carnegie Mellon University Program for Computational Biology, Pittsburgh, PA, USA
| | - Lirane Bitton
- School of Computer Science and Engineering, Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | - Jianquan Xu
- Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yang Liu
- Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dina Schneidman-Duhovny
- School of Computer Science and Engineering, Institute of Life Sciences, The Hebrew University of Jerusalem, Israel.
| | - Yi Shi
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA; University of Pittsburgh, Carnegie Mellon University Program for Computational Biology, Pittsburgh, PA, USA.
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8
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Davis CW, Jackson KJL, McCausland MM, Darce J, Chang C, Linderman SL, Chennareddy C, Gerkin R, Brown SJ, Wrammert J, Mehta AK, Cheung WC, Boyd SD, Waller EK, Ahmed R. Influenza vaccine-induced human bone marrow plasma cells decline within a year after vaccination. Science 2020; 370:237-241. [PMID: 32792465 PMCID: PMC10155619 DOI: 10.1126/science.aaz8432] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 08/02/2020] [Indexed: 01/09/2023]
Abstract
A universal vaccine against influenza would ideally generate protective immune responses that are not only broadly reactive against multiple influenza strains but also long-lasting. Because long-term serum antibody levels are maintained by bone marrow plasma cells (BMPCs), we investigated the production and maintenance of these cells after influenza vaccination. We found increased numbers of influenza-specific BMPCs 4 weeks after immunization with the seasonal inactivated influenza vaccine, but numbers returned to near their prevaccination levels after 1 year. This decline was driven by the loss of BMPCs induced by the vaccine, whereas preexisting BMPCs were maintained. Our results suggest that most BMPCs generated by influenza vaccination in adults are short-lived. Designing strategies to enhance their persistence will be a key challenge for the next generation of influenza vaccines.
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Affiliation(s)
- Carl W Davis
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA.,Emory-UGA Center of Excellence of Influenza Research and Surveillance (CEIRS), Atlanta GA, USA
| | | | - Megan M McCausland
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA.,Emory-UGA Center of Excellence of Influenza Research and Surveillance (CEIRS), Atlanta GA, USA
| | - Jaime Darce
- Cell Signaling Technology, Inc., Danvers, MA, USA
| | - Cathy Chang
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA.,Emory-UGA Center of Excellence of Influenza Research and Surveillance (CEIRS), Atlanta GA, USA
| | - Susanne L Linderman
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA.,Emory-UGA Center of Excellence of Influenza Research and Surveillance (CEIRS), Atlanta GA, USA
| | - Chakravarthy Chennareddy
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA.,Emory-UGA Center of Excellence of Influenza Research and Surveillance (CEIRS), Atlanta GA, USA
| | - Rebecca Gerkin
- Emory-UGA Center of Excellence of Influenza Research and Surveillance (CEIRS), Atlanta GA, USA.,Department of Hematology and Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, USA
| | - Shantoria J Brown
- Emory-UGA Center of Excellence of Influenza Research and Surveillance (CEIRS), Atlanta GA, USA.,Department of Hematology and Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, USA
| | - Jens Wrammert
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA.,Department of Pediatrics, Division of Infectious Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Aneesh K Mehta
- Emory-UGA Center of Excellence of Influenza Research and Surveillance (CEIRS), Atlanta GA, USA.,Division of Infectious Diseases, School of Medicine, Emory University, Atlanta, GA, USA
| | | | - Scott D Boyd
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Edmund K Waller
- Emory-UGA Center of Excellence of Influenza Research and Surveillance (CEIRS), Atlanta GA, USA.,Department of Hematology and Oncology, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, USA
| | - Rafi Ahmed
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA. .,Emory-UGA Center of Excellence of Influenza Research and Surveillance (CEIRS), Atlanta GA, USA
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9
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Marks C, Deane CM. How repertoire data are changing antibody science. J Biol Chem 2020; 295:9823-9837. [PMID: 32409582 DOI: 10.1074/jbc.rev120.010181] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/28/2020] [Indexed: 12/13/2022] Open
Abstract
Antibodies are vital proteins of the immune system that recognize potentially harmful molecules and initiate their removal. Mammals can efficiently create vast numbers of antibodies with different sequences capable of binding to any antigen with high affinity and specificity. Because they can be developed to bind to many disease agents, antibodies can be used as therapeutics. In an organism, after antigen exposure, antibodies specific to that antigen are enriched through clonal selection, expansion, and somatic hypermutation. The antibodies present in an organism therefore report on its immune status, describe its innate ability to deal with harmful substances, and reveal how it has previously responded. Next-generation sequencing technologies are being increasingly used to query the antibody, or B-cell receptor (BCR), sequence repertoire, and the amount of BCR data in public repositories is growing. The Observed Antibody Space database, for example, currently contains over a billion sequences from 68 different studies. Repertoires are available that represent both the naive state (i.e. antigen-inexperienced) and that after immunization. This wealth of data has created opportunities to learn more about our immune system. In this review, we discuss the many ways in which BCR repertoire data have been or could be exploited. We highlight its utility for providing insights into how the naive immune repertoire is generated and how it responds to antigens. We also consider how structural information can be used to enhance these data and may lead to more accurate depictions of the sequence space and to applications in the discovery of new therapeutics.
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Affiliation(s)
- Claire Marks
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Charlotte M Deane
- Department of Statistics, University of Oxford, Oxford, United Kingdom
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10
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Shaw JB, Liu W, Vasil′ev YV, Bracken CC, Malhan N, Guthals A, Beckman JS, Voinov VG. Direct Determination of Antibody Chain Pairing by Top-down and Middle-down Mass Spectrometry Using Electron Capture Dissociation and Ultraviolet Photodissociation. Anal Chem 2020; 92:766-773. [PMID: 31769659 PMCID: PMC7819135 DOI: 10.1021/acs.analchem.9b03129] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
One challenge associated with the discovery and development of monoclonal antibody (mAb) therapeutics is the determination of heavy chain and light chain pairing. Advances in MS instrumentation and MS/MS methods have greatly enhanced capabilities for the analysis of large intact proteins yielding much more detailed and accurate proteoform characterization. Consequently, direct interrogation of intact antibodies or F(ab')2 and Fab fragments has the potential to significantly streamline therapeutic mAb discovery processes. Here, we demonstrate for the first time the ability to efficiently cleave disulfide bonds linking heavy and light chains of mAbs using electron capture dissociation (ECD) and 157 nm ultraviolet photodissociation (UVPD). The combination of intact mAb, Fab, or F(ab')2 mass, intact LC and Fd masses, and CDR3 sequence coverage enabled determination of heavy chain and light chain pairing from a single experiment and experimental condition. These results demonstrate the potential of top-down and middle-down proteomics to significantly streamline therapeutic antibody discovery.
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Affiliation(s)
- Jared B. Shaw
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
| | - Weijing Liu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
| | - Yury V. Vasil′ev
- e-MSion Inc., 2121 NE Jack London Drive, Corvallis, Oregon 97330, United States
- Linus Pauling Institute and the Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Carter C. Bracken
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
| | - Neha Malhan
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 3335 Innovation Boulevard, Richland, Washington 99354, United States
| | - Adrian Guthals
- Mapp Biopharmaceutical Inc., 6160 Lusk Boulevard #105, San Diego, California 92121, United States
| | - Joseph S. Beckman
- e-MSion Inc., 2121 NE Jack London Drive, Corvallis, Oregon 97330, United States
- Linus Pauling Institute and the Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
| | - Valery G. Voinov
- e-MSion Inc., 2121 NE Jack London Drive, Corvallis, Oregon 97330, United States
- Linus Pauling Institute and the Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331, United States
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11
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Dibo M, Battocchio EC, dos Santos Souza LM, da Silva MDV, Banin-Hirata BK, Sapla MM, Marinello P, Rocha SP, Faccin-Galhardi LC. Antibody Therapy for the Control of Viral Diseases: An Update. Curr Pharm Biotechnol 2019; 20:1108-1121. [DOI: 10.2174/1389201020666190809112704] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 04/22/2019] [Accepted: 08/01/2019] [Indexed: 12/29/2022]
Abstract
The epidemiological impact of viral diseases, combined with the emergence and reemergence of some viruses, and the difficulties in identifying effective therapies, have encouraged several studies to develop new therapeutic strategies for viral infections. In this context, the use of immunotherapy for the treatment of viral diseases is increasing. One of the strategies of immunotherapy is the use of antibodies, particularly the monoclonal antibodies (mAbs) and multi-specific antibodies, which bind directly to the viral antigen and bring about activation of the immune system. With current advancements in science and technology, several such antibodies are being tested, and some are already approved and are undergoing clinical trials. The present work aims to review the status of mAb development for the treatment of viral diseases.
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Affiliation(s)
- Miriam Dibo
- Department of Microbiology, Biological Sciences Center, State University of Londrina, Parana, Brazil
| | - Eduardo C. Battocchio
- Department of Microbiology, Biological Sciences Center, State University of Londrina, Parana, Brazil
| | - Lucas M. dos Santos Souza
- Department of Microbiology, Biological Sciences Center, State University of Londrina, Parana, Brazil
| | | | - Bruna K. Banin-Hirata
- Department of Pathological Sciences, Biological Sciences Center, State University of Londrina, Parana, Brazil
| | - Milena M.M. Sapla
- Department of Pathological Sciences, Biological Sciences Center, State University of Londrina, Parana, Brazil
| | - Poliana Marinello
- Department of Pathological Sciences, Biological Sciences Center, State University of Londrina, Parana, Brazil
| | - Sérgio P.D. Rocha
- Department of Microbiology, Biological Sciences Center, State University of Londrina, Parana, Brazil
| | - Lígia C. Faccin-Galhardi
- Department of Microbiology, Biological Sciences Center, State University of Londrina, Parana, Brazil
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12
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Engineered peptide barcodes for in-depth analyses of binding protein libraries. Nat Methods 2019; 16:421-428. [PMID: 31011184 DOI: 10.1038/s41592-019-0389-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 03/08/2019] [Indexed: 01/02/2023]
Abstract
Binding protein generation typically relies on laborious screening cascades that process candidate molecules individually. We have developed NestLink, a binder selection and identification technology able to biophysically characterize thousands of library members at once without the need to handle individual clones at any stage of the process. NestLink uses genetically encoded barcoding peptides termed flycodes, which were designed for maximal detectability by mass spectrometry and support accurate deep sequencing. We demonstrate NestLink's capacity to overcome the current limitations of binder-generation methods in three applications. First, we show that hundreds of binder candidates can be simultaneously ranked according to kinetic parameters. Next, we demonstrate deep mining of a nanobody immune repertoire for membrane protein binders, carried out entirely in solution without target immobilization. Finally, we identify rare binders against an integral membrane protein directly in the cellular environment of a human pathogen. NestLink opens avenues for the selection of tailored binder characteristics directly in tissues or in living organisms.
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13
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Bidmos FA, Siris S, Gladstone CA, Langford PR. Bacterial Vaccine Antigen Discovery in the Reverse Vaccinology 2.0 Era: Progress and Challenges. Front Immunol 2018; 9:2315. [PMID: 30349542 PMCID: PMC6187972 DOI: 10.3389/fimmu.2018.02315] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 09/17/2018] [Indexed: 11/13/2022] Open
Abstract
The ongoing, and very serious, threat from antimicrobial resistance necessitates the development and use of preventative measures, predominantly vaccination. Polysaccharide-based vaccines have provided a degree of success in limiting morbidity from disseminated bacterial infections, including those caused by the major human obligate pathogens, Neisseria meningitidis, and Streptococcus pneumoniae. Limitations of these polysaccharide vaccines, such as partial coverage and induced escape leading to persistence of disease, provide a compelling argument for the development of protein vaccines. In this review, we briefly chronicle approaches that have yielded licensed vaccines before highlighting reverse vaccinology 2.0 and its potential application in the discovery of novel bacterial protein vaccine candidates. Technical challenges and research gaps are also discussed.
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Affiliation(s)
- Fadil A Bidmos
- Department of Medicine, Imperial College London, London, United Kingdom
| | - Sara Siris
- Department of Medicine, Imperial College London, London, United Kingdom
| | | | - Paul R Langford
- Department of Medicine, Imperial College London, London, United Kingdom
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14
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Antibody-Mediated Therapy against HIV/AIDS: Where Are We Standing Now? J Pathog 2018; 2018:8724549. [PMID: 29973995 PMCID: PMC6009031 DOI: 10.1155/2018/8724549] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 04/10/2018] [Accepted: 04/26/2018] [Indexed: 11/17/2022] Open
Abstract
Acquired immunodeficiency syndrome (AIDS) cases are on the rise globally. To date, there is still no effective measure to eradicate the causative agent, human immunodeficiency virus (HIV). Highly active antiretroviral therapy (HAART) is being used in HIV/AIDS management, but it results in long-term medication and has major drawbacks such as multiple side effects, high cost, and increasing the generation rate of escape mutants. In addition, HAART does not control HIV-related complications, and hence more medications and further management are required. With this, other alternatives are urgently needed. In the past, small-molecule inhibitors have shown potent antiviral effects, and some of them are now being evaluated in clinical trials. The challenges in developing these small molecules for clinical use include the off-target effect, poor stability, and low bioavailability. On the other hand, antibody-mediated therapy has emerged as an important therapeutic modality for anti-HIV therapeutics development. Many antiviral antibodies, namely, broad neutralizing antibodies (bnAbs) against multiple strains of HIV, have shown promising effects in vitro and in animal studies; further studies are ongoing in clinical trials to evaluate their uses in clinical applications. This short review aims to discuss the current development of therapeutic antibodies against HIV and the challenges in adopting them for clinical use.
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15
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High-throughput sequencing of the immune repertoire in oncology: Applications for clinical diagnosis, monitoring, and immunotherapies. Cancer Lett 2017; 416:42-56. [PMID: 29247824 DOI: 10.1016/j.canlet.2017.12.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 12/11/2017] [Accepted: 12/11/2017] [Indexed: 12/21/2022]
Abstract
The diagnostic, monitoring and therapeutic options for cancers currently remain limited. These limitations represent a large threat to human health. Adaptive immunity, which is dependent on diverse repertoires of B cell receptors (BCRs) and T cell receptors (TCRs), plays a critical role in the anti-tumor immune response. Modulation and surveillance of adaptive immunity has become a powerful weapon to combat cancers. Recently, the high-throughput sequencing of immune repertoire (HTS-IR) technology, which provides a robust tool for deep sequencing repertoires of BCRs or TCRs, has been applied in the development of tumor biomarkers and immunotherapeutics for cancers. This review will first provide an overview of the advancement of HTS-IR technology at the population-cell and single-cell levels. It will then provide a current summary of the applications of HTS-IR technology in the diagnosis and monitoring of minimal residual disease (MRD), focusing on immune reconstitution after the treatment of allogeneic hematopoietic stem cell transplantation (allo-HSCT) in B/T-cell malignancies, and the precise detection of tumor-infiltrating lymphocytes (TILs) in non-B/T-cell malignancies. Finally, current advances of HTS-IR technology in cancer immunotherapeutic applications, such as therapeutic antibodies, CAR-T cell based-adoptive immunotherapies, and neoantigen-specific TCR-T cell-based adoptive immunotherapies, will be introduced.
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16
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Kovaltsuk A, Krawczyk K, Galson JD, Kelly DF, Deane CM, Trück J. How B-Cell Receptor Repertoire Sequencing Can Be Enriched with Structural Antibody Data. Front Immunol 2017; 8:1753. [PMID: 29276518 PMCID: PMC5727015 DOI: 10.3389/fimmu.2017.01753] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 11/27/2017] [Indexed: 12/24/2022] Open
Abstract
Next-generation sequencing of immunoglobulin gene repertoires (Ig-seq) allows the investigation of large-scale antibody dynamics at a sequence level. However, structural information, a crucial descriptor of antibody binding capability, is not collected in Ig-seq protocols. Developing systematic relationships between the antibody sequence information gathered from Ig-seq and low-throughput techniques such as X-ray crystallography could radically improve our understanding of antibodies. The mapping of Ig-seq datasets to known antibody structures can indicate structurally, and perhaps functionally, uncharted areas. Furthermore, contrasting naïve and antigenically challenged datasets using structural antibody descriptors should provide insights into antibody maturation. As the number of antibody structures steadily increases and more and more Ig-seq datasets become available, the opportunities that arise from combining the two types of information increase as well. Here, we review how these data types enrich one another and show potential for advancing our knowledge of the immune system and improving antibody engineering.
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Affiliation(s)
| | - Konrad Krawczyk
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Jacob D Galson
- Division of Immunology and the Children's Research Center, University Children's Hospital, University of Zürich, Zürich, Switzerland
| | - Dominic F Kelly
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Center, Oxford, United Kingdom
| | - Charlotte M Deane
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Johannes Trück
- Division of Immunology and the Children's Research Center, University Children's Hospital, University of Zürich, Zürich, Switzerland
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17
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VanDuijn MM, Dekker LJ, van IJcken WFJ, Sillevis Smitt PAE, Luider TM. Immune Repertoire after Immunization As Seen by Next-Generation Sequencing and Proteomics. Front Immunol 2017; 8:1286. [PMID: 29085363 PMCID: PMC5650670 DOI: 10.3389/fimmu.2017.01286] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 09/25/2017] [Indexed: 01/24/2023] Open
Abstract
The immune system produces a diverse repertoire of immunoglobulins in response to foreign antigens. During B-cell development, VDJ recombination and somatic mutations generate diversity, whereas selection processes remove it. Using both proteomic and NGS approaches, we characterized the immune repertoires in groups of rats after immunization with purified antigens. Proteomics and NGS data on the repertoire are in qualitative agreement, but did show quantitative differences that may relate to differences between the biological niches that were sampled for these approaches. Both methods contributed complementary information in the characterization of the immune repertoire. It was found that the immune repertoires resulting from each antigen had many similarities that allowed samples to cluster together, and that mutated immunoglobulin peptides were shared among animals with a response to the same antigen significantly more than for different antigens. However, the number of shared sequences decreased in a log-linear fashion relative to the number of animals that share them, which may affect future applications. A phylogenetic analysis on the NGS reads showed that reads from different individuals immunized with the same antigen populated distinct branches of the phylogram, an indication that the repertoire had converged. Also, similar mutation patterns were found in branches of the phylogenetic tree that were associated with antigen-specific immunoglobulins through proteomics data. Thus, data from different analysis methods and different experimental platforms show that the immunoglobulin repertoires of immunized animals have overlapping and converging features. With additional research, this may enable interesting applications in biotechnology and clinical diagnostics.
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Affiliation(s)
| | | | | | | | - Theo M Luider
- Department of Neurology, Erasmus MC, Rotterdam, Netherlands
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18
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Antibody therapies for the prevention and treatment of viral infections. NPJ Vaccines 2017; 2:19. [PMID: 29263875 PMCID: PMC5627241 DOI: 10.1038/s41541-017-0019-3] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 05/08/2017] [Accepted: 05/16/2017] [Indexed: 12/18/2022] Open
Abstract
Antibodies are an important component in host immune responses to viral pathogens. Because of their unique maturation process, antibodies can evolve to be highly specific to viral antigens. Physicians and researchers have been relying on such high specificity in their quest to understand host–viral interaction and viral pathogenesis mechanisms and to find potential cures for viral infection and disease. With more than 60 recombinant monoclonal antibodies developed for human use in the last 20 years, monoclonal antibodies are now considered a viable therapeutic modality for infectious disease targets, including newly emerging viral pathogens such as Ebola representing heightened public health concerns, as well as pathogens that have long been known, such as human cytomegalovirus. Here, we summarize some recent advances in identification and characterization of monoclonal antibodies suitable as drug candidates for clinical evaluation, and review some promising candidates in the development pipeline.
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19
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Guthals A, Gan Y, Murray L, Chen Y, Stinson J, Nakamura G, Lill JR, Sandoval W, Bandeira N. De Novo MS/MS Sequencing of Native Human Antibodies. J Proteome Res 2016; 16:45-54. [PMID: 27779884 DOI: 10.1021/acs.jproteome.6b00608] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One direct route for the discovery of therapeutic human monoclonal antibodies (mAbs) involves the isolation of peripheral B cells from survivors/sero-positive individuals after exposure to an infectious reagent or disease etiology, followed by single-cell sequencing or hybridoma generation. Peripheral B cells, however, are not always easy to obtain and represent only a small percentage of the total B-cell population across all bodily tissues. Although it has been demonstrated that tandem mass spectrometry (MS/MS) techniques can interrogate the full polyclonal antibody (pAb) response to an antigen in vivo, all current approaches identify MS/MS spectra against databases derived from genetic sequencing of B cells from the same patient. In this proof-of-concept study, we demonstrate the feasibility of a novel MS/MS antibody discovery approach in which only serum antibodies are required without the need for sequencing of genetic material. Peripheral pAbs from a cytomegalovirus-exposed individual were purified by glycoprotein B antigen affinity and de novo sequenced from MS/MS data. Purely MS-derived mAbs were then manufactured in mammalian cells to validate potency via antigen-binding ELISA. Interestingly, we found that these mAbs accounted for 1 to 2% of total donor IgG but were not detected in parallel sequencing of memory B cells from the same patient.
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Affiliation(s)
- Adrian Guthals
- Mapp Biopharmaceutical, Inc. , 6160 Lusk Boulevard #C105, San Diego, California 92121, United States
| | - Yutian Gan
- Department of Proteomics & Biological Resources, Genentech, Inc. , South San Francisco, California 94080, United States
| | - Laura Murray
- Department of Protein Chemistry, Genentech, Inc. , South San Francisco, California 94080, United States
| | - Yongmei Chen
- Department of Antibody Engineering, Genentech, Inc. , South San Francisco, California 94080, United States
| | - Jeremy Stinson
- Department of Molecular Biology, Genentech, Inc. , South San Francisco, California 94080, United States
| | - Gerald Nakamura
- Department of Antibody Engineering, Genentech, Inc. , South San Francisco, California 94080, United States
| | - Jennie R Lill
- Department of Proteomics & Biological Resources, Genentech, Inc. , South San Francisco, California 94080, United States
| | - Wendy Sandoval
- Department of Proteomics & Biological Resources, Genentech, Inc. , South San Francisco, California 94080, United States
| | - Nuno Bandeira
- Department of Computer Science and Engineering, University of California, San Diego , 9500 Gilman Drive, Mail Code 0404, La Jolla, California 92093, United States.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego , 9500 Gilman Drive, Mail Code 0657, La Jolla, California 92093, United States
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20
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Han Y, Li H, Guan Y, Huang J. Immune repertoire: A potential biomarker and therapeutic for hepatocellular carcinoma. Cancer Lett 2016; 379:206-12. [DOI: 10.1016/j.canlet.2015.06.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 06/29/2015] [Accepted: 06/30/2015] [Indexed: 12/27/2022]
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21
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Antibodies elicited by the first non-viral prophylactic cancer vaccine show tumor-specificity and immunotherapeutic potential. Sci Rep 2016; 6:31740. [PMID: 27545199 PMCID: PMC4992835 DOI: 10.1038/srep31740] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 07/25/2016] [Indexed: 01/30/2023] Open
Abstract
MUC1 is a shared tumor antigen expressed on >80% of human cancers. We completed the first prophylactic cancer vaccine clinical trial based on a non-viral antigen, MUC1, in healthy individuals at-risk for colon cancer. This trial provided a unique source of potentially effective and safe immunotherapeutic drugs, fully-human antibodies affinity-matured in a healthy host to a tumor antigen. We purified, cloned, and characterized 13 IgGs specific for several tumor-associated MUC1 epitopes with a wide range of binding affinities. These antibodies bind hypoglycosylated MUC1 on human cancer cell lines and tumor tissues but show no reactivity against fully-glycosylated MUC1 on normal cells and tissues. We found that several antibodies activate complement-mediated cytotoxicity and that T cells carrying chimeric antigen receptors with the antibody variable regions kill MUC1(+) target cells, express activation markers, and produce interferon gamma. Fully-human and tumor-specific, these antibodies are candidates for further testing and development as immunotherapeutic drugs.
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22
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Ogishi M, Yotsuyanagi H, Moriya K, Koike K. Delineation of autoantibody repertoire through differential proteogenomics in hepatitis C virus-induced cryoglobulinemia. Sci Rep 2016; 6:29532. [PMID: 27403724 PMCID: PMC4941579 DOI: 10.1038/srep29532] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/17/2016] [Indexed: 12/21/2022] Open
Abstract
Antibodies cross-reactive to pathogens and autoantigens are considered pivotal in both infection control and accompanying autoimmunity. However, the pathogenic roles of autoantibodies largely remain elusive without a priori knowledge of disease-specific autoantigens. Here, through a novel quantitative proteogenomics approach, we demonstrated a successful identification of immunoglobulin variable heavy chain (VH) sequences highly enriched in pathological immune complex from clinical specimens obtained from a patient with hepatitis C virus-induced cryoglobulinemia (HCV-CG). Reconstructed single-domain antibodies were reactive to both HCV antigens and potentially liver-derived human proteins. Moreover, over the course of antiviral therapy, a substantial "de-evolution" of a distinct sub-repertoire was discovered, to which proteomically identified cryoprecipitation-prone autoantibodies belonged. This sub-repertoire was characterized by IGHJ6*03-derived, long, hydrophobic complementarity determining region (CDR-H3). This study provides a proof-of-concept of de novo mining of autoantibodies and corresponding autoantigen candidates in a disease-specific context in human, thus facilitating future reverse-translational research for the discovery of novel biomarkers and the development of antigen-specific immunotherapy against various autoantibody-related disorders.
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Affiliation(s)
- Masato Ogishi
- Department of Infectious Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Yotsuyanagi
- Department of Infectious Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kyoji Moriya
- Department of Infectious Control and Prevention, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kazuhiko Koike
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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23
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Liu J, Li R, Liu K, Li L, Zai X, Chi X, Fu L, Xu J, Chen W. Identification of antigen-specific human monoclonal antibodies using high-throughput sequencing of the antibody repertoire. Biochem Biophys Res Commun 2016; 473:23-28. [PMID: 26979754 DOI: 10.1016/j.bbrc.2016.03.038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 03/08/2016] [Indexed: 12/26/2022]
Abstract
High-throughput sequencing of the antibody repertoire provides a large number of antibody variable region sequences that can be used to generate human monoclonal antibodies. However, current screening methods for identifying antigen-specific antibodies are inefficient. In the present study, we developed an antibody clone screening strategy based on clone dynamics and relative frequency, and used it to identify antigen-specific human monoclonal antibodies. Enzyme-linked immunosorbent assay showed that at least 52% of putative positive immunoglobulin heavy chains composed antigen-specific antibodies. Combining information on dynamics and relative frequency improved identification of positive clones and elimination of negative clones. and increase the credibility of putative positive clones. Therefore the screening strategy could simplify the subsequent experimental screening and may facilitate the generation of antigen-specific antibodies.
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Affiliation(s)
- Ju Liu
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing 100071, China
| | - Ruihua Li
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing 100071, China
| | - Kun Liu
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing 100071, China
| | - Liangliang Li
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing 100071, China
| | - Xiaodong Zai
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing 100071, China
| | - Xiangyang Chi
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing 100071, China
| | - Ling Fu
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing 100071, China
| | - Junjie Xu
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing 100071, China.
| | - Wei Chen
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing 100071, China.
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24
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Al Kindi MA, Colella AD, Chataway TK, Jackson MW, Wang JJ, Gordon TP. Secreted autoantibody repertoires in Sjögren's syndrome and systemic lupus erythematosus: A proteomic approach. Autoimmun Rev 2016; 15:405-10. [PMID: 26804757 DOI: 10.1016/j.autrev.2016.01.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 01/13/2016] [Indexed: 12/18/2022]
Abstract
The structures of epitopes bound by autoantibodies against RNA-protein complexes have been well-defined over several decades, but little is known of the clonality, immunoglobulin (Ig) variable (V) gene usage and mutational status of the autoantibodies themselves at the level of the secreted (serum) proteome. A novel proteomic workflow is presented based on affinity purification of specific Igs from serum, high-resolution two-dimensional gel electrophoresis, and de novo and database-driven sequencing of V-region proteins by mass spectrometry. Analysis of anti-Ro52/Ro60/La proteomes in primary Sjögren's syndrome (SS) and anti-Sm and anti-ribosomal P proteomes in systemic lupus erythematosus (SLE) has revealed that these antibody responses are dominated by restricted sets of public (shared) clonotypes, consistent with common pathways of production across unrelated individuals. The discovery of shared sets of specific V-region peptides can be exploited for diagnostic biomarkers in targeted mass spectrometry platforms and for tracking and removal of pathogenic clones.
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Affiliation(s)
- Mahmood A Al Kindi
- Department of Immunology, Flinders Medical Centre and Flinders University, SA Pathology, Bedford Park, 5042, South Australia, Australia
| | - Alex D Colella
- Department of Immunology, Flinders Medical Centre and Flinders University, SA Pathology, Bedford Park, 5042, South Australia, Australia; Flinders Proteomic Facility, Flinders University, Australia
| | - Tim K Chataway
- Flinders Proteomic Facility, Flinders University, Australia
| | - Michael W Jackson
- Department of Immunology, Flinders Medical Centre and Flinders University, SA Pathology, Bedford Park, 5042, South Australia, Australia
| | - Jing J Wang
- Department of Immunology, Flinders Medical Centre and Flinders University, SA Pathology, Bedford Park, 5042, South Australia, Australia.
| | - Tom P Gordon
- Department of Immunology, Flinders Medical Centre and Flinders University, SA Pathology, Bedford Park, 5042, South Australia, Australia.
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25
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Safonova Y, Bonissone S, Kurpilyansky E, Starostina E, Lapidus A, Stinson J, DePalatis L, Sandoval W, Lill J, Pevzner PA. IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis. Bioinformatics 2015; 31:i53-61. [PMID: 26072509 PMCID: PMC4542777 DOI: 10.1093/bioinformatics/btv238] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
UNLABELLED The analysis of concentrations of circulating antibodies in serum (antibody repertoire) is a fundamental, yet poorly studied, problem in immunoinformatics. The two current approaches to the analysis of antibody repertoires [next generation sequencing (NGS) and mass spectrometry (MS)] present difficult computational challenges since antibodies are not directly encoded in the germline but are extensively diversified by somatic recombination and hypermutations. Therefore, the protein database required for the interpretation of spectra from circulating antibodies is custom for each individual. Although such a database can be constructed via NGS, the reads generated by NGS are error-prone and even a single nucleotide error precludes identification of a peptide by the standard proteomics tools. Here, we present the IgRepertoireConstructor algorithm that performs error-correction of immunosequencing reads and uses mass spectra to validate the constructed antibody repertoires. AVAILABILITY AND IMPLEMENTATION IgRepertoireConstructor is open source and freely available as a C++ and Python program running on all Unix-compatible platforms. The source code is available from http://bioinf.spbau.ru/igtools. CONTACT ppevzner@ucsd.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yana Safonova
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Stefano Bonissone
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Eugene Kurpilyansky
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Ekaterina Starostina
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Alla Lapidus
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Jeremy Stinson
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Laura DePalatis
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Wendy Sandoval
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Jennie Lill
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Pavel A Pevzner
- Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia, Algorithmic Biology Laboratory, St. Petersburg Academic University, St. Petersburg, Russia, Bioinformatics Program, University of California, San Diego, CA, USA, Genentech, South San Francisco, CA, USA and Department of Computer Science and Engineering, University of California, San Diego, CA, USA
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26
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Ohlin M, Söderberg-Nauclér C. Human antibody technology and the development of antibodies against cytomegalovirus. Mol Immunol 2015; 67:153-70. [DOI: 10.1016/j.molimm.2015.02.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 02/13/2015] [Accepted: 02/15/2015] [Indexed: 02/08/2023]
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Halliley JL, Tipton CM, Liesveld J, Rosenberg AF, Darce J, Gregoretti IV, Popova L, Kaminiski D, Fucile CF, Albizua I, Kyu S, Chiang KY, Bradley KT, Burack R, Slifka M, Hammarlund E, Wu H, Zhao L, Walsh EE, Falsey AR, Randall TD, Cheung WC, Sanz I, Lee FEH. Long-Lived Plasma Cells Are Contained within the CD19(-)CD38(hi)CD138(+) Subset in Human Bone Marrow. Immunity 2015; 43:132-45. [PMID: 26187412 DOI: 10.1016/j.immuni.2015.06.016] [Citation(s) in RCA: 342] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Revised: 01/16/2015] [Accepted: 04/28/2015] [Indexed: 01/09/2023]
Abstract
Antibody responses to viral infections are sustained for decades by long-lived plasma cells (LLPCs). However, LLPCs have yet to be characterized in humans. Here we used CD19, CD38, and CD138 to identify four PC subsets in human bone marrow (BM). We found that the CD19(-)CD38(hi)CD138(+) subset was morphologically distinct, differentially expressed PC-associated genes, and exclusively contained PCs specific for viral antigens to which the subjects had not been exposed for more than 40 years. Protein sequences of measles- and mumps-specific circulating antibodies were encoded for by CD19(-)CD38(hi)CD138(+) PCs in the BM. Finally, we found that CD19(-)CD38(hi)CD138(+) PCs had a distinct RNA transcriptome signature and human immunoglobulin heavy chain (VH) repertoire that was relatively uncoupled from other BM PC subsets and probably represents the B cell response's "historical record" of antigenic exposure. Thus, our studies define human LLPCs and provide a mechanism for the life-long maintenance of anti-viral antibodies in the serum.
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Affiliation(s)
- Jessica L Halliley
- Divisions of Pulmonary, Allergy, & Critical Care Medicine, Emory University, Atlanta, GA 30322, USA; Pulmonary & Critical Care Medicine, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Christopher M Tipton
- Division of Rheumatology, Emory University, Atlanta, GA 30322, USA; Lowance Center for Human Immunology in the Departments of Medicine and Pediatrics, Emory University, Atlanta, GA 30322, USA
| | - Jane Liesveld
- Divisions of Hematology/Oncology/James P. Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Alexander F Rosenberg
- Division of Allergy, Immunology, and Rheumatology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Jaime Darce
- Cell Signaling Technology, Inc., Danvers, MA 01923, USA
| | | | - Lana Popova
- Cell Signaling Technology, Inc., Danvers, MA 01923, USA
| | - Denise Kaminiski
- Division of Allergy, Immunology, and Rheumatology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Christopher F Fucile
- Division of Allergy, Immunology, and Rheumatology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Igor Albizua
- Divisions of Pulmonary, Allergy, & Critical Care Medicine, Emory University, Atlanta, GA 30322, USA
| | - Shuya Kyu
- Divisions of Pulmonary, Allergy, & Critical Care Medicine, Emory University, Atlanta, GA 30322, USA
| | - Kuang-Yueh Chiang
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Emory University, Atlanta, GA 30322, USA
| | - Kyle T Bradley
- Department of Pathology & Laboratory Medicine, Emory University, Atlanta, GA 30322, USA
| | - Richard Burack
- Department of Pathology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Mark Slifka
- Oregon Health & Sciences University, Beaverton, OR 97006, USA
| | | | - Hao Wu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA
| | - Liping Zhao
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA
| | - Edward E Walsh
- Division of Infectious Diseases, University of Rochester Medical Center & Rochester General Hospital, Rochester, NY 14621, USA
| | - Ann R Falsey
- Division of Infectious Diseases, University of Rochester Medical Center & Rochester General Hospital, Rochester, NY 14621, USA
| | - Troy D Randall
- Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | | | - Iñaki Sanz
- Division of Rheumatology, Emory University, Atlanta, GA 30322, USA; Lowance Center for Human Immunology in the Departments of Medicine and Pediatrics, Emory University, Atlanta, GA 30322, USA
| | - F Eun-Hyung Lee
- Divisions of Pulmonary, Allergy, & Critical Care Medicine, Emory University, Atlanta, GA 30322, USA; Lowance Center for Human Immunology in the Departments of Medicine and Pediatrics, Emory University, Atlanta, GA 30322, USA.
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Wine Y, Horton AP, Ippolito GC, Georgiou G. Serology in the 21st century: the molecular-level analysis of the serum antibody repertoire. Curr Opin Immunol 2015; 35:89-97. [PMID: 26172290 DOI: 10.1016/j.coi.2015.06.009] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 06/22/2015] [Accepted: 06/22/2015] [Indexed: 12/11/2022]
Abstract
The ensemble of antibodies found in serum and secretions represents the key adaptive component of B-cell mediated humoral immunity. The antibody repertoire is shaped by the historical record of exposure to exogenous factors such as pathogens and vaccines, as well as by endogenous host-intrinsic factors such as genetics, self-antigens, and age. Thanks to very recent technology advancements it is now becoming possible to identify and quantify the individual antibodies comprising the serological repertoire. In parallel, the advent of high throughput methods for antigen and immunosignature discovery opens up unprecedented opportunities to transform our understanding of numerous key questions in adaptive humoral immunity, including the nature and dynamics of serological memory, the role of polyspecific antibodies in health and disease and how protective responses to infections or vaccine challenge arise. Additionally, these technologies also hold great promise for therapeutic antibody and biomarker discovery in a variety of settings.
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Affiliation(s)
- Yariv Wine
- Department of Molecular Microbiology and Biotechnology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Andrew P Horton
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA; Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA
| | - Gregory C Ippolito
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - George Georgiou
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX, USA; Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, USA; Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA; Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX, USA.
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29
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Calis JJA, Rosenberg BR. Characterizing immune repertoires by high throughput sequencing: strategies and applications. Trends Immunol 2014; 35:581-590. [PMID: 25306219 PMCID: PMC4390416 DOI: 10.1016/j.it.2014.09.004] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 09/05/2014] [Accepted: 09/09/2014] [Indexed: 01/09/2023]
Abstract
As the key cellular effectors of adaptive immunity, T and B lymphocytes utilize specialized receptors to recognize, respond to, and neutralize a diverse array of extrinsic threats. These receptors (immunoglobulins in B lymphocytes, T cell receptors in T lymphocytes) are incredibly variable, the products of specialized genetic diversification mechanisms that generate complex lymphocyte repertoires with extensive collections of antigen specificities. Recent advances in high throughput sequencing (HTS) technologies have transformed our ability to examine antigen receptor repertoires at single nucleotide, and more recently, single cell, resolution. Here we review current approaches to examining antigen receptor repertoires by HTS, and discuss inherent biological and technical challenges. We further describe emerging applications of this powerful methodology for exploring the adaptive immune system.
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Affiliation(s)
| | - Brad R Rosenberg
- The Rockefeller University, New York, NY, USA; John C. Whitehead Presidential Fellows Program, The Rockefeller University, New York, NY, USA.
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30
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Tan YC, Kongpachith S, Blum LK, Ju CH, Lahey LJ, Lu DR, Cai X, Wagner CA, Lindstrom TM, Sokolove J, Robinson WH. Barcode-enabled sequencing of plasmablast antibody repertoires in rheumatoid arthritis. Arthritis Rheumatol 2014; 66:2706-15. [PMID: 24965753 DOI: 10.1002/art.38754] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 06/17/2014] [Indexed: 12/29/2022]
Abstract
OBJECTIVE A hallmark of rheumatoid arthritis (RA) is the production of autoantibodies, including anti-citrullinated protein antibodies (ACPAs). Nevertheless, the specific targets of these autoantibodies remain incompletely defined. During an immune response, B cells specific for the inciting antigen(s) are activated and differentiate into plasmablasts, which are released into the blood. We undertook this study to sequence the plasmablast antibody repertoire to define the targets of the active immune response in RA. METHODS We developed a novel DNA barcoding method to sequence the cognate heavy- and light-chain pairs of antibodies expressed by individual blood plasmablasts in RA. The method uses a universal 5' adapter that enables full-length sequencing of the antibodies' variable regions and recombinant expression of the paired antibody chains. The sequence data sets were bioinformatically analyzed to generate phylogenetic trees that identify clonal families of antibodies sharing heavy- and light-chain VJ sequences. Representative antibodies were expressed, and their binding properties were characterized using anti-cyclic citrullinated peptide 2 (anti-CCP-2) enzyme-linked immunosorbent assay (ELISA) and antigen microarrays. RESULTS We used our sequencing method to generate phylogenetic trees representing the antibody repertoires of peripheral blood plasmablasts from 4 individuals with anti-CCP+ RA, and recombinantly expressed 14 antibodies that were either "singleton" antibodies or representative of clonal antibody families. Anti-CCP-2 ELISA identified 4 ACPAs, and antigen microarray analysis identified ACPAs that differentially targeted epitopes on α-enolase, citrullinated fibrinogen, and citrullinated histone H2B. CONCLUSION Our data provide evidence that autoantibodies targeting α-enolase, citrullinated fibrinogen, and citrullinated histone H2B are produced by the ongoing activated B cell response in, and thus may contribute to the pathogenesis of, RA.
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Affiliation(s)
- Yann-Chong Tan
- Stanford University, Stanford, California, and VA Palo Alto Health Care System, Palo Alto, California
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31
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Lavinder JJ, Horton AP, Georgiou G, Ippolito GC. Next-generation sequencing and protein mass spectrometry for the comprehensive analysis of human cellular and serum antibody repertoires. Curr Opin Chem Biol 2014; 24:112-20. [PMID: 25461729 DOI: 10.1016/j.cbpa.2014.11.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 11/08/2014] [Accepted: 11/10/2014] [Indexed: 12/19/2022]
Abstract
Recent developments of high-throughput technologies are enabling the molecular-level analysis and bioinformatic mining of antibody-mediated (humoral) immunity in humans at an unprecedented level. These approaches explore either the sequence space of B-cell receptor repertoires using next-generation deep sequencing (BCR-seq), or the amino acid identities of antibody in blood using protein mass spectrometry (Ig-seq), or both. Generalizable principles about the molecular composition of the protective humoral immune response are being defined, and as such, the field could supersede traditional methods for the development of diagnostics, vaccines, and antibody therapeutics. Three key challenges remain and have driven recent advances: (1) incorporation of innovative techniques for paired BCR-seq to ascertain the complete antibody variable-domain VH:VL clonotype, (2) integration of proteomic Ig-seq with BCR-seq to reveal how the serum antibody repertoire compares with the antibody repertoire encoded by circulating B cells, and (3) a demand to link antibody sequence data to functional meaning (binding and protection).
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Affiliation(s)
- Jason J Lavinder
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712-1062, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712-1062, USA
| | - Andrew P Horton
- Center for Systems & Synthetic Biology, University of Texas at Austin, Austin, TX 78712-1062, USA; Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712-1062, USA
| | - George Georgiou
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX 78712-1062, USA; Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712-1062, USA; Center for Systems & Synthetic Biology, University of Texas at Austin, Austin, TX 78712-1062, USA; Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712-1062, USA; Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712-1062, USA
| | - Gregory C Ippolito
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712-1062, USA.
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32
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Greiff V, Menzel U, Haessler U, Cook SC, Friedensohn S, Khan TA, Pogson M, Hellmann I, Reddy ST. Quantitative assessment of the robustness of next-generation sequencing of antibody variable gene repertoires from immunized mice. BMC Immunol 2014; 15:40. [PMID: 25318652 PMCID: PMC4233042 DOI: 10.1186/s12865-014-0040-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 09/15/2014] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) of antibody variable regions has emerged as a powerful tool in systems immunology by providing quantitative molecular information on polyclonal humoral immune responses. Reproducible and robust information on antibody repertoires is valuable for basic and applied immunology studies: thus, it is essential to establish the reliability of antibody NGS data. RESULTS We isolated RNA from antibody-secreting cells (ASCs) from either 1 mouse or a pool of 9 immunized mice in order to simulate both normal and high diversity populations. Next, we prepared three technical replicates of antibody libraries by RT-PCR from each diversity scenario, which were sequenced using the Illumina MiSeq platform resulting in >106 250 bp paired-end reads per replicate. We then assessed the robustness of antibody repertoire data based on clonal identification defined by amino acid sequence of either full-length VDJ region or the complementarity determining region 3 (CDR3). Leveraging modeling approaches adapted from mathematical ecology, we found that in either diversity scenario both CDR3 and VDJ detection nears completeness indicating deep coverage of ASC repertoires. Additionally, we defined reliability thresholds for accurate quantification and ranking of CDR3s and VDJs. Importantly, we show that both factors-(i) replicate sequencing and (ii) sequencing depth-are crucial for robust CDR3 and VDJ detection and ranking. CONCLUSIONS In summary, we established widely applicable experimental and computational guidelines for robust antibody NGS and analysis, which will help advance systems immunology studies related to the quantitative profiling of antibody responses following infection and vaccination.
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Affiliation(s)
- Victor Greiff
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Ulrike Menzel
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Ulrike Haessler
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Skylar C Cook
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Simon Friedensohn
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Tarik A Khan
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Mark Pogson
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Ina Hellmann
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
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33
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Boutz DR, Horton AP, Wine Y, Lavinder JJ, Georgiou G, Marcotte EM. Proteomic identification of monoclonal antibodies from serum. Anal Chem 2014; 86:4758-66. [PMID: 24684310 PMCID: PMC4033631 DOI: 10.1021/ac4037679] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Characterizing the in vivo dynamics of the polyclonal antibody repertoire in serum, such as that which might arise in response to stimulation with an antigen, is difficult due to the presence of many highly similar immunoglobulin proteins, each specified by distinct B lymphocytes. These challenges have precluded the use of conventional mass spectrometry for antibody identification based on peptide mass spectral matches to a genomic reference database. Recently, progress has been made using bottom-up analysis of serum antibodies by nanoflow liquid chromatography/high-resolution tandem mass spectrometry combined with a sample-specific antibody sequence database generated by high-throughput sequencing of individual B cell immunoglobulin variable domains (V genes). Here, we describe how intrinsic features of antibody primary structure, most notably the interspersed segments of variable and conserved amino acid sequences, generate recurring patterns in the corresponding peptide mass spectra of V gene peptides, greatly complicating the assignment of correct sequences to mass spectral data. We show that the standard method of decoy-based error modeling fails to account for the error introduced by these highly similar sequences, leading to a significant underestimation of the false discovery rate. Because of these effects, antibody-derived peptide mass spectra require increased stringency in their interpretation. The use of filters based on the mean precursor ion mass accuracy of peptide-spectrum matches is shown to be particularly effective in distinguishing between "true" and "false" identifications. These findings highlight important caveats associated with the use of standard database search and error-modeling methods with nonstandard data sets and custom sequence databases.
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Affiliation(s)
- Daniel R Boutz
- Center for Systems & Synthetic Biology, †Institute for Cellular and Molecular Biology, ⊥Department of Biomedical Engineering, §Department of Chemical Engineering, and ∥Department of Molecular Biosciences, University of Texas at Austin , Austin, Texas 78712, United States
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34
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Dekker L, Wu S, Vanduijn M, Tolić N, Stingl C, Zhao R, Luider T, Paša-Tolić L. An integrated top-down and bottom-up proteomic approach to characterize the antigen-binding fragment of antibodies. Proteomics 2014; 14:1239-48. [DOI: 10.1002/pmic.201300366] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 02/14/2014] [Accepted: 03/07/2014] [Indexed: 11/10/2022]
Affiliation(s)
- Lennard Dekker
- Department of Neurology; Erasmus MC; Rotterdam The Netherlands
| | - Si Wu
- Environmental Molecular Sciences Laboratory; Pacific Northwest National Laboratories; Richland WA USA
| | | | - Nikolai Tolić
- Environmental Molecular Sciences Laboratory; Pacific Northwest National Laboratories; Richland WA USA
| | | | - Rui Zhao
- Environmental Molecular Sciences Laboratory; Pacific Northwest National Laboratories; Richland WA USA
| | - Theo Luider
- Department of Neurology; Erasmus MC; Rotterdam The Netherlands
| | - Ljiljana Paša-Tolić
- Environmental Molecular Sciences Laboratory; Pacific Northwest National Laboratories; Richland WA USA
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35
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Lu DR, Tan YC, Kongpachith S, Cai X, Stein EA, Lindstrom TM, Sokolove J, Robinson WH. Identifying functional anti-Staphylococcus aureus antibodies by sequencing antibody repertoires of patient plasmablasts. Clin Immunol 2014; 152:77-89. [PMID: 24589749 DOI: 10.1016/j.clim.2014.02.010] [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] [Received: 11/09/2013] [Revised: 02/15/2014] [Accepted: 02/15/2014] [Indexed: 01/16/2023]
Abstract
Infection by Staphylococcus aureus is on the rise, and there is a need for a better understanding of host immune responses that combat S. aureus. Here we use DNA barcoding to enable deep sequencing of the paired heavy- and light-chain immunoglobulin genes expressed by individual plasmablasts derived from S. aureus-infected humans. Bioinformatic analysis of the antibody repertoires revealed clonal families of heavy-chain sequences and enabled rational selection of antibodies for recombinant expression. Of the ten recombinant antibodies produced, seven bound to S. aureus, of which four promoted opsonophagocytosis of S. aureus. Five of the antibodies bound to known S. aureus cell-surface antigens, including fibronectin-binding protein A. Fibronectin-binding protein A-specific antibodies were isolated from two independent S. aureus-infected patients and mediated neutrophil killing of S. aureus in in vitro assays. Thus, our DNA barcoding approach enabled efficient identification of antibodies involved in protective host antibody responses against S. aureus.
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Affiliation(s)
- Daniel R Lu
- Division of Immunology and Rheumatology, Stanford University, CCSR 4135, 269 Campus Dr., Stanford, CA 94305, USA; VA Palo Alto Health Care System, 3801 Miranda Ave, Palo Alto, CA 94304, USA; Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yann-Chong Tan
- Division of Immunology and Rheumatology, Stanford University, CCSR 4135, 269 Campus Dr., Stanford, CA 94305, USA; VA Palo Alto Health Care System, 3801 Miranda Ave, Palo Alto, CA 94304, USA; Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sarah Kongpachith
- Division of Immunology and Rheumatology, Stanford University, CCSR 4135, 269 Campus Dr., Stanford, CA 94305, USA; VA Palo Alto Health Care System, 3801 Miranda Ave, Palo Alto, CA 94304, USA; Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Xiaoyong Cai
- Division of Immunology and Rheumatology, Stanford University, CCSR 4135, 269 Campus Dr., Stanford, CA 94305, USA; VA Palo Alto Health Care System, 3801 Miranda Ave, Palo Alto, CA 94304, USA
| | - Emily A Stein
- Division of Immunology and Rheumatology, Stanford University, CCSR 4135, 269 Campus Dr., Stanford, CA 94305, USA; VA Palo Alto Health Care System, 3801 Miranda Ave, Palo Alto, CA 94304, USA
| | - Tamsin M Lindstrom
- Division of Immunology and Rheumatology, Stanford University, CCSR 4135, 269 Campus Dr., Stanford, CA 94305, USA
| | - Jeremy Sokolove
- Division of Immunology and Rheumatology, Stanford University, CCSR 4135, 269 Campus Dr., Stanford, CA 94305, USA; VA Palo Alto Health Care System, 3801 Miranda Ave, Palo Alto, CA 94304, USA
| | - William H Robinson
- Division of Immunology and Rheumatology, Stanford University, CCSR 4135, 269 Campus Dr., Stanford, CA 94305, USA; VA Palo Alto Health Care System, 3801 Miranda Ave, Palo Alto, CA 94304, USA; Stanford Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA.
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36
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The promise and challenge of high-throughput sequencing of the antibody repertoire. Nat Biotechnol 2014; 32:158-68. [PMID: 24441474 PMCID: PMC4113560 DOI: 10.1038/nbt.2782] [Citation(s) in RCA: 471] [Impact Index Per Article: 47.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 12/04/2013] [Indexed: 12/16/2022]
Abstract
Georgiou and colleagues discuss rapidly evolving methods for high-throughput sequencing of the antibody repertoire, and how the resulting data may be applied to answer basic and translational research questions. Efforts to determine the antibody repertoire encoded by B cells in the blood or lymphoid organs using high-throughput DNA sequencing technologies have been advancing at an extremely rapid pace and are transforming our understanding of humoral immune responses. Information gained from high-throughput DNA sequencing of immunoglobulin genes (Ig-seq) can be applied to detect B-cell malignancies with high sensitivity, to discover antibodies specific for antigens of interest, to guide vaccine development and to understand autoimmunity. Rapid progress in the development of experimental protocols and informatics analysis tools is helping to reduce sequencing artifacts, to achieve more precise quantification of clonal diversity and to extract the most pertinent biological information. That said, broader application of Ig-seq, especially in clinical settings, will require the development of a standardized experimental design framework that will enable the sharing and meta-analysis of sequencing data generated by different laboratories.
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37
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Thurgood LA, Arentz G, Lindop R, Jackson MW, Whyte AF, Colella AD, Chataway TK, Gordon TP. An immunodominant La/SSB autoantibody proteome derives from public clonotypes. Clin Exp Immunol 2013; 174:237-44. [PMID: 23841690 PMCID: PMC3828827 DOI: 10.1111/cei.12171] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2013] [Indexed: 01/31/2023] Open
Abstract
The La/SSB autoantigen is a major target of long-term humoral autoimmunity in primary Sjögren's Syndrome (SS) and systemic lupus erythematosus. A majority of patients with linked anti-Ro60/Ro52/La responses target an NH2-terminal epitope designated LaA that is expressed on Ro/La ribonucleoprotein complexes and the surface membrane of apoptotic cells. In this study, we used high-resolution Orbitrap mass spectrometry to determine the clonality, isotype and V-region sequences of LaA-specific autoantibodies in seven patients with primary SS. Anti-LaA immunoglobulin (Ig)Gs purified from polyclonal sera by epitope-specific affinity chromatography were analysed by combined database and de-novo mass spectrometric sequencing. Autoantibody responses comprised two heavily mutated IgG1 kappa-restricted monoclonal species that were shared (public) across unrelated patients; one clonotype was specified by an IGHV3-30 heavy chain paired with IGKV3-15 light chain and the second by an IGHV3-43/IGKV3-20 pairing. Shared amino acid replacement mutations were also seen within heavy and light chain complementarity-determining regions, consistent with a common breach of B cell tolerance followed by antigen-driven clonal selection. The discovery of public clonotypic autoantibodies directed against an immunodominant epitope on La, taken together with recent findings for the linked Ro52 and Ro60 autoantigens, supports a model of systemic autoimmunity in which humoral responses against protein-RNA complexes are mediated by public sets of autoreactive B cell clonotypes.
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Affiliation(s)
- L A Thurgood
- Department of Immunology, Flinders Medical Centre, Flinders University, Adelaide, SA, Australia
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Genetic manipulation of B cells for the isolation of rare therapeutic antibodies from the human repertoire. Methods 2013; 65:38-43. [PMID: 23867338 DOI: 10.1016/j.ymeth.2013.07.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 06/28/2013] [Accepted: 07/06/2013] [Indexed: 01/12/2023] Open
Abstract
Antibody based therapies are increasingly applied to prevent and treat human disease. While the majority of antibodies currently on the market are chimeric or humanized antibodies from rodents, the focus has now shifted to the isolation and development of fully human antibodies. By retroviral transduction of B cell lymphoma-6 (BCL-6), which prevents terminal differentiation of B cells and, the anti-apoptotic gene B-cell lymphoma-extra large (Bcl-xL) into primary human B cells we efficiently immortalize antibody-producing B cells allowing the isolation of therapeutic antibodies. Selection of antigen-specific B cell clones was greatly facilitated because the transduced B cells retain surface immunoglobulin expression and secrete immunoglobulin into the culture supernatant. Surface immunoglobulin expression can be utilized to stain and isolate antigen specific B cell clones with labeled antigen. Immunoglobulins secreted in culture supernatant can directly be tested in functional assays to identify unique B cell clones. Here we describe the key features of our Bcl-6/Bcl-xL culture platform (AIMSelect).
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Klöhn PC, Wuellner U, Zizlsperger N, Zhou Y, Tavares D, Berger S, Zettlitz KA, Proetzel G, Yong M, Begent RH, Reichert JM. IBC's 23rd Annual Antibody Engineering, 10th Annual Antibody Therapeutics international conferences and the 2012 Annual Meeting of The Antibody Society: December 3-6, 2012, San Diego, CA. MAbs 2013; 5:178-201. [PMID: 23575266 PMCID: PMC3893229 DOI: 10.4161/mabs.23655] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 01/17/2013] [Indexed: 01/13/2023] Open
Abstract
The 23rd Annual Antibody Engineering, 10th Annual Antibody Therapeutics international conferences, and the 2012 Annual Meeting of The Antibody Society, organized by IBC Life Sciences with contributions from The Antibody Society and two Scientific Advisory Boards, were held December 3-6, 2012 in San Diego, CA. The meeting drew over 800 participants who attended sessions on a wide variety of topics relevant to antibody research and development. As a prelude to the main events, a pre-conference workshop held on December 2, 2012 focused on intellectual property issues that impact antibody engineering. The Antibody Engineering Conference was composed of six sessions held December 3-5, 2012: (1) From Receptor Biology to Therapy; (2) Antibodies in a Complex Environment; (3) Antibody Targeted CNS Therapy: Beyond the Blood Brain Barrier; (4) Deep Sequencing in B Cell Biology and Antibody Libraries; (5) Systems Medicine in the Development of Antibody Therapies/Systematic Validation of Novel Antibody Targets; and (6) Antibody Activity and Animal Models. The Antibody Therapeutics conference comprised four sessions held December 4-5, 2012: (1) Clinical and Preclinical Updates of Antibody-Drug Conjugates; (2) Multifunctional Antibodies and Antibody Combinations: Clinical Focus; (3) Development Status of Immunomodulatory Therapeutic Antibodies; and (4) Modulating the Half-Life of Antibody Therapeutics. The Antibody Society's special session on applications for recording and sharing data based on GIATE was held on December 5, 2012, and the conferences concluded with two combined sessions on December 5-6, 2012: (1) Development Status of Early Stage Therapeutic Antibodies; and (2) Immunomodulatory Antibodies for Cancer Therapy.
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Affiliation(s)
- Peter-Christian Klöhn
- MRC Prion Unit; Department of Neurodegenerative Diseases; UCL Institute of Neurology; London, UK
| | | | - Nora Zizlsperger
- Protein Engineering and Antibody Technologies; EMD Serono Research Institute, Inc.; Billerica MA USA
| | - Yu Zhou
- Department of Anesthesia; University of California, San Francisco; San Francisco, CA USA
| | | | - Sven Berger
- Institut de Recherche, Centre d'Immunologie Pierre Fabre; St Julien en Genevois, France
| | - Kirstin A. Zettlitz
- Crump Institute for Molecular Imaging; Department of Molecular and Medical Pharmacology; David Geffen School of Medicine at UCLA; California NanoSystems Institute; University of California Los Angeles; Los Angeles, CA USA
| | | | - May Yong
- UCL Cancer Institute; London, UK
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Molecular deconvolution of the monoclonal antibodies that comprise the polyclonal serum response. Proc Natl Acad Sci U S A 2013; 110:2993-8. [PMID: 23382245 DOI: 10.1073/pnas.1213737110] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
We have developed and validated a methodology for determining the antibody composition of the polyclonal serum response after immunization. Pepsin-digested serum IgGs were subjected to standard antigen-affinity chromatography, and resulting elution, wash, and flow-through fractions were analyzed by bottom-up, liquid chromatography-high-resolution tandem mass spectrometry. Identification of individual monoclonal antibodies required the generation of a database of IgG variable gene (V-gene) sequences constructed by NextGen sequencing of mature B cells. Antibody V-gene sequences are characterized by short complementarity determining regions (CDRs) of high diversity adjacent to framework regions shared across thousands of IgGs, greatly complicating the identification of antigen-specific IgGs from proteomically observed peptides. By mapping peptides marking unique V(H) CDRH3 sequences, we identified a set of V-genes heavily enriched in the affinity chromatography elution, constituting the serum polyclonal response. After booster immunization in a rabbit, we find that the antigen-specific serum immune response is oligoclonal, comprising antibodies encoding 34 different CDRH3s that group into 30 distinct antibody V(H) clonotypes. Of these 34 CDRH3s, 12 account for ∼60% of the antigen-specific CDRH3 peptide mass spectral counts. For comparison, antibodies with 18 different CDRH3s (12 clonotypes) were represented in the antigen-specific IgG fraction from an unimmunized rabbit that fortuitously displayed a moderate titer for BSA. Proteomically identified antibodies were synthesized and shown to display subnanomolar affinities. The ability to deconvolute the polyclonal serum response is likely to be of key importance for analyzing antibody responses after vaccination and for more completely understanding adaptive immune responses in health and disease.
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DeKosky BJ, Ippolito GC, Deschner RP, Lavinder JJ, Wine Y, Rawlings BM, Varadarajan N, Giesecke C, Dörner T, Andrews SF, Wilson PC, Hunicke-Smith SP, Willson CG, Ellington AD, Georgiou G. High-throughput sequencing of the paired human immunoglobulin heavy and light chain repertoire. Nat Biotechnol 2013; 31:166-9. [PMID: 23334449 DOI: 10.1038/nbt.2492] [Citation(s) in RCA: 327] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 01/02/2013] [Indexed: 02/07/2023]
Abstract
Each B-cell receptor consists of a pair of heavy and light chains. High-throughput sequencing can identify large numbers of heavy- and light-chain variable regions (V(H) and V(L)) in a given B-cell repertoire, but information about endogenous pairing of heavy and light chains is lost after bulk lysis of B-cell populations. Here we describe a way to retain this pairing information. In our approach, single B cells (>5 × 10(4) capacity per experiment) are deposited in a high-density microwell plate (125 pl/well) and lysed in situ. mRNA is then captured on magnetic beads, reverse transcribed and amplified by emulsion V(H):V(L) linkage PCR. The linked transcripts are analyzed by Illumina high-throughput sequencing. We validated the fidelity of V(H):V(L) pairs identified by this approach and used the method to sequence the repertoire of three human cell subsets-peripheral blood IgG(+) B cells, peripheral plasmablasts isolated after tetanus toxoid immunization and memory B cells isolated after seasonal influenza vaccination.
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Affiliation(s)
- Brandon J DeKosky
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA
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BiotecVisions 2013, January. Biotechnol J 2013. [DOI: 10.1002/biot.201200060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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