1
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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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Schulte D, Snijder J. A Handle on Mass Coincidence Errors in De Novo Sequencing of Antibodies by Bottom-up Proteomics. J Proteome Res 2024. [PMID: 38932690 DOI: 10.1021/acs.jproteome.4c00188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
Antibody sequences can be determined at 99% accuracy directly from the polypeptide product by using bottom-up proteomics techniques. Sequencing accuracy at the peptide level is limited by the isobaric residues leucine and isoleucine, incomplete fragmentation spectra in which the order of two or more residues remains ambiguous due to lacking fragment ions for the intermediate positions, and isobaric combinations of amino acids, of potentially different lengths, for example, GG = N and GA = Q. Here, we present several updates to Stitch (v1.5), which performs template-based assembly of de novo peptides to reconstruct antibody sequences. This version introduces a mass-based alignment algorithm that explicitly accounts for mass coincidence errors. In addition, it incorporates a postprocessing procedure to assign I/L residues based on secondary fragments (satellite ions, i.e., w-ions). Moreover, evidence for sequence assignments can now be directly evaluated with the addition of an integrated spectrum viewer. Lastly, input data from a wider selection of de novo peptide sequencing algorithms are allowed, now including Casanovo, PEAKS, Novor.Cloud, pNovo, and MaxNovo, in addition to flat text and FASTA. Combined, these changes make Stitch compatible with a larger range of data processing pipelines and improve its tolerance to peptide-level sequencing errors.
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Affiliation(s)
- Douwe Schulte
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Joost Snijder
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands
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3
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Stingl C, VanDuijn MM, Dejoie T, Sillevis Smitt PAE, Luider TM. Improved detection of tryptic immunoglobulin variable region peptides by chromatographic and gas-phase fractionation techniques. CELL REPORTS METHODS 2024; 4:100795. [PMID: 38861989 PMCID: PMC11228375 DOI: 10.1016/j.crmeth.2024.100795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 03/30/2024] [Accepted: 05/20/2024] [Indexed: 06/13/2024]
Abstract
The polyclonal repertoire of circulating antibodies potentially holds valuable information about an individual's humoral immune state. While bottom-up proteomics is well suited for serum proteomics, the vast number of antibodies and dynamic range of serum challenge this analysis. To acquire the serum proteome more comprehensively, we incorporated high-field asymmetric waveform ion-mobility spectrometry (FAIMS) or two-dimensional chromatography into standard trypsin-based bottom-up proteomics. Thereby, the number of variable region (VR)-related spectra increased 1.7-fold with FAIMS and 10-fold with chromatography fractionation. To match antibody VRs to spectra, we combined de novo searching and BLAST alignment. Validation of this approach showed that, as peptide length increased, the de novo accuracy decreased and BLAST performance increased. Through in silico calculations on antibody repository sequences, we determined the uniqueness of tryptic VR peptides and their suitability as antibody surrogate. Approximately one-third of these peptides were unique, and about one-third of all antibodies contained at least one unique peptide.
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Affiliation(s)
- Christoph Stingl
- Clinical and Cancer Proteomics, Department of Neurology, Erasmus MC, 3000 CA Rotterdam, the Netherlands.
| | - Martijn M VanDuijn
- Clinical and Cancer Proteomics, Department of Neurology, Erasmus MC, 3000 CA Rotterdam, the Netherlands
| | - Thomas Dejoie
- Laboratoire de Biochimie, Centre Hospitalier Universitaire (CHU), 44000 Nantes, France
| | - Peter A E Sillevis Smitt
- Clinical and Cancer Proteomics, Department of Neurology, Erasmus MC, 3000 CA Rotterdam, the Netherlands
| | - Theo M Luider
- Clinical and Cancer Proteomics, Department of Neurology, Erasmus MC, 3000 CA Rotterdam, the Netherlands
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4
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Wang Z, Huang AS, Tang L, Wang J, Wang G. Microfluidic-assisted single-cell RNA sequencing facilitates the development of neutralizing monoclonal antibodies against SARS-CoV-2. LAB ON A CHIP 2024; 24:642-657. [PMID: 38165771 DOI: 10.1039/d3lc00749a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
As a class of antibodies that specifically bind to a virus and block its entry, neutralizing monoclonal antibodies (neutralizing mAbs) have been recognized as a top choice for combating COVID-19 due to their high specificity and efficacy in treating serious infections. Although conventional approaches for neutralizing mAb development have been optimized for decades, there is an urgent need for workflows with higher efficiency due to time-sensitive concerns, including the high mutation rate of SARS-CoV-2. One promising approach is the identification of neutralizing mAb candidates via single-cell RNA sequencing (RNA-seq), as each B cell has a unique transcript sequence corresponding to its secreted antibody. The state-of-the-art high-throughput single-cell sequencing technologies, which have been greatly facilitated by advances in microfluidics, have greatly accelerated the process of neutralizing mAb development. Here, we provide an overview of the general procedures for high-throughput single-cell RNA-seq enabled by breakthroughs in droplet microfluidics, introduce revolutionary approaches that combine single-cell RNA-seq to facilitate the development of neutralizing mAbs against SARS-CoV-2, and outline future steps that need to be taken to further improve development strategies for effective treatments against infectious diseases.
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Affiliation(s)
- Ziwei Wang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Amelia Siqi Huang
- Dalton Academy, The Affiliated High School of Peking University, Beijing, 100190, China
| | - Lingfang Tang
- Dalton Academy, The Affiliated High School of Peking University, Beijing, 100190, China
| | - Jianbin Wang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Guanbo Wang
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen, 518132, China.
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5
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Wang S, Zhou Y, Li Z. A microfluidic cover converts a standard 96-well plate into a mass-transport-controlled immunoassay system. BIOMICROFLUIDICS 2024; 18:014102. [PMID: 38249129 PMCID: PMC10798817 DOI: 10.1063/5.0183651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/01/2024] [Indexed: 01/23/2024]
Abstract
96-well microtiter plates, widely used in immunoassays, face challenges such as prolonged assay time and limited sensitivity due to the lack of analyte transport control. Orbital shakers, commonly employed to facilitate mass transport, offer limited improvements and can introduce assay inconsistencies. While microfluidic devices offer performance enhancements, their complexity and incompatibility with existing platforms limit their wide adoption. This study introduces a novel microfluidic 96-well cover designed to convert a standard 96-well plate to a mass-transport-controlled surface bioreactor. The cover employs microfluidic methods to enhance the diffusion flux of analytes toward the receptors immobilized on the well bottom. Both simulation and experimental results demonstrated that the cover significantly enhances the capture rate of analyte molecules, resulting in increased signal strength for various detection methods and a lower detection limit. The cover serves as an effective add-on to standard 96-well plates, offering enhanced assay performance without requiring modifications to existing infrastructure or reagents. This innovation holds promise for improving the efficiency and reliability of microtiter plate based immunoassays.
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Affiliation(s)
- Sheng Wang
- Department of Biomedical Engineering, The George Washington University, District of Columbia, 20052, USA
| | - You Zhou
- Department of Electrical and Computer Engineering, The George Washington University, District of Columbia, 20052, USA
| | - Zhenyu Li
- Department of Biomedical Engineering, The George Washington University, District of Columbia, 20052, USA
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6
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Wu X, Zhang J, Fang L. Next-Generation Sequencing and Proteomics-Enabled Approach for Rapid and High-Throughput Isolation of Virus-Neutralizing Nanobodies. Methods Mol Biol 2024; 2824:135-146. [PMID: 39039411 DOI: 10.1007/978-1-0716-3926-9_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Compared with traditional antibodies, nanobodies from camelids have various advantages, including small molecular weight, high affinity, low immunogenicity, convenient production through genetic engineering, etc. Here we combined next-generation sequencing (NGS) with proteomics technology based on affinity purification-mass spectrometry (AP-MS) and bioinformatics analysis to high-throughput screen monoclonal nanobodies from camels immunized with surface glycoprotein (glycoprotein N, Gn) of severe fever with thrombocytopenia syndrome virus and fulfilled production of the screened anti-Gn monoclonal nanobody with high affinity by genetic engineering. The innovative high-throughput technical route developed here could also be expanded to the production of neutralizing nanobodies specific for Rift Valley fever virus.
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Affiliation(s)
- Xilin Wu
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center, Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, China
| | - Jingzi Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, Nanjing, China
- Chemistry and Biomedicine Innovation Center, Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, China
| | - Lei Fang
- State Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, Nanjing, China.
- Chemistry and Biomedicine Innovation Center, Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing, China.
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7
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Walter J, Eludin Z, Drabovich AP. Redefining serological diagnostics with immunoaffinity proteomics. Clin Proteomics 2023; 20:42. [PMID: 37821808 PMCID: PMC10568870 DOI: 10.1186/s12014-023-09431-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023] Open
Abstract
Serological diagnostics is generally defined as the detection of specific human immunoglobulins developed against viral, bacterial, or parasitic diseases. Serological tests facilitate the detection of past infections, evaluate immune status, and provide prognostic information. Serological assays were traditionally implemented as indirect immunoassays, and their design has not changed for decades. The advantages of straightforward setup and manufacturing, analytical sensitivity and specificity, affordability, and high-throughput measurements were accompanied by limitations such as semi-quantitative measurements, lack of universal reference standards, potential cross-reactivity, and challenges with multiplexing the complete panel of human immunoglobulin isotypes and subclasses. Redesign of conventional serological tests to include multiplex quantification of immunoglobulin isotypes and subclasses, utilize universal reference standards, and minimize cross-reactivity and non-specific binding will facilitate the development of assays with higher diagnostic specificity. Improved serological assays with higher diagnostic specificity will enable screenings of asymptomatic populations and may provide earlier detection of infectious diseases, autoimmune disorders, and cancer. In this review, we present the major clinical needs for serological diagnostics, overview conventional immunoassay detection techniques, present the emerging immunoassay detection technologies, and discuss in detail the advantages and limitations of mass spectrometry and immunoaffinity proteomics for serological diagnostics. Finally, we explore the design of novel immunoaffinity-proteomic assays to evaluate cell-mediated immunity and advance the sequencing of clinically relevant immunoglobulins.
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Affiliation(s)
- Jonathan Walter
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, 10-102 Clinical Sciences Building, Edmonton, AB, T6G 2G3, Canada
| | - Zicki Eludin
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, 10-102 Clinical Sciences Building, Edmonton, AB, T6G 2G3, Canada
| | - Andrei P Drabovich
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, 10-102 Clinical Sciences Building, Edmonton, AB, T6G 2G3, Canada.
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8
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Wang Z, Li D, Chen Y, Sun Y, Jin C, Hu C, Feng Y, Su J, Ren L, Hao Y, Wang S, Zhu M, Liu Y, Qi J, Zhu B, Shao Y. Characterization of RBD-specific cross-neutralizing antibodies responses against SARS-CoV-2 variants from COVID-19 convalescents. Front Immunol 2023; 14:1160283. [PMID: 37234155 PMCID: PMC10207940 DOI: 10.3389/fimmu.2023.1160283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 04/25/2023] [Indexed: 05/27/2023] Open
Abstract
Introduction The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been posing a severe threat to global public health. Although broadly neutralizing antibodies have been used to prevent or treat corona virus disease 2019 (COVID-19), new emerging variants have been proven resistant to these antibodies. Methods In this study, we isolated receptor binding domain (RBD)-specific memory B cells using single-cell sorting method from two COVID-19 convalescents and expressed the antibody to test their neutralizing activity against diverse SARS-CoV-2 variants. Then, we resolved antibody-RBD complex structures of potent RBD-specific neutralizing antibodies by X-ray diffraction method. Finally, we analyzed the whole antibody repertoires of the two donors and studied the evolutionary pathway of potent neutralizing antibodies. Results and discussion We identified three potent RBD-specific neutralizing antibodies (1D7, 3G10 and 3C11) from two COVID-19 convalescents that neutralized authentic SARS-CoV-2 WH-1 and Delta variant, and one of them, 1D7, presented broadly neutralizing activity against WH-1, Beta, Gamma, Delta and Omicron authentic viruses. The resolved antibody-RBD complex structures of two antibodies, 3G10 and 3C11, indicate that both of them interact with the external subdomain of the RBD and that they belong to the RBD-1 and RBD-4 communities, respectively. From the antibody repertoire analysis, we found that the CDR3 frequencies of the light chain, which shared high degrees of amino acid identity with these three antibodies, were higher than those of the heavy chain. This research will contribute to the development of RBD-specific antibody-based drugs and immunogens against multiple variants.
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Affiliation(s)
- Zheng Wang
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Dan Li
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yulu Chen
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yeping Sun
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Changzhong Jin
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Caiqin Hu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yi Feng
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Junwei Su
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Li Ren
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yanling Hao
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shuo Wang
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Meiling Zhu
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ying Liu
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Biao Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yiming Shao
- State Key Laboratory of Infectious Disease Prevention and Control, Division of Research of Virology and Immunology, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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9
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Wang B, Huang B, Li X, Guo Y, Qi G, Ding Y, Gao H, Zhang J, Wu X, Fang L. Development of functional anti-Gn nanobodies specific for SFTSV based on next-generation sequencing and proteomics. Protein Sci 2022; 31:e4461. [PMID: 36177742 PMCID: PMC9601861 DOI: 10.1002/pro.4461] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 09/21/2022] [Accepted: 09/24/2022] [Indexed: 11/10/2022]
Abstract
Severe fever with thrombocytopenia syndrome (SFTS) is an acute infectious disease caused by novel bunyavirus (SFTSV), with a mortality rate of 6.3% ~ 30%. To date, there is no specific treatment for SFTS. Previously, we demonstrated that SFTSV surface glycoprotein (Glycoprotein N, Gn) was a potential target for the development of SFTS vaccine or therapeutic antibodies, and anti-Gn neutralizing antibodies played a protective role in SFTS infection. Compared with traditional antibodies, nanobodies from camelids have various advantages, including small molecular weight, high affinity, low immunogenicity, convenient production by gene engineering, etc. In this study, we combined next-generation sequencing (NGS) with proteomics technology based on affinity purification-mass spectrometry (AP-MS) and bioinformatics analysis to high-throughput screen monoclonal anti-Gn nanobodies from camel immunized with Gn protein. We identified 19 anti-Gn monoclonal nanobody sequences, of which six sequences were selected for recombinant protein expression and purification. Among these six anti-Gn nanobodies, nanobody 57,493 was validated to be highly specific for Gn. The innovative high-throughput technical route developed in this study could also be expanded to the production of nanobodies specific for other viruses like SARS-CoV-2.
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Affiliation(s)
- Binghao Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation CenterMedical School of Nanjing UniversityNanjingChina
| | - Bilian Huang
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation CenterMedical School of Nanjing UniversityNanjingChina
| | - Xinyu Li
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation CenterMedical School of Nanjing UniversityNanjingChina
| | - Yan Guo
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation CenterMedical School of Nanjing UniversityNanjingChina
| | - Guantong Qi
- School of Life ScienceNanjing UniversityNanjingChina
| | - Yibing Ding
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation CenterMedical School of Nanjing UniversityNanjingChina
| | - Haidong Gao
- Genepioneer Biotechnologies Co. Ltd.NanjingChina
| | - Jingzi Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation CenterMedical School of Nanjing UniversityNanjingChina
| | - Xilin Wu
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation CenterMedical School of Nanjing UniversityNanjingChina
| | - Lei Fang
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation CenterMedical School of Nanjing UniversityNanjingChina
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10
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Schulte D, Peng W, Snijder J. Template-Based Assembly of Proteomic Short Reads For De Novo Antibody Sequencing and Repertoire Profiling. Anal Chem 2022; 94:10391-10399. [PMID: 35834437 PMCID: PMC9330293 DOI: 10.1021/acs.analchem.2c01300] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Antibodies can target a vast molecular diversity of antigens.
This
is achieved by generating a complementary diversity of antibody sequences
through somatic recombination and hypermutation. A full understanding
of the antibody repertoire in health and disease therefore requires
dedicated de novo sequencing methods. Next-generation
cDNA sequencing methods have laid the foundation of our current understanding
of the antibody repertoire, but these methods share one major limitation
in that they target the antibody-producing B-cells, rather than the
functional secreted product in bodily fluids. Mass spectrometry-based
methods offer an opportunity to bridge this gap between antibody repertoire
profiling and bulk serological assays, as they can access antibody
sequence information straight from the secreted polypeptide products.
In a step to meeting the challenge of mass spectrometry (MS)-based
antibody sequencing, we present a fast and simple software tool (Stitch)
to map proteomic short reads to user-defined templates with dedicated
features for both monoclonal antibody sequencing and profiling of
polyclonal antibody repertoires. We demonstrate the use of Stitch
by fully reconstructing two monoclonal antibody sequences with >98%
accuracy (including I/L assignment); sequencing a Fab from patient
serum isolated by reversed-phase liquid chromatography (LC) fractionation
against a high background of homologous antibody sequences; sequencing
antibody light chains from the urine of multiple-myeloma patients;
and profiling the IgG repertoire in sera from patients hospitalized
with COVID-19. We demonstrate that Stitch assembles a comprehensive
overview of the antibody sequences that are represented in the dataset
and provides an important first step toward analyzing polyclonal antibodies
and repertoire profiling.
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Affiliation(s)
- Douwe Schulte
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Weiwei Peng
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Joost Snijder
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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11
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Wu H, Zhou Z, Xie S, Yan R, Gong M, Tian X, Wang Z. Similarity measurements of B cell receptor repertoire in baseline mice showed spectrum convergence of IgM. BMC Immunol 2022; 23:11. [PMID: 35246036 PMCID: PMC8895918 DOI: 10.1186/s12865-022-00482-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 02/18/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The B cell receptor (BCR) repertoire is highly diverse among individuals. Poor similarity of the spectrum among inbred baseline mice may limit the ability to discriminate true signals from those involving specific experimental factors. The repertoire similarity of the baseline status lacks intensive measurements. RESULTS We measured the repertoire similarity of IgH in blood and spleen samples from untreated BALB/c and C57BL/6J mice to investigate the baseline status of the two inbred strains. The antibody pool was stratified by the isotype of IgA, IgG and IgM. Between individuals, the results showed better convergence of CDR3 and clonal lineage profiles in IgM than in IgA and IgG, and better robustness of somatic mutation networks in IgM than in IgA and IgG. It also showed that the CDR3 clonotypes and clonal lineages shared better in the spleen samples than in the blood samples. The animal batch differences were detected in CDR3 evenness, mutated clonotype proportions, and maximal network degrees. A cut-off of 95% identity in the CDR3 nucleotide sequences was suitable for clonal lineage establishment. CONCLUSIONS Our findings reveal a natural landscape of BCR repertoire similarities between baseline mice and provide a solid reference for designing studies of mouse BCR repertoires.
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Affiliation(s)
- Hongkai Wu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Zhichao Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Shi Xie
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Rong Yan
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Mingxing Gong
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xingui Tian
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China.
| | - Zhanhui Wang
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China.
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12
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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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13
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Melani RD, Des Soye BJ, Kafader JO, Forte E, Hollas M, Blagojevic V, Negrão F, McGee JP, Drown B, Lloyd-Jones C, Seckler HS, Camarillo JM, Compton PD, LeDuc RD, Early B, Fellers RT, Cho BK, Mattamana BB, Goo YA, Thomas PM, Ash MK, Bhimalli PP, Al-Harthi L, Sha BE, Schneider JR, Kelleher NL. Next-Generation Serology by Mass Spectrometry: Readout of the SARS-CoV-2 Antibody Repertoire. J Proteome Res 2022; 21:274-288. [PMID: 34878788 PMCID: PMC8673472 DOI: 10.1021/acs.jproteome.1c00882] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Indexed: 01/03/2023]
Abstract
Methods of antibody detection are used to assess exposure or immunity to a pathogen. Here, we present Ig-MS, a novel serological readout that captures the immunoglobulin (Ig) repertoire at molecular resolution, including entire variable regions in Ig light and heavy chains. Ig-MS uses recent advances in protein mass spectrometry (MS) for multiparametric readout of antibodies, with new metrics like Ion Titer (IT) and Degree of Clonality (DoC) capturing the heterogeneity and relative abundance of individual clones without sequencing of B cells. We applied Ig-MS to plasma from subjects with severe and mild COVID-19 and immunized subjects after two vaccine doses, using the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2 as the bait for antibody capture. Importantly, we report a new data type for human serology, that could use other antigens of interest to gauge immune responses to vaccination, pathogens, or autoimmune disorders.
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Affiliation(s)
- Rafael D. Melani
- Departments of Molecular Biosciences, Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Benjamin J. Des Soye
- Departments of Molecular Biosciences, Chemistry, Northwestern University, Evanston, IL, 60208, USA
- Proteomics Center of Excellence, Evanston, IL, 60208, USA
| | - Jared O. Kafader
- Departments of Molecular Biosciences, Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Eleonora Forte
- Proteomics Center of Excellence, Evanston, IL, 60208, USA
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Michael Hollas
- Departments of Molecular Biosciences, Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Voislav Blagojevic
- Departments of Molecular Biosciences, Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Fernanda Negrão
- Departments of Molecular Biosciences, Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - John P. McGee
- Departments of Molecular Biosciences, Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Bryon Drown
- Departments of Molecular Biosciences, Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Cameron Lloyd-Jones
- Departments of Molecular Biosciences, Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Henrique S. Seckler
- Departments of Molecular Biosciences, Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Jeannie M. Camarillo
- Departments of Molecular Biosciences, Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Philip D. Compton
- Departments of Molecular Biosciences, Chemistry, Northwestern University, Evanston, IL, 60208, USA
- Integrated Protein Technologies, Evanston, IL, 60201, USA
| | - Richard D. LeDuc
- Departments of Molecular Biosciences, Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Bryan Early
- Departments of Molecular Biosciences, Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Ryan T. Fellers
- Departments of Molecular Biosciences, Chemistry, Northwestern University, Evanston, IL, 60208, USA
| | - Byoung-Kyu Cho
- Proteomics Center of Excellence, Evanston, IL, 60208, USA
| | | | - Young Ah Goo
- Departments of Molecular Biosciences, Chemistry, Northwestern University, Evanston, IL, 60208, USA
- Proteomics Center of Excellence, Evanston, IL, 60208, USA
| | - Paul M. Thomas
- Departments of Molecular Biosciences, Chemistry, Northwestern University, Evanston, IL, 60208, USA
- Proteomics Center of Excellence, Evanston, IL, 60208, USA
| | - Michelle K. Ash
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Pavan P. Bhimalli
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Lena Al-Harthi
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Beverly E. Sha
- Division of Infectious Diseases, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Jeffrey R. Schneider
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Neil L. Kelleher
- Departments of Molecular Biosciences, Chemistry, Northwestern University, Evanston, IL, 60208, USA
- Proteomics Center of Excellence, Evanston, IL, 60208, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611 USA
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14
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Huang Y, Tang X, Zheng L, Huang J, Zhang Q, Liu H. Development of Generic Immuno-Magnetic Bead-Based Enzyme-Linked Immunoassay for Ustiloxins in Rice Coupled with Enrichment. Toxins (Basel) 2021; 13:toxins13120907. [PMID: 34941744 PMCID: PMC8705705 DOI: 10.3390/toxins13120907] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/09/2021] [Accepted: 12/15/2021] [Indexed: 11/16/2022] Open
Abstract
Ustiloxins are a group of mycotoxins produced by rice false smut pathogen. Previous studies have shown that the false smut balls contain six types of ustiloxins, and these toxins are toxic to living organisms. Thus, immunoassay for on-site monitoring of ustiloxins in rice is urgently required. The current immunoassays are only for detecting single ustiloxin, and they cannot meet the demand for synchronous and rapid detection of the group toxins. Therefore, this study designed and synthesized a generic antigen with ustiloxin G as material based on the common structure of the mycotoxins. Ustiloxin G was conjugated to two carrier proteins including bovine serum albumin (BSA) and ovalbvmin (OVA) by carbon diimide method. The mice were immunized with ustiloxin-G-BSA to generate the antibody serum, which was further purified to obtain the generic antibody against ustiloxins. The conjugated ustiloxin G-OVA and generic antibodies were used for establishing the enzyme-linked immunosorbent assay (ELISA) for ustiloxin detection and optimizing experiment conditions. The characterization of the antibody showed that the semi-inhibitory concentrations (IC50) of ustiloxin A, B, and G were 0.53, 0.34, and 0.06 µg/mL, respectively, and that their corresponding cross-reactivities were 11.9%, 18.4%, and 100%, respectively. To increase ELISA detection efficiency, generic antibody was combined with magnetic beads to obtain sensitive and class-specific immune-magnetic beads. Based on these immuno-magnetic beads, a high-efficiency enzyme-linked immunoassay method was developed for ustiloxin detection, whose sensitivity to ustiloxin A, B, and G was improved to 0.15 µg/mL, 0.14 µg/mL, and 0.04 µg/mL, respectively. The method accuracy was evaluated by spiking ustiloxin G as standard, and the spiked samples were tested by the immune-magnetic bead-based ELISA. The result showed the ustiloxin G recoveries ranged from 101.9% to 116.4% and were accepted by a standard HPLC method, indicating that our developed method would be promising for on-site monitoring of ustiloxins in rice.
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Affiliation(s)
- Yi Huang
- The Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China; (Y.H.); (L.Z.); (J.H.)
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China;
| | - Xiaoqian Tang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China;
| | - Lu Zheng
- The Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China; (Y.H.); (L.Z.); (J.H.)
| | - Junbin Huang
- The Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China; (Y.H.); (L.Z.); (J.H.)
| | - Qi Zhang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China;
- Correspondence: (Q.Z.); (H.L.)
| | - Hao Liu
- The Key Lab of Plant Pathology of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China; (Y.H.); (L.Z.); (J.H.)
- Correspondence: (Q.Z.); (H.L.)
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15
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Chen Y, Zhu L, Huang W, Tong X, Wu H, Tao Y, Tong B, Huang H, Chen J, Zhao X, Lou Y, Wu C. Potent RBD-specific neutralizing rabbit monoclonal antibodies recognize emerging SARS-CoV-2 variants elicited by DNA prime-protein boost vaccination. Emerg Microbes Infect 2021; 10:1390-1403. [PMID: 34120577 PMCID: PMC8274519 DOI: 10.1080/22221751.2021.1942227] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/11/2021] [Accepted: 06/06/2021] [Indexed: 01/10/2023]
Abstract
Global concerns arose as the emerged and rapidly spreading SARS-CoV-2 variants might escape host immunity induced by vaccination. In this study, a heterologous prime-boost immunization strategy for COVID-19 was designed to prime with a DNA vaccine encoding wild type (WT) spike protein receptor-binding domain (RBD) followed by S1 protein-based vaccine in rabbits. Four vaccine-elicited rabbit monoclonal antibodies (RmAbs), including 1H1, 9H1, 7G5, and 5E1, were isolated for biophysical property, neutralization potency and sequence analysis. All RmAbs recognized RBD or S1 protein with KD in the low nM or sub nM range. 1H1 and 9H1, but neither 7G5 nor 5E1, can bind to all RBD protein variants derived from B.1.351. All four RmAbs were able to neutralize wild type (WT) SARS-CoV-2 strain in pseudovirus assay, and 1H1 and 9H1 could neutralize the SARS-CoV-2 WT authentic virus with IC50 values of 0.136 and 0.026 μg/mL, respectively. Notably, 1H1 was able to neutralize all 6 emerging SARS-CoV-2 variants tested including D614G, B.1.1.7, B.1.429, P.1, B.1.526, and B.1.351 variants, and 5E1 could neutralize against the above 5 variants except P.1. Epitope binning analysis revealed that 9H1, 5E1 and 1H1 recognized distinct epitopes, while 9H1 and 7G5 may have overlapping but not identical epitope. In conclusion, DNA priming protein boost vaccination was an effective strategy to induce RmAbs with potent neutralization capability against not only SARS-CoV-2 WT strain but also emergent variants, which may provide a new avenue for effective therapeutics and point-of-care diagnostic measures.
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Affiliation(s)
- Yuxin Chen
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, People’s Republic of China
| | - Liguo Zhu
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, People’s Republic of China
| | - Weijin Huang
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institute for Food and Drug Control, Beijing, People’s Republic of China
| | - Xin Tong
- Department of Infectious Diseases, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, People’s Republic of China
| | - Hai Wu
- Yurogen Biosystem LLC, Worcester, MA, USA
| | - Yue Tao
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, People’s Republic of China
| | - Bei Tong
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, People’s Republic of China
| | | | | | - Xiangan Zhao
- Department of Gastroenterology, Northern Jiangsu People’s Hospital, Clinical Medical College of Yangzhou University, Yangzhou, People’s Republic of China
| | - Yang Lou
- Yurogen Biosystem LLC, Worcester, MA, USA
| | - Chao Wu
- Department of Infectious Diseases, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, People’s Republic of China
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16
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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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17
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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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18
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Dupré M, Duchateau M, Sternke-Hoffmann R, Boquoi A, Malosse C, Fenk R, Haas R, Buell AK, Rey M, Chamot-Rooke J. De Novo Sequencing of Antibody Light Chain Proteoforms from Patients with Multiple Myeloma. Anal Chem 2021; 93:10627-10634. [PMID: 34292722 DOI: 10.1021/acs.analchem.1c01955] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In multiple myeloma diseases, monoclonal immunoglobulin light chains (LCs) are abundantly produced, with, as a consequence in some cases, the formation of deposits affecting various organs, such as the kidney, while in other cases remaining soluble up to concentrations of several g·L-1 in plasma. The exact factors crucial for the solubility of LCs are poorly understood, but it can be hypothesized that their amino acid sequence plays an important role. Determining the precise sequences of patient-derived LCs is therefore highly desirable. We establish here a novel de novo sequencing workflow for patient-derived LCs, based on the combination of bottom-up and top-down proteomics without database search. PEAKS is used for the de novo sequencing of peptides that are further assembled into full length LC sequences using ALPS. Top-down proteomics provides the molecular masses of proteoforms and allows the exact determination of the amino acid sequence including all posttranslational modifications. This pipeline is then used for the complete de novo sequencing of LCs extracted from the urine of 10 patients with multiple myeloma. We show that for the bottom-up part, digestions with trypsin and Nepenthes digestive fluid are sufficient to produce overlapping peptides able to generate the best sequence candidates. Top-down proteomics is absolutely required to achieve 100% final sequence coverage and characterize clinical samples containing several LCs. Our work highlights an unexpected range of modifications.
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Affiliation(s)
- Mathieu Dupré
- Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, CNRS, 28 rue du Dr Roux, Paris 75015, France
| | - Magalie Duchateau
- Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, CNRS, 28 rue du Dr Roux, Paris 75015, France
| | - Rebecca Sternke-Hoffmann
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, Düsseldorf 40225, Germany
| | - Amelie Boquoi
- Department of Hematology, Oncology and Clinical Oncology, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany, Moorenstr. 5, Düsseldorf 40225, Germany
| | - Christian Malosse
- Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, CNRS, 28 rue du Dr Roux, Paris 75015, France
| | - Roland Fenk
- Department of Hematology, Oncology and Clinical Oncology, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany, Moorenstr. 5, Düsseldorf 40225, Germany
| | - Rainer Haas
- Department of Hematology, Oncology and Clinical Oncology, Heinrich-Heine Universität Düsseldorf, Düsseldorf, Germany, Moorenstr. 5, Düsseldorf 40225, Germany
| | - Alexander K Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Kgs. Lyngby 2800, Denmark
| | - Martial Rey
- Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, CNRS, 28 rue du Dr Roux, Paris 75015, France
| | - Julia Chamot-Rooke
- Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, CNRS, 28 rue du Dr Roux, Paris 75015, France
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19
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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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20
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Melani RD, Soye BJD, Kafader JO, Forte E, Hollas M, Blagojevic V, Negrão F, McGee JP, Drown B, Lloyd-Jones C, Seckler HS, Camarillo JM, Compton PD, LeDuc RD, Early B, Fellers RT, Cho BK, Mattamana BB, Goo YA, Thomas PM, Ash MK, Bhimalli PP, Al-Harthi L, Sha BE, Schneider JR, Kelleher NL. Next-generation Serology by Mass Spectrometry: Readout of the SARS-CoV-2 Antibody Repertoire. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021. [PMID: 34268518 DOI: 10.1101/2021.07.06.21259226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Methods of antibody detection are used to assess exposure or immunity to a pathogen. Here, we present Ig-MS , a novel serological readout that captures the immunoglobulin (Ig) repertoire at molecular resolution, including entire variable regions in Ig light and heavy chains. Ig-MS uses recent advances in protein mass spectrometry (MS) for multi-parametric readout of antibodies, with new metrics like Ion Titer (IT) and Degree of Clonality (DoC) capturing the heterogeneity and relative abundance of individual clones without sequencing of B cells. We apply Ig-MS to plasma from subjects with severe & mild COVID-19, using the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2 as the bait for antibody capture. Importantly, we report a new data type for human serology, with compatibility to any recombinant antigen to gauge our immune responses to vaccination, pathogens, or autoimmune disorders.
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21
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Peng W, Pronker MF, Snijder J. Mass Spectrometry-Based De Novo Sequencing of Monoclonal Antibodies Using Multiple Proteases and a Dual Fragmentation Scheme. J Proteome Res 2021; 20:3559-3566. [PMID: 34121409 PMCID: PMC8256418 DOI: 10.1021/acs.jproteome.1c00169] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Indexed: 12/20/2022]
Abstract
Antibody sequence information is crucial to understanding the structural basis for antigen binding and enables the use of antibodies as therapeutics and research tools. Here, we demonstrate a method for direct de novo sequencing of monoclonal IgG from the purified antibody products. The method uses a panel of multiple complementary proteases to generate suitable peptides for de novo sequencing by liquid chromatography-tandem mass spectrometry (LC-MS/MS) in a bottom-up fashion. Furthermore, we apply a dual fragmentation scheme, using both stepped high-energy collision dissociation (stepped HCD) and electron-transfer high-energy collision dissociation (EThcD), on all peptide precursors. The method achieves full sequence coverage of the monoclonal antibody herceptin, with an accuracy of 99% in the variable regions. We applied the method to sequence the widely used anti-FLAG-M2 mouse monoclonal antibody, which we successfully validated by remodeling a high-resolution crystal structure of the Fab and demonstrating binding to a FLAG-tagged target protein in Western blot analysis. The method thus offers robust and reliable sequences of monoclonal antibodies.
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Affiliation(s)
| | | | - Joost Snijder
- Biomolecular Mass Spectrometry
and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht
Institute of Pharmaceutical Sciences, Utrecht
University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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22
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Santos-Neto JF, Oliveira FO, Hodel KVS, Fonseca LMS, Badaró R, Machado BAS. Technological Advancements in Monoclonal Antibodies. ScientificWorldJournal 2021; 2021:6663708. [PMID: 33628140 PMCID: PMC7892242 DOI: 10.1155/2021/6663708] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/11/2021] [Accepted: 01/21/2021] [Indexed: 12/20/2022] Open
Abstract
Biopharmaceuticals are innovative solutions that have revolutionized the treatment of important chronic diseases and malignancies. The approval of biosimilar products has become a complex and balanced process, and there are versions of drugs with established biosimilarity that can offer a more accessible treatment option to patients. The objective of this work was to identify the advancement of these technologies by means of patent and article analysis based on technological and scientific prospection. In patent document recovery, Derwent Innovation Index (DWPI) and PatentInspiration databases were used. The research was based on the search of the selected terms in the title, summary, and claims of the documents through a search strategy containing IPC code and keywords. In articles recovery, the Web of Science tool was used in the search of scientific publications dated from the last 5 years. The search resulted in a total of 2295 individual patent documents and 467 families using DWPI database, 769 individual patents and 205 families using PatentInspiration, and 2602 articles using Web of Science database. Additionally, this work describes the number of organizations that contribute to this area, where they are, how much development they have undergone, and the inventors/authors involved. Based on the number of publications registered, there is an important prominence for scientific research in mAbs. In terms of innovation, it is expected that several therapeutic drugs are already under regulatory review, which will allow drugs to be approved over the next few years and will thus generate a continuous flow of new products based on immunotherapies, mAbs, and biosimilar drugs. These drugs have become essential weapons for the treatment of significant diseases, and the increasing trend in the number of related scientific and technological publications contributes to making these therapies available to the greatest number of people.
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Affiliation(s)
- José F. Santos-Neto
- University Center SENAI/CIMATEC, National Service of Industrial Learning–SENAI, Salvador, Bahia, Brazil
| | - Fabricia O. Oliveira
- SENAI Institute of Innovation (ISI) in Advanced Health Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, National Service of Industrial Learning–SENAI, Salvador, Bahia, Brazil
| | - Katharine V. S. Hodel
- SENAI Institute of Innovation (ISI) in Advanced Health Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, National Service of Industrial Learning–SENAI, Salvador, Bahia, Brazil
| | - Larissa M. S. Fonseca
- SENAI Institute of Innovation (ISI) in Advanced Health Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, National Service of Industrial Learning–SENAI, Salvador, Bahia, Brazil
| | - Roberto Badaró
- SENAI Institute of Innovation (ISI) in Advanced Health Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, National Service of Industrial Learning–SENAI, Salvador, Bahia, Brazil
| | - Bruna A. S. Machado
- University Center SENAI/CIMATEC, National Service of Industrial Learning–SENAI, Salvador, Bahia, Brazil
- SENAI Institute of Innovation (ISI) in Advanced Health Systems (CIMATEC ISI SAS), University Center SENAI/CIMATEC, National Service of Industrial Learning–SENAI, Salvador, Bahia, Brazil
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23
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A general strategy to control antibody specificity against targets showing molecular and biological similarity: Salmonella case study. Sci Rep 2020; 10:18439. [PMID: 33116156 PMCID: PMC7595100 DOI: 10.1038/s41598-020-75285-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 10/12/2020] [Indexed: 11/10/2022] Open
Abstract
The control of antibody specificity plays pivotal roles in key technological fields such as diagnostics and therapeutics. During the development of immunoassays (IAs) for the biosensing of pathogens in food matrices, we have found a way to rationalize and control the specificity of polyclonal antibodies (sera) for a complex analytical target (the Salmonella genus), in terms of number of analytes (Salmonella species) and potential cross-reactivity with similar analytes (other bacteria strains). Indeed, the biosensing of Salmonella required the development of sera and serum mixtures displaying homogeneous specificity for a large set of strains showing broad biochemical variety (54 Salmonella serovars tested in this study), which partially overlaps with the molecular features of other class of bacteria (like specific serogroups of E. coli). To achieve a trade-off between specificity harmonisation and maximization, we have developed a strategy based on the conversion of the specificity profiles of individual sera in to numerical descriptors, which allow predicting the capacity of serum mixtures to detect multiple bacteria strains. This approach does not imply laborious purification steps and results advantageous for process scaling-up, and may help in the customization of the specificity profiles of antibodies needed for diagnostic and therapeutic applications such as multi-analyte detection and recombinant antibody engineering, respectively.
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24
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Zhang W, Wang L, Liu K, Wei X, Yang K, Du W, Wang S, Guo N, Ma C, Luo L, Wu J, Lin L, Yang F, Gao F, Wang X, Li T, Zhang R, Saksena NK, Yang H, Wang J, Fang L, Hou Y, Xu X, Liu X. PIRD: Pan Immune Repertoire Database. Bioinformatics 2020; 36:897-903. [PMID: 31373607 DOI: 10.1093/bioinformatics/btz614] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/17/2019] [Accepted: 08/01/2019] [Indexed: 02/06/2023] Open
Abstract
MOTIVATION T and B cell receptors (TCRs and BCRs) play a pivotal role in the adaptive immune system by recognizing an enormous variety of external and internal antigens. Understanding these receptors is critical for exploring the process of immunoreaction and exploiting potential applications in immunotherapy and antibody drug design. Although a large number of samples have had their TCR and BCR repertoires sequenced using high-throughput sequencing in recent years, very few databases have been constructed to store these kinds of data. To resolve this issue, we developed a database. RESULTS We developed a database, the Pan Immune Repertoire Database (PIRD), located in China National GeneBank (CNGBdb), to collect and store annotated TCR and BCR sequencing data, including from Homo sapiens and other species. In addition to data storage, PIRD also provides functions of data visualization and interactive online analysis. Additionally, a manually curated database of TCRs and BCRs targeting known antigens (TBAdb) was also deposited in PIRD. AVAILABILITY AND IMPLEMENTATION PIRD can be freely accessed at https://db.cngb.org/pird.
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Affiliation(s)
- Wei Zhang
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Longlong Wang
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.,BGI-Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Ke Liu
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Xiaofeng Wei
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Kai Yang
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Wensi Du
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Shiyu Wang
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.,BGI-Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Nannan Guo
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Chuanchuan Ma
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Lihua Luo
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.,BGI-Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Jinghua Wu
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.,BGI-Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Liya Lin
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Fan Yang
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Fei Gao
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xie Wang
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Tao Li
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Ruifang Zhang
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Nitin K Saksena
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Lin Fang
- BGI-Shenzhen, Shenzhen 518083, China.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Yong Hou
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Xiao Liu
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
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25
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Srzentić K, Fornelli L, Tsybin YO, Loo JA, Seckler H, Agar JN, Anderson LC, Bai DL, Beck A, Brodbelt JS, van der Burgt YEM, Chamot-Rooke J, Chatterjee S, Chen Y, Clarke DJ, Danis PO, Diedrich JK, D'Ippolito RA, Dupré M, Gasilova N, Ge Y, Goo YA, Goodlett DR, Greer S, Haselmann KF, He L, Hendrickson CL, Hinkle JD, Holt MV, Hughes S, Hunt DF, Kelleher NL, Kozhinov AN, Lin Z, Malosse C, Marshall AG, Menin L, Millikin RJ, Nagornov KO, Nicolardi S, Paša-Tolić L, Pengelley S, Quebbemann NR, Resemann A, Sandoval W, Sarin R, Schmitt ND, Shabanowitz J, Shaw JB, Shortreed MR, Smith LM, Sobott F, Suckau D, Toby T, Weisbrod CR, Wildburger NC, Yates JR, Yoon SH, Young NL, Zhou M. Interlaboratory Study for Characterizing Monoclonal Antibodies by Top-Down and Middle-Down Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1783-1802. [PMID: 32812765 PMCID: PMC7539639 DOI: 10.1021/jasms.0c00036] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The Consortium for Top-Down Proteomics (www.topdownproteomics.org) launched the present study to assess the current state of top-down mass spectrometry (TD MS) and middle-down mass spectrometry (MD MS) for characterizing monoclonal antibody (mAb) primary structures, including their modifications. To meet the needs of the rapidly growing therapeutic antibody market, it is important to develop analytical strategies to characterize the heterogeneity of a therapeutic product's primary structure accurately and reproducibly. The major objective of the present study is to determine whether current TD/MD MS technologies and protocols can add value to the more commonly employed bottom-up (BU) approaches with regard to confirming protein integrity, sequencing variable domains, avoiding artifacts, and revealing modifications and their locations. We also aim to gather information on the common TD/MD MS methods and practices in the field. A panel of three mAbs was selected and centrally provided to 20 laboratories worldwide for the analysis: Sigma mAb standard (SiLuLite), NIST mAb standard, and the therapeutic mAb Herceptin (trastuzumab). Various MS instrument platforms and ion dissociation techniques were employed. The present study confirms that TD/MD MS tools are available in laboratories worldwide and provide complementary information to the BU approach that can be crucial for comprehensive mAb characterization. The current limitations, as well as possible solutions to overcome them, are also outlined. A primary limitation revealed by the results of the present study is that the expert knowledge in both experiment and data analysis is indispensable to practice TD/MD MS.
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Affiliation(s)
- Kristina Srzentić
- Northwestern University, Evanston, Illinois 60208-0001, United States
| | - Luca Fornelli
- Northwestern University, Evanston, Illinois 60208-0001, United States
| | - Yury O Tsybin
- Spectroswiss, EPFL Innovation Park, Building I, 1015 Lausanne, Switzerland
| | - Joseph A Loo
- University of California-Los Angeles, Los Angeles, California 90095, United States
| | - Henrique Seckler
- Northwestern University, Evanston, Illinois 60208-0001, United States
| | - Jeffrey N Agar
- Northeastern University, Boston, Massachusetts 02115, United States
| | - Lissa C Anderson
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Dina L Bai
- University of Virginia, Charlottesville, Virginia 22901, United States
| | - Alain Beck
- Centre d'immunologie Pierre Fabre, 74160 Saint-Julien-en-Genevois, France
| | | | | | | | | | - Yunqiu Chen
- Biogen, Inc., Cambridge, Massachusetts 02142-1031, United States
| | - David J Clarke
- The University of Edinburgh, EH9 3FJ Edinburgh, United Kingdom
| | - Paul O Danis
- Consortium for Top-Down Proteomics, Cambridge, Massachusetts 02142, United States
| | - Jolene K Diedrich
- The Scripps Research Institute, La Jolla, California 92037, United States
| | | | | | - Natalia Gasilova
- Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Ying Ge
- University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Young Ah Goo
- University of Maryland, Baltimore, Maryland 21201, United States
| | - David R Goodlett
- University of Maryland, Baltimore, Maryland 21201, United States
| | - Sylvester Greer
- University of Texas at Austin, Austin, Texas 78712-1224, United States
| | | | - Lidong He
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | | | - Joshua D Hinkle
- University of Virginia, Charlottesville, Virginia 22901, United States
| | - Matthew V Holt
- Baylor College of Medicine, Houston, Texas 77030-3411, United States
| | - Sam Hughes
- The University of Edinburgh, EH9 3FJ Edinburgh, United Kingdom
| | - Donald F Hunt
- University of Virginia, Charlottesville, Virginia 22901, United States
| | - Neil L Kelleher
- Northwestern University, Evanston, Illinois 60208-0001, United States
| | - Anton N Kozhinov
- Spectroswiss, EPFL Innovation Park, Building I, 1015 Lausanne, Switzerland
| | - Ziqing Lin
- University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | | | - Alan G Marshall
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
- Florida State University, Tallahassee, Florida 32310-4005, United States
| | - Laure Menin
- Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Robert J Millikin
- University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | | | - Simone Nicolardi
- Leiden University Medical Centre, 2300 RC Leiden, The Netherlands
| | - Ljiljana Paša-Tolić
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | | | - Neil R Quebbemann
- University of California-Los Angeles, Los Angeles, California 90095, United States
| | | | - Wendy Sandoval
- Genentech, Inc., South San Francisco, California 94080-4990, United States
| | - Richa Sarin
- Biogen, Inc., Cambridge, Massachusetts 02142-1031, United States
| | | | | | - Jared B Shaw
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | | | - Lloyd M Smith
- University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Frank Sobott
- University of Antwerp, 2000 Antwerp, Belgium
- University of Leeds, LS2 9JT Leeds, United Kingdom
| | | | - Timothy Toby
- Northwestern University, Evanston, Illinois 60208-0001, United States
| | - Chad R Weisbrod
- National High Magnetic Field Laboratory, Tallahassee, Florida 32310, United States
| | - Norelle C Wildburger
- Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - John R Yates
- The Scripps Research Institute, La Jolla, California 92037, United States
| | - Sung Hwan Yoon
- University of Maryland, Baltimore, Maryland 21201, United States
| | - Nicolas L Young
- Baylor College of Medicine, Houston, Texas 77030-3411, United States
| | - Mowei Zhou
- Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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26
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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: 69] [Impact Index Per Article: 17.3] [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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27
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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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28
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Li FF, Gasser RB, Liu F, Shan JN, Di WD, He L, Zhou CX, Wang CQ, Fang R, Hu M. Identification and characterization of an R-Smad homologue (Hco-DAF-8) from Haemonchus contortus. Parasit Vectors 2020; 13:164. [PMID: 32245505 PMCID: PMC7119156 DOI: 10.1186/s13071-020-04034-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 03/25/2020] [Indexed: 01/18/2023] Open
Abstract
Background Smad proteins are essential cellular mediators within the transforming growth factor-β (TGF-β) superfamily. They directly transmit incoming signals from the cell surface receptors to the nucleus. In spite of their functional importance, almost nothing is known about Smad proteins in parasitic nematodes including Haemonchus contortus, an important blood-sucking nematode of small ruminants. Methods Based on genomic and transcriptome data for H. contortus and using bioinformatics methods, a Smad homologue (called Hco-daf-8) was inferred from H. contortus and the structural characteristics of this gene and its encoded protein Hco-DAF-8 established. Using real-time PCR and immunofluorescence assays, temporal transcriptional and spatial expression profiles of Hco-daf-8 were studied. Gene rescue in Caenorhabditis elegans was then applied to assess the function of Hco-daf-8 and a specific inhibitor of human Smad3 (called SIS3) was employed to evaluate the roles of Hco-DAF-8 in H. contortus development. Results The features of Hco-DAF-8 (502 amino acids), including conserved R-Smad domains and residues of the L3-loop that determine pathway specificity, are consistent with a TGF-β type I receptor-activated R-Smad. The Hco-daf-8 gene was transcribed in all developmental stages of H. contortus studied, with a higher level of transcription in the fourth-stage larval (L4) females and the highest level in adult males. Hco-DAF-8 was expressed in the platymyarian muscular cells, intestine and reproductive system of adult stages. Gene rescue experiments showed that Hco-daf-8 was able to partially rescue gene function in a daf-8 deficient mutant strain of C. elegans, leading to a resumption of normal development. In H. contortus, SIS3 was shown to affect H. contortus development from the exsheathed third-stage larvae (L3s) to L4s in vitro. Conclusions These findings suggest that Hco-DAF-8, encoded by the gene Hco-daf-8, is an important cellular mediator of H. contortus development via the TGF-β signalling pathway. They provide a basis for future explorations of Hco-DAF-8 and associated pathways in H. contortus and other important parasitic nematodes.![]()
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Affiliation(s)
- Fang-Fang Li
- State Key Laboratory of Agricultural Microbiology, Key Laboratory for the Development of Veterinary Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Robin B Gasser
- State Key Laboratory of Agricultural Microbiology, Key Laboratory for the Development of Veterinary Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,Melbourne Veterinary School, Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Feng Liu
- State Key Laboratory of Agricultural Microbiology, Key Laboratory for the Development of Veterinary Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Jia-Nan Shan
- State Key Laboratory of Agricultural Microbiology, Key Laboratory for the Development of Veterinary Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Wen-Da Di
- State Key Laboratory of Agricultural Microbiology, Key Laboratory for the Development of Veterinary Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Li He
- State Key Laboratory of Agricultural Microbiology, Key Laboratory for the Development of Veterinary Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Cai-Xian Zhou
- State Key Laboratory of Agricultural Microbiology, Key Laboratory for the Development of Veterinary Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Chun-Qun Wang
- State Key Laboratory of Agricultural Microbiology, Key Laboratory for the Development of Veterinary Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Rui Fang
- State Key Laboratory of Agricultural Microbiology, Key Laboratory for the Development of Veterinary Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Min Hu
- State Key Laboratory of Agricultural Microbiology, Key Laboratory for the Development of Veterinary Products, Ministry of Agriculture, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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29
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Hashimoto A, Takeuchi S, Kajita R, Yamagata A, Kakui R, Tanaka T, Nakata K. Proteogenomic analysis of granulocyte macrophage colony- stimulating factor autoantibodies in the blood of a patient with autoimmune pulmonary alveolar proteinosis. Sci Rep 2020; 10:4923. [PMID: 32188922 PMCID: PMC7080758 DOI: 10.1038/s41598-020-61934-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 03/02/2020] [Indexed: 11/18/2022] Open
Abstract
Recently, attempts to reveal the structures of autoantibodies comprehensively using improved proteogenomics technology, have become popular. This technology identifies peptides in highly purified antibodies by using an Orbitrap device to compare spectra from liquid chromatography-tandem mass spectrometry against a cDNA database obtained through next-generation sequencing. In this study, we first analyzed granulocyte-macrophage colony-stimulating factor (GM-CSF) autoantibodies in a patient with autoimmune pulmonary alveolar proteinosis, using the trapped ion mobility spectrometry coupled with quadrupole time-of-flight (TIMS-TOF) instrument. The TIMS-TOF instrument identified peptides that partially matched sequences in up to 156 out of 162 cDNA clones. Complementarity-determining region 3 (CDR3) was fully and partially detected in nine and 132 clones, respectively. Moreover, we confirmed one unique framework region 4 (FR4) and at least three unique across CDR3 to FR4 peptides via de novo peptide sequencing. This new technology may thus permit the comprehensive identification of autoantibody structure.
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Affiliation(s)
| | - Shiho Takeuchi
- Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | | | | | | | - Takahiro Tanaka
- Niigata University Medical & Dental Hospital, Niigata, Japan
| | - Koh Nakata
- Niigata University Medical & Dental Hospital, Niigata, Japan.
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30
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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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31
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Lee AYS, Chataway T, Colella AD, Gordon TP, Wang JJ. Quantitative Mass Spectrometric Analysis of Autoantibodies as a Paradigm Shift in Autoimmune Serology. Front Immunol 2019; 10:2845. [PMID: 31867009 PMCID: PMC6904311 DOI: 10.3389/fimmu.2019.02845] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/19/2019] [Indexed: 12/11/2022] Open
Affiliation(s)
- Adrian Y S Lee
- Department of Immunology, SA Pathology, Flinders Medical Centre, Adelaide, SA, Australia.,College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Tim Chataway
- College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Alex D Colella
- Department of Immunology, SA Pathology, Flinders Medical Centre, Adelaide, SA, Australia.,College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Tom P Gordon
- Department of Immunology, SA Pathology, Flinders Medical Centre, Adelaide, SA, Australia.,College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
| | - Jing J Wang
- Department of Immunology, SA Pathology, Flinders Medical Centre, Adelaide, SA, Australia.,College of Medicine and Public Health, Flinders University, Adelaide, SA, Australia
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32
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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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33
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Li X, Zhang W, Huang M, Ren Z, Nie C, Liu X, Yang S, Zhang X, Yang N. Selection of potential cytokeratin-18 monoclonal antibodies following IGH repertoire evaluation in mice. J Immunol Methods 2019; 474:112647. [PMID: 31421082 DOI: 10.1016/j.jim.2019.112647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 07/12/2019] [Accepted: 08/13/2019] [Indexed: 12/12/2022]
Abstract
Cytokeratin 18 (CK18), the main scaffold protein of keratinocyte, is distributed in epithelial cells. This structural protein maintains the integrity and continuity of epithelial tissue. Cytokeratin is also frequently used as an immunohistochemical marker of tumor growth. In recent years, immune repertoire (IR) evaluation using next-generation sequencing (NGS) have become increasingly efficient. Here we deep sequenced the mouse IR of the immunoglobulin heavy chain (IGH) after CK18 immunization. We comprehensively analyzed the IR based on complementarity determining region 3 (CDR3) abundance, germline gene usage polarization, clone diversity, and lineage. We found many convergence characteristics after CK18 immunization. Convergence represents a phenomenon that antigen stimulation or pathogen exposure induces the antigen specific clone expansion and enrichment. The convergence could be used for the immune evaluation and antibody screen. After immunization, the IGHV5 gene clusters became preponderant. The abundance and length of the most frequent CDR3 both increased, nevertheless the IR diversity level decreased. From the convergent IGH repertoires, we selected and expressed six antibodies with the most frequent CDR3s and IGH V-J combinations. The ELISA results suggested all screened six antibodies bound CK18 specifically. The most potential antibody had 9.424E-10M M affinity for the interaction with the CK18. Therefore, this is the NGS platform has been first used for anti-CK18 monoclonal antibodies (MAbs) discovery. These analyses methods could also be used for vaccine evaluation.
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Affiliation(s)
- Xinyang Li
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Wei Zhang
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Mi Huang
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Zhe Ren
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Chao Nie
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Xiao Liu
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Shuang Yang
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Xiuqing Zhang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Naibo Yang
- BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China; Complete Genomics, Inc., 2904 Orchard Parkway, San Jose, CA 95134, USA.
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34
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Lewis GK, Ackerman ME, Scarlatti G, Moog C, Robert-Guroff M, Kent SJ, Overbaugh J, Reeves RK, Ferrari G, Thyagarajan B. Knowns and Unknowns of Assaying Antibody-Dependent Cell-Mediated Cytotoxicity Against HIV-1. Front Immunol 2019; 10:1025. [PMID: 31134085 PMCID: PMC6522882 DOI: 10.3389/fimmu.2019.01025] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 04/23/2019] [Indexed: 12/15/2022] Open
Abstract
It is now well-accepted that Fc-mediated effector functions, including antibody-dependent cellular cytotoxicity (ADCC), can contribute to vaccine-elicited protection as well as post-infection control of HIV viremia. This picture was derived using a wide array of ADCC assays, no two of which are strictly comparable, and none of which is qualified at the clinical laboratory level. An earlier comparative study of assay protocols showed that while data from different ADCC assay formats were often correlated, they remained distinct in terms of target cells and the epitopes and antigen(s) available for recognition by antibodies, the effector cells, and the readout of cytotoxicity. This initial study warrants expanded analyses of the relationships among all current assay formats to determine where they detect overlapping activities and where they do not. Here we summarize knowns and unknowns of assaying ADCC against HIV-1.
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Affiliation(s)
- George K. Lewis
- Division of Vaccine Research, Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
| | | | - Gabriella Scarlatti
- Viral Evolution and Transmission Unit, Department of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Christiane Moog
- INSERM U1109, Fédération Hospitalo-Universitaire (FHU) OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Marjorie Robert-Guroff
- Vaccine Branch, Center for Cancer Research, National Cancer Institute, National Institues of Health, Bethesda, MD, United States
| | - Stephen J. Kent
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Julie Overbaugh
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - R. Keith Reeves
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, MA, United States
| | - Guido Ferrari
- Department of Surgery and Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, United States
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35
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Miyamoto K, Aoki W, Ohtani Y, Miura N, Aburaya S, Matsuzaki Y, Kajiwara K, Kitagawa Y, Ueda M. Peptide barcoding for establishment of new types of genotype-phenotype linkages. PLoS One 2019; 14:e0215993. [PMID: 31013333 PMCID: PMC6478338 DOI: 10.1371/journal.pone.0215993] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/06/2019] [Indexed: 01/15/2023] Open
Abstract
Measuring binding properties of binders (e.g., antibodies) is essential for developing useful experimental reagents, diagnostics, and pharmaceuticals. Display technologies can evaluate a large number of binders in a high-throughput manner, but the immobilization effect and the avidity effect prohibit the precise evaluation of binding properties. In this paper, we propose a novel methodology, peptide barcoding, to quantitatively measure the binding properties of multiple binders without immobilization. In the experimental scheme, unique peptide barcodes are fused with each binder, and they represent genotype information. These peptide barcodes are designed to have high detectability for mass spectrometry, leading to low identification bias and a high identification rate. A mixture of different peptide-barcoded nanobodies is reacted with antigen-coated magnetic beads in one pot. Peptide barcodes of functional nanobodies are cleaved on beads by a specific protease, and identified by selected reaction monitoring using triple quadrupole mass spectrometry. To demonstrate proof-of-principle for peptide barcoding, we generated peptide-barcoded anti-CD4 nanobody and anti-GFP nanobody, and determined whether we could simultaneously quantify their binding activities. We showed that peptide barcoding did not affect the properties of the nanobodies, and succeeded in measuring the binding activities of these nanobodies in one shot. The results demonstrate the advantages of peptide barcoding, new types of genotype–phenotype linkages.
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Affiliation(s)
- Kana Miyamoto
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, Japan
| | - Wataru Aoki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 7 Goban-cho, Chiyoda-ku, Tokyo, Japan
- Kyoto Integrated Science & Technology Bio-Analysis Center, 134 Chudoji Minamimachi, Simogyo-ku, Kyoto, Japan
| | - Yuta Ohtani
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, Japan
| | - Natsuko Miura
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1–1 Gakuen-cho, Naka-ku, Sakai, Osaka, Japan
| | - Shunsuke Aburaya
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, Japan
- Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo, Japan
| | - Yusei Matsuzaki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, Japan
| | - Kaho Kajiwara
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, Japan
| | - Yoshinori Kitagawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, Japan
| | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 7 Goban-cho, Chiyoda-ku, Tokyo, Japan
- Kyoto Integrated Science & Technology Bio-Analysis Center, 134 Chudoji Minamimachi, Simogyo-ku, Kyoto, Japan
- * E-mail:
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36
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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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37
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Yang H, Li YC, Zhao MZ, Wu FL, Wang X, Xiao WD, Wang YH, Zhang JL, Wang FQ, Xu F, Zeng WF, Overall CM, He SM, Chi H, Xu P. Precision De Novo Peptide Sequencing Using Mirror Proteases of Ac-LysargiNase and Trypsin for Large-scale Proteomics. Mol Cell Proteomics 2019; 18:773-785. [PMID: 30622160 PMCID: PMC6442358 DOI: 10.1074/mcp.tir118.000918] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 11/20/2018] [Indexed: 11/06/2022] Open
Abstract
De novo peptide sequencing for large-scale proteomics remains challenging because of the lack of full coverage of ion series in tandem mass spectra. We developed a mirror protease of trypsin, acetylated LysargiNase (Ac-LysargiNase), with superior activity and stability. The mirror spectrum pairs derived from the Ac-LysargiNase and trypsin treated samples can generate full b and y ion series, which provide mutual complementarity of each other, and allow us to develop a novel algorithm, pNovoM, for de novo sequencing. Using pNovoM to sequence peptides of purified proteins, the accuracy of the sequence was close to 100%. More importantly, from a large-scale yeast proteome sample digested with trypsin and Ac-LysargiNase individually, 48% of all tandem mass spectra formed mirror spectrum pairs, 97% of which contained full coverage of ion series, resulting in precision de novo sequencing of full-length peptides by pNovoM. This enabled pNovoM to successfully sequence 21,249 peptides from 3,753 proteins and interpreted 44-152% more spectra than pNovo+ and PEAKS at a 5% FDR at the spectrum level. Moreover, the mirror protease strategy had an obvious advantage in sequencing long peptides. We believe that the combination of mirror protease strategy and pNovoM will be an effective approach for precision de novo sequencing on both single proteins and proteome samples.
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Affiliation(s)
- Hao Yang
- From the ‡Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS; University of Chinese Academy of Sciences; Institute of Computing Technology, CAS, Beijing 100190, China
| | - Yan-Chang Li
- §State Key Laboratory of Proteomics; Beijing Proteome Research Center; National Center for Protein Sciences Beijing; Beijing Institute of Lifeomics, Beijing 102206, China
| | - Ming-Zhi Zhao
- §State Key Laboratory of Proteomics; Beijing Proteome Research Center; National Center for Protein Sciences Beijing; Beijing Institute of Lifeomics, Beijing 102206, China
| | - Fei-Lin Wu
- §State Key Laboratory of Proteomics; Beijing Proteome Research Center; National Center for Protein Sciences Beijing; Beijing Institute of Lifeomics, Beijing 102206, China
| | - Xi Wang
- From the ‡Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS; University of Chinese Academy of Sciences; Institute of Computing Technology, CAS, Beijing 100190, China
| | - Wei-Di Xiao
- §State Key Laboratory of Proteomics; Beijing Proteome Research Center; National Center for Protein Sciences Beijing; Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yi-Hao Wang
- §State Key Laboratory of Proteomics; Beijing Proteome Research Center; National Center for Protein Sciences Beijing; Beijing Institute of Lifeomics, Beijing 102206, China
| | - Jun-Ling Zhang
- §State Key Laboratory of Proteomics; Beijing Proteome Research Center; National Center for Protein Sciences Beijing; Beijing Institute of Lifeomics, Beijing 102206, China
| | - Fu-Qiang Wang
- §State Key Laboratory of Proteomics; Beijing Proteome Research Center; National Center for Protein Sciences Beijing; Beijing Institute of Lifeomics, Beijing 102206, China
| | - Feng Xu
- §State Key Laboratory of Proteomics; Beijing Proteome Research Center; National Center for Protein Sciences Beijing; Beijing Institute of Lifeomics, Beijing 102206, China
| | - Wen-Feng Zeng
- From the ‡Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS; University of Chinese Academy of Sciences; Institute of Computing Technology, CAS, Beijing 100190, China
| | - Christopher M Overall
- ‖Centre for Blood Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Si-Min He
- From the ‡Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS; University of Chinese Academy of Sciences; Institute of Computing Technology, CAS, Beijing 100190, China;.
| | - Hao Chi
- From the ‡Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS; University of Chinese Academy of Sciences; Institute of Computing Technology, CAS, Beijing 100190, China;.
| | - Ping Xu
- §State Key Laboratory of Proteomics; Beijing Proteome Research Center; National Center for Protein Sciences Beijing; Beijing Institute of Lifeomics, Beijing 102206, China;; ¶Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education Wuhan University, Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China;; College of Life Sciences, Hebei University, Baoding 071002, China.
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Xi Y, Miao X, Li Y, Lai K, Du X, Jiang Z, Wang Y, Yang G. BMP2-mimicking peptide modified with E7 coupling to calcined bovine bone enhanced bone regeneration associating with activation of the Runx2/SP7 signaling axis. J Biomed Mater Res B Appl Biomater 2019; 108:80-93. [PMID: 30912295 DOI: 10.1002/jbm.b.34368] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 02/26/2019] [Accepted: 02/27/2019] [Indexed: 12/14/2022]
Abstract
Commercial bone substitute, such as calcined bovine bone (CBB), is currently extensively used as an alternative to autogenous bone. However, CBB lacks osteoinductivity and merely serves as a scaffold for native bone formation. To address this issue, we designed and prepared a heptaglutamate (E7)-modified BMP2-mimicking peptide (7E) and carried out a series of comprehensive physical characterizations and in vivo and in vitro studies to evaluate its role in the repair of cranial defects. The data elucidated that the amount of peptide anchoring to the bone graft materials was remarkably increased after modified with E7. Of note, 7E had a relatively stable and durable release, which promoted the osteogenic differentiation of rat derived bone marrow mesenchymal stem cells (BMSCs) and enhanced the bone regeneration of a rabbit calvarial defect by regulating the expression of the Runx2/SP7 axis. In summary, the composite biomaterials incorporating the E7-modified BMP2-mimicking peptide and CBB prepared in this study is a novel bone augmentation material with the merits of non-immunotoxicity, convenience, and low cost. © 2019 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater 108B:80-93, 2020.
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Affiliation(s)
- Yue Xi
- Department of Implantology, Stomatology Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Xiaoyan Miao
- Department of Science and Education, Stomatology Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Yongzheng Li
- Department of Implantology, Stomatology Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Kaichen Lai
- Department of Implantology, Stomatology Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Xue Du
- Department of Implantology, Stomatology Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Zhiwei Jiang
- Department of Implantology, Stomatology Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Ying Wang
- Department of Oral Medicine, Stomatology Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Guoli Yang
- Department of Implantology, Stomatology Hospital, School of Medicine, Zhejiang University, Hangzhou, People's Republic of China
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39
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Wang Z, Liu X, Muther J, James JA, Smith K, Wu S. Top-down Mass Spectrometry Analysis of Human Serum Autoantibody Antigen-Binding Fragments. Sci Rep 2019; 9:2345. [PMID: 30787393 PMCID: PMC6382847 DOI: 10.1038/s41598-018-38380-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 12/18/2018] [Indexed: 12/26/2022] Open
Abstract
Detecting autoimmune diseases at an early stage is crucial for effective treatment and disease management to slow disease progression and prevent irreversible organ damage. In many autoimmune diseases, disease-specific autoantibodies are produced by B cells in response to soluble autoantigens due to defects in B cell tolerance mechanisms. Autoantibodies accrue early in disease development, and several are so disease-specific they serve as classification criteria. In this study, we established a high-throughput, sensitive, intact serum autoantibody analysis platform based on the optimization of a one dimensional ultra-high-pressure liquid chromatography top-down mass spectrometry platform (1D UPLC-TDMS). This approach has been successfully applied to a 12 standard monoclonal antibody antigen-binding fragment (Fab) mixture, demonstrating the feasibility to separate and sequence intact antibodies with high sequence coverage and high sensitivity. We then applied the optimized platform to characterize total serum antibody Fabs in a systemic lupus erythematosus (SLE) patient sample and compared it to healthy control samples. From this analysis, we show that the SLE sample has many dominant antibody Fab-related mass features unlike the healthy controls. To our knowledge, this is the first top-down demonstration of serum autoantibody pool analysis. Our proposed approach holds great promise for discovering novel serum autoantibody biomarkers that are of interest for diagnosis, prognosis, and tolerance induction, as well as improving our understanding of pathogenic autoimmune processes.
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Affiliation(s)
- Zhe Wang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA
| | - Xiaowen Liu
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Jennifer Muther
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Judith A James
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
- Departments of Medicine and Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Kenneth Smith
- Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA.
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA.
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40
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Shah HB, Smith K, Wren JD, Webb CF, Ballard JD, Bourn RL, James JA, Lang ML. Insights From Analysis of Human Antigen-Specific Memory B Cell Repertoires. Front Immunol 2019; 9:3064. [PMID: 30697210 PMCID: PMC6340933 DOI: 10.3389/fimmu.2018.03064] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 12/11/2018] [Indexed: 12/17/2022] Open
Abstract
Memory B cells that are generated during an infection or following vaccination act as sentinels to guard against future infections. Upon repeat antigen exposure memory B cells differentiate into new antibody-secreting plasma cells to provide rapid and sustained protection. Some pathogens evade or suppress the humoral immune system, or induce memory B cells with a diminished ability to differentiate into new plasma cells. This leaves the host vulnerable to chronic or recurrent infections. Single cell approaches coupled with next generation antibody gene sequencing facilitate a detailed analysis of the pathogen-specific memory B cell repertoire. Monoclonal antibodies that are generated from antibody gene sequences allow a functional analysis of the repertoire. This review discusses what has been learned thus far from analysis of diverse pathogen-specific memory B cell compartments and describes major differences in their repertoires. Such information may illuminate ways to advance the goal of improving vaccine and therapeutic antibody design.
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Affiliation(s)
- Hemangi B Shah
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Kenneth Smith
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Jonathan D Wren
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States.,Department of Biochemistry and Molecular Biology and Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Carol F Webb
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States.,Division of Rheumatology, Immunology and Allergy, Department of Cell Biology and Internal Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Jimmy D Ballard
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Rebecka L Bourn
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Judith A James
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States.,Department of Medicine and Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Mark L Lang
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
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41
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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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42
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Srzentić K, Nagornov KO, Fornelli L, Lobas AA, Ayoub D, Kozhinov AN, Gasilova N, Menin L, Beck A, Gorshkov MV, Aizikov K, Tsybin YO. Multiplexed Middle-Down Mass Spectrometry as a Method for Revealing Light and Heavy Chain Connectivity in a Monoclonal Antibody. Anal Chem 2018; 90:12527-12535. [DOI: 10.1021/acs.analchem.8b02398] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Kristina Srzentić
- Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | | | - Luca Fornelli
- Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Anna A. Lobas
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Daniel Ayoub
- Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | | | - Natalia Gasilova
- Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Laure Menin
- Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Alain Beck
- Centre d’Immunologie Pierre Fabre, 74160 St. Julien-en-Genevois, France
| | - Mikhail V. Gorshkov
- Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
- Moscow Institute of Physics and Technology State University, 141707 Dolgoprudny, Moscow Region, Russia
| | | | - Yury O. Tsybin
- Spectroswiss, EPFL Innovation Park, 1015 Lausanne, Switzerland
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43
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Wang JJ, Reed JH, Colella AD, Russell AJ, Murray-Brown W, Chataway TK, Jackson KJL, Goodnow CC, Gordon TP. Molecular Profiling and Clonal Tracking of Secreted Rheumatoid Factors in Primary Sjögren's Syndrome. Arthritis Rheumatol 2018; 70:1617-1625. [PMID: 29697211 DOI: 10.1002/art.40539] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 04/19/2018] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Rheumatoid factors (RFs) are associated with systemic disease in primary Sjögren's syndrome (SS) and may be pathogenic as mixed cryoglobulins. Current detection methods cannot resolve RFs at a molecular level. This study was undertaken to perform the first proteomic and transcriptomic analysis of secreted and membrane-bound IgM-RF in primary SS and identify unique heavy-chain peptide signatures for RF clonotype tracking. METHODS Purified heavy chains of serum RFs from 15 patients with primary SS were subjected to de novo mass spectrometric sequencing. The circulating B cell Ig repertoire was determined by massively parallel sequencing of IGH RNA from matched peripheral blood mononuclear cells (n = 7). RF-specific heavy-chain third complementarity-determining region (CDR3) peptides were identified by searching RF heavy-chain peptide sequences against the corresponding IGH RNA sequence libraries. Heavy-chain CDR3 peptides were used as biomarkers to track serum RF clonotypes using quantitative multiple reaction monitoring. RESULTS Serum RFs were clonally restricted and composed of shared sets of IgM heavy-chain variable region (Ig VH ) 1-69, 3-15, 3-7, and 3-74 subfamilies. Cryoprecipitable RFs from patients with mixed cryoglobulinemia (MC) were distinguishable from nonprecipitating RFs by a higher frequency of amino acid substitutions and identification of stereotypic heavy-chain CDR3 transcripts. Potentially pathogenic RF clonotypes were detected in serum by multiple reaction monitoring years before patients presented with MC. Levels of Ig VH 4-34 IgM-RF decreased following immunosuppression and remission of MC. CONCLUSION Cryoprecipitable RF clonotypes linked to vasculitis in primary SS have different molecular profiles than nonprecipitating RFs, suggesting different underlying mechanisms of production. The combined omics workflow presented herein provides molecular biomarkers for tracking and removal of pathogenic RF clones.
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Affiliation(s)
- Jing J Wang
- Flinders University and SA Pathology, Bedford Park, South Australia, Australia
| | - Joanne H Reed
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Alex D Colella
- Flinders University and SA Pathology, Bedford Park, South Australia, Australia
| | - Amanda J Russell
- Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | | | - Tim K Chataway
- Flinders University, Bedford Park, South Australia, Australia
| | | | | | - Tom P Gordon
- Flinders University and SA Pathology, Bedford Park, South Australia, Australia
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44
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Avram O, Vaisman-Mentesh A, Yehezkel D, Ashkenazy H, Pupko T, Wine Y. ASAP - A Webserver for Immunoglobulin-Sequencing Analysis Pipeline. Front Immunol 2018; 9:1686. [PMID: 30105017 PMCID: PMC6077260 DOI: 10.3389/fimmu.2018.01686] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/09/2018] [Indexed: 12/16/2022] Open
Abstract
Reproducible and robust data on antibody repertoires are invaluable for basic and applied immunology. Next-generation sequencing (NGS) of antibody variable regions has emerged as a powerful tool in systems immunology, providing quantitative molecular information on antibody polyclonal composition. However, major computational challenges exist when analyzing antibody sequences, from error handling to hypermutation profiles and clonal expansion analyses. In this work, we developed the ASAP (A webserver for Immunoglobulin-Seq Analysis Pipeline) webserver (https://asap.tau.ac.il). The input to ASAP is a paired-end sequence dataset from one or more replicates, with or without unique molecular identifiers. These datasets can be derived from NGS of human or murine antibody variable regions. ASAP first filters and annotates the sequence reads using public or user-provided germline sequence information. The ASAP webserver next performs various calculations, including somatic hypermutation level, CDR3 lengths, V(D)J family assignments, and V(D)J combination distribution. These analyses are repeated for each replicate. ASAP provides additional information by analyzing the commonalities and differences between the repeats (“joint” analysis). For example, ASAP examines the shared variable regions and their frequency in each replicate to determine which sequences are less likely to be a result of a sample preparation derived and/or sequencing errors. Moreover, ASAP clusters the data to clones and reports the identity and prevalence of top ranking clones (clonal expansion analysis). ASAP further provides the distribution of synonymous and non-synonymous mutations within the V genes somatic hypermutations. Finally, ASAP provides means to process the data for proteomic analysis of serum/secreted antibodies by generating a variable region database for liquid chromatography high resolution tandem mass spectrometry (LC-MS/MS) interpretation. ASAP is user-friendly, free, and open to all users, with no login requirement. ASAP is applicable for researchers interested in basic questions related to B cell development and differentiation, as well as applied researchers who are interested in vaccine development and monoclonal antibody engineering. By virtue of its user-friendliness, ASAP opens the antibody analysis field to non-expert users who seek to boost their research with immune repertoire analysis.
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Affiliation(s)
- Oren Avram
- George S. Wise Faculty of Life Sciences, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Anna Vaisman-Mentesh
- George S. Wise Faculty of Life Sciences, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Dror Yehezkel
- George S. Wise Faculty of Life Sciences, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Haim Ashkenazy
- George S. Wise Faculty of Life Sciences, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Tal Pupko
- George S. Wise Faculty of Life Sciences, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Yariv Wine
- George S. Wise Faculty of Life Sciences, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
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45
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Lin YY, Gawronski A, Hach F, Li S, Numanagić I, Sarrafi I, Mishra S, McPherson A, Collins CC, Radovich M, Tang H, Sahinalp SC. Computational identification of micro-structural variations and their proteogenomic consequences in cancer. Bioinformatics 2018; 34:1672-1681. [PMID: 29267878 PMCID: PMC5946953 DOI: 10.1093/bioinformatics/btx807] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 11/24/2017] [Accepted: 12/15/2017] [Indexed: 12/18/2022] Open
Abstract
Motivation Rapid advancement in high throughput genome and transcriptome sequencing (HTS) and mass spectrometry (MS) technologies has enabled the acquisition of the genomic, transcriptomic and proteomic data from the same tissue sample. We introduce a computational framework, ProTIE, to integratively analyze all three types of omics data for a complete molecular profile of a tissue sample. Our framework features MiStrVar, a novel algorithmic method to identify micro structural variants (microSVs) on genomic HTS data. Coupled with deFuse, a popular gene fusion detection method we developed earlier, MiStrVar can accurately profile structurally aberrant transcripts in tumors. Given the breakpoints obtained by MiStrVar and deFuse, our framework can then identify all relevant peptides that span the breakpoint junctions and match them with unique proteomic signatures. Observing structural aberrations in all three types of omics data validates their presence in the tumor samples. Results We have applied our framework to all The Cancer Genome Atlas (TCGA) breast cancer Whole Genome Sequencing (WGS) and/or RNA-Seq datasets, spanning all four major subtypes, for which proteomics data from Clinical Proteomic Tumor Analysis Consortium (CPTAC) have been released. A recent study on this dataset focusing on SNVs has reported many that lead to novel peptides. Complementing and significantly broadening this study, we detected 244 novel peptides from 432 candidate genomic or transcriptomic sequence aberrations. Many of the fusions and microSVs we discovered have not been reported in the literature. Interestingly, the vast majority of these translated aberrations, fusions in particular, were private, demonstrating the extensive inter-genomic heterogeneity present in breast cancer. Many of these aberrations also have matching out-of-frame downstream peptides, potentially indicating novel protein sequence and structure. Availability and implementation MiStrVar is available for download at https://bitbucket.org/compbio/mistrvar, and ProTIE is available at https://bitbucket.org/compbio/protie. Contact cenksahi@indiana.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yen-Yi Lin
- School of Computing Science, Simon Fraser University, Burnaby, BC, Canada
- Vancouver Prostate Centre, Vancouver, BC, Canada
| | | | - Faraz Hach
- School of Computing Science, Simon Fraser University, Burnaby, BC, Canada
- Vancouver Prostate Centre, Vancouver, BC, Canada
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Sujun Li
- Department of Computer Science, Indiana University, Bloomington, IN, USA
| | - Ibrahim Numanagić
- School of Computing Science, Simon Fraser University, Burnaby, BC, Canada
| | - Iman Sarrafi
- School of Computing Science, Simon Fraser University, Burnaby, BC, Canada
- Vancouver Prostate Centre, Vancouver, BC, Canada
| | - Swati Mishra
- Department of Surgery, Indiana University, School of Medicine, Indianapolis, IN, USA
| | - Andrew McPherson
- School of Computing Science, Simon Fraser University, Burnaby, BC, Canada
| | - Colin C Collins
- Vancouver Prostate Centre, Vancouver, BC, Canada
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Milan Radovich
- Department of Surgery, Indiana University, School of Medicine, Indianapolis, IN, USA
| | - Haixu Tang
- Department of Computer Science, Indiana University, Bloomington, IN, USA
| | - S Cenk Sahinalp
- Vancouver Prostate Centre, Vancouver, BC, Canada
- Department of Computer Science, Indiana University, Bloomington, IN, USA
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46
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Iversen R, Snir O, Stensland M, Kroll JE, Steinsbø Ø, Korponay-Szabó IR, Lundin KEA, de Souza GA, Sollid LM. Strong Clonal Relatedness between Serum and Gut IgA despite Different Plasma Cell Origins. Cell Rep 2018; 20:2357-2367. [PMID: 28877470 PMCID: PMC5603730 DOI: 10.1016/j.celrep.2017.08.036] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 07/14/2017] [Accepted: 08/07/2017] [Indexed: 01/02/2023] Open
Abstract
Mucosal antigens induce generation of lamina propria plasma cells (PCs) that secrete dimeric immunoglobulin A (IgA) destined for transport across the epithelium. In addition, blood contains monomeric IgA. To study the relationship between mucosal and systemic antibody responses, we took advantage of celiac disease patient samples for isolation of gut PCs as well as serum IgA and IgG reactive with a gluten-derived peptide or the autoantigen transglutaminase 2. Proteomic analysis of serum IgA revealed antigen-specific V-gene preferences, which matched those found in gut PCs. Further, gut PC CDR-H3 sequences were abundant in serum IgA but also detectable in serum IgG. Our data indicate that the same B cell clones that give rise to gut PCs also contribute to the serum antibody pool. However, serum IgA antibodies had a molecular composition distinct from that of IgA antibodies secreted in the gut, suggesting that individual B cell clones give rise to different PC populations.
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Affiliation(s)
- Rasmus Iversen
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, NO-0372 Oslo, Norway
| | - Omri Snir
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, NO-0372 Oslo, Norway
| | - Maria Stensland
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, NO-0372 Oslo, Norway; Proteomics Core Facility, Oslo University Hospital-Rikshospitalet, NO-0372 Oslo, Norway
| | - José E Kroll
- Brain Institute, Federal University of Rio Grande do Norte, RN 59056-450 Natal, Brazil
| | - Øyvind Steinsbø
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, NO-0372 Oslo, Norway
| | | | - Knut E A Lundin
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, NO-0372 Oslo, Norway; Department of Gastroenterology, Oslo University Hospital-Rikshospitalet, NO-0372 Oslo, Norway; KG Jebsen Coeliac Disease Research Centre, University of Oslo, NO-0372 Oslo, Norway
| | - Gustavo A de Souza
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, NO-0372 Oslo, Norway; Proteomics Core Facility, Oslo University Hospital-Rikshospitalet, NO-0372 Oslo, Norway; Brain Institute, Federal University of Rio Grande do Norte, RN 59056-450 Natal, Brazil
| | - Ludvig M Sollid
- Centre for Immune Regulation and Department of Immunology, University of Oslo and Oslo University Hospital-Rikshospitalet, NO-0372 Oslo, Norway; KG Jebsen Coeliac Disease Research Centre, University of Oslo, NO-0372 Oslo, Norway.
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47
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Cheng HD, Grimm SK, Gilman MS, Gwom LC, Sok D, Sundling C, Donofrio G, Karlsson Hedestam GB, Bonsignori M, Haynes BF, Lahey TP, Maro I, von Reyn CF, Gorny MK, Zolla-Pazner S, Walker BD, Alter G, Burton DR, Robb ML, Krebs SJ, Seaman MS, Bailey-Kellogg C, Ackerman ME. Fine epitope signature of antibody neutralization breadth at the HIV-1 envelope CD4-binding site. JCI Insight 2018. [PMID: 29515029 PMCID: PMC5922287 DOI: 10.1172/jci.insight.97018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Major advances in donor identification, antigen probe design, and experimental methods to clone pathogen-specific antibodies have led to an exponential growth in the number of newly characterized broadly neutralizing antibodies (bnAbs) that recognize the HIV-1 envelope glycoprotein. Characterization of these bnAbs has defined new epitopes and novel modes of recognition that can result in potent neutralization of HIV-1. However, the translation of envelope recognition profiles in biophysical assays into an understanding of in vivo activity has lagged behind, and identification of subjects and mAbs with potent antiviral activity has remained reliant on empirical evaluation of neutralization potency and breadth. To begin to address this discrepancy between recombinant protein recognition and virus neutralization, we studied the fine epitope specificity of a panel of CD4-binding site (CD4bs) antibodies to define the molecular recognition features of functionally potent humoral responses targeting the HIV-1 envelope site bound by CD4. Whereas previous studies have used neutralization data and machine-learning methods to provide epitope maps, here, this approach was reversed, demonstrating that simple binding assays of fine epitope specificity can prospectively identify broadly neutralizing CD4bs-specific mAbs. Building on this result, we show that epitope mapping and prediction of neutralization breadth can also be accomplished in the assessment of polyclonal serum responses. Thus, this study identifies a set of CD4bs bnAb signature amino acid residues and demonstrates that sensitivity to mutations at signature positions is sufficient to predict neutralization breadth of polyclonal sera with a high degree of accuracy across cohorts and across clades.
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Affiliation(s)
- Hao D Cheng
- Thayer School of Engineering and.,Molecular and Cellular Biology Program, Dartmouth College, Hanover, New Hampshire, USA
| | | | - Morgan Sa Gilman
- Thayer School of Engineering and.,Molecular and Cellular Biology Program, Dartmouth College, Hanover, New Hampshire, USA
| | - Luc Christian Gwom
- Thayer School of Engineering and.,Faculty of Medicine and Biomedical Sciences, University of Yaoundé 1, Yaoundé, Cameroon
| | - Devin Sok
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
| | - Christopher Sundling
- Unit of Infectious Diseases, Department of Medicine, Solna, Karolinska Institute, Stockholm, Sweden
| | - Gina Donofrio
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | | | | | | | - Timothy P Lahey
- Department of Medicine, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Isaac Maro
- Department of Medicine, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA.,DarDar Health Programs, Dar es salaam, Tanzania.,Tokyo Medical and Dental University, Tokyo, Japan
| | - C Fordham von Reyn
- Department of Medicine, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Miroslaw K Gorny
- Department of Pathology, NYU School of Medicine, New York, New York, USA
| | - Susan Zolla-Pazner
- Departments of Medicine and Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT, and Harvard University, Cambridge, Massachusetts, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard University, Cambridge, Massachusetts, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA.,Ragon Institute of MGH, MIT, and Harvard University, Cambridge, Massachusetts, USA
| | - Merlin L Robb
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Shelly J Krebs
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Michael S Seaman
- Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
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48
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Liu X, Wu J. History, applications, and challenges of immune repertoire research. Cell Biol Toxicol 2018; 34:441-457. [PMID: 29484527 DOI: 10.1007/s10565-018-9426-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 02/14/2018] [Indexed: 12/19/2022]
Abstract
The diversity of T and B cells in terms of their receptor sequences is huge in the vertebrate's immune system and provides broad protection against the vast diversity of pathogens. Immune repertoire is defined as the sum of T cell receptors and B cell receptors (also named immunoglobulin) that makes the organism's adaptive immune system. Before the emergence of high-throughput sequencing, the studies on immune repertoire were limited by the underdeveloped methodologies, since it was impossible to capture the whole picture by the low-throughput tools. The massive paralleled sequencing technology suits perfectly the researches on immune repertoire. In this article, we review the history of immune repertoire studies, in terms of technologies and research applications. Particularly, we discuss several aspects of challenges in this field and highlight the efforts to develop potential solutions, in the era of high-throughput sequencing of the immune repertoire.
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Affiliation(s)
- Xiao Liu
- BGI-Shenzhen, Shenzhen, 518083, China.
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49
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Bozekowski JD, Graham AJ, Daugherty PS. High-titer antibody depletion enhances discovery of diverse serum antibody specificities. J Immunol Methods 2018; 455:1-9. [PMID: 29360471 DOI: 10.1016/j.jim.2018.01.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 12/26/2017] [Accepted: 01/16/2018] [Indexed: 12/15/2022]
Abstract
The human antibody repertoire is a unique repository of information regarding infection, inflammation, and autoimmunity of the past, present, and future. However, antibodies can span vast ranges of concentrations with varying affinities and the repertoire is often heavily polarized by a few species. These complexities lead to difficulties detecting and characterizing low abundance antibody species that may be relevant to disease. We therefore developed a method to selectively remove antibodies from a sample in proportion to the titer of the species prior to analysis, referred to as high-titer depletion (HTD). Peptides from a large random peptide display library were enriched towards binding high-titer antibody species and utilized as binding reagents to deplete the corresponding species from the specimen. HTD enabled the discovery of antibody binding specificities using random peptide library screening with reduced cross-reactivity and background signal and improved coverage of low abundance species. With HTD, three monoclonal antibody species were detected at concentrations at least an order of magnitude lower than without HTD. Additionally, 92 serum antibody specificities were readily discovered from an individual specimen using HTD compared to only 25 specificities without HTD. Parameters affecting the extent of depletion such as the concentration of depleted serum were also adjusted to reproducibly improve the coverage of antibody specificities. These results demonstrate that HTD could be employed for the discovery of rare specificities related to disease and enable extensive characterization of the antibody repertoire. Moreover, the strategy of depletion in proportion to titer could be extended to other applications with complex biological samples to improve discovery.
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Affiliation(s)
- Joel D Bozekowski
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Austin J Graham
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Patrick S Daugherty
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA..
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50
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Abstract
Next-generation sequencing is making it possible to study the antibody repertoire of an organism in unprecedented detail, and, by so doing, to characterize its behavior in the response to infection and in pathological conditions such as autoimmunity and cancer. The polymorphic nature of the repertoire poses unique challenges that rule out the use of many commonly used NGS methods and require tradeoffs to be made when considering experimental design.We outline the main contexts in which antibody repertoire analysis has been used, and summarize the key tools that are available. The humoral immune response to vaccination has been a particular focus of repertoire analyses, and we review the key conclusions and methods used in these studies.
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Affiliation(s)
- William D Lees
- Department of Biological Sciences and Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London, WC1E 7HX, UK
| | - Adrian J Shepherd
- Department of Biological Sciences and Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London, WC1E 7HX, UK.
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