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Gervásio J, Ferreira A, Felicori LF. Yclon: Ultrafast clustering of B cell clones from high-throughput immunoglobulin repertoire sequencing data. J Immunol Methods 2023; 523:113576. [PMID: 37966818 DOI: 10.1016/j.jim.2023.113576] [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: 05/18/2023] [Accepted: 10/17/2023] [Indexed: 11/16/2023]
Abstract
MOTIVATION The next-generation sequencing technologies have transformed our understanding of immunoglobulin (Ig) profiles in various immune states. Clonotyping, which groups Ig sequences into B cell clones, is crucial in investigating the diversity of repertoires and changes in antigen exposure. Despite its importance, there is no widely accepted method for clonotyping, and existing methods are computationally intensive for large sequencing datasets. RESULTS To address this challenge, we introduce YClon, a fast and efficient approach for clonotyping Ig repertoire data. YClon uses a hierarchical clustering approach, similar to other methods, to group Ig sequences into B cell clones in a highly sensitive and specific manner. Notably, our approach outperforms other methods by being more than 30 to 5000 times faster in processing the repertoires analyzed. Astonishingly, YClon can effortlessly handle up to 2 million Ig sequences on a standard laptop computer. This enables in-depth analysis of large and numerous antibody repertoires. AVAILABILITY AND IMPLEMENTATION YClon was implemented in Python3 and is freely available on GitHub.
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Affiliation(s)
- João Gervásio
- Laboratory of Synthetic Biology and Biomimetics, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Alice Ferreira
- Laboratory of Synthetic Biology and Biomimetics, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Liza F Felicori
- Laboratory of Synthetic Biology and Biomimetics, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil.
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2
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Pelissier A, Luo S, Stratigopoulou M, Guikema JEJ, Rodríguez Martínez M. Exploring the impact of clonal definition on B-cell diversity: implications for the analysis of immune repertoires. Front Immunol 2023; 14:1123968. [PMID: 37138881 PMCID: PMC10150052 DOI: 10.3389/fimmu.2023.1123968] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/13/2023] [Indexed: 05/05/2023] Open
Abstract
The adaptive immune system has the extraordinary ability to produce a broad range of immunoglobulins that can bind a wide variety of antigens. During adaptive immune responses, activated B cells duplicate and undergo somatic hypermutation in their B-cell receptor (BCR) genes, resulting in clonal families of diversified B cells that can be related back to a common ancestor. Advances in high-throughput sequencing technologies have enabled the high-throughput characterization of B-cell repertoires, however, the accurate identification of clonally related BCR sequences remains a major challenge. In this study, we compare three different clone identification methods on both simulated and experimental data, and investigate their impact on the characterization of B-cell diversity. We observe that different methods lead to different clonal definitions, which affects the quantification of clonal diversity in repertoire data. Our analyses show that direct comparisons between clonal clusterings and clonal diversity of different repertoires should be avoided if different clone identification methods were used to define the clones. Despite this variability, the diversity indices inferred from the repertoires' clonal characterization across samples show similar patterns of variation regardless of the clonal identification method used. We find the Shannon entropy to be the most robust in terms of the variability of diversity rank across samples. Our analysis also suggests that the traditional germline gene alignment-based method for clonal identification remains the most accurate when the complete information about the sequence is known, but that alignment-free methods may be preferred for shorter sequencing read lengths. We make our implementation freely available as a Python library cdiversity.
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Affiliation(s)
- Aurelien Pelissier
- IBM Research Europe, Rüschlikon, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Siyuan Luo
- IBM Research Europe, Rüschlikon, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Maria Stratigopoulou
- Department of Pathology, Amsterdam University Medical Centers, location AMC, Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam, Netherlands
| | - Jeroen E. J. Guikema
- Department of Pathology, Amsterdam University Medical Centers, location AMC, Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam, Netherlands
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3
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Lower Somatic Mutation Levels in the λ Light-Chain Repertoires with Chronic HBV Infection. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2021; 2021:5525369. [PMID: 34239579 PMCID: PMC8203402 DOI: 10.1155/2021/5525369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 05/27/2021] [Indexed: 11/21/2022]
Abstract
To investigate the characteristics of the immunoglobulin light-chain repertoires with chronic HBV infection, the high-throughput sequencing and IMGT/HighV-QUEST were adapted to analyze the κ (IgK) and λ (IgL) light-chain repertoires from the inactive HBV carriers (IHB) and the healthy adults (HH). The comparative analysis revealed high similarity between the κ light-chain repertoires of the HBV carriers and the healthy adults. Nevertheless, the proportion of IGLV genes with ≥90% identity as the germline genes was higher in the IgL light-chain repertoire of the IHB library compared with that of HH library (74.6% vs. 69.1%). Besides, the frequency of amino acid mutations in the CDR1 regions was significantly lower in the IgL light-chain repertoire of the IHB library than that of the HH library (65.52% vs. 56.0%). These results suggested the lower somatic mutation level in the IgL repertoire of IHB library, which might indicate the biased selection of IGLV genes in the IgL repertoire with chronic HBV infection. These findings might lead to a better understanding of the characteristics of the light-chain repertoires of HBV chronically infected individuals.
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4
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Zhan Q, Xu JH, Yu YY, Lo KK E, El-Nezami H, Zeng Z. Human immune repertoire in hepatitis B virus infection. World J Gastroenterol 2021; 27:3790-3801. [PMID: 34321844 PMCID: PMC8291018 DOI: 10.3748/wjg.v27.i25.3790] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/08/2021] [Accepted: 05/27/2021] [Indexed: 02/06/2023] Open
Abstract
Hepatitis B virus (HBV) infection is a public health threat that affects 257 million people worldwide and can progress to liver cirrhosis, liver failure, and hepatocellular carcinoma. The HBV antigen- induced adaptive immune response plays an important role in HBV clearance. Immune repertoire sequencing (IRS) has been used to investigate the molecular mechanisms behind the immune system, find novel ways to treat HBV infection, and evaluate the genetic responses and immune characteristics of individuals infected by HBV or immunized by HBV vaccine. This review summarizes the human immune repertoire analysis methodology, and the application of the IRS in the prediction of HBV infection progression, treatment, and vaccination.
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Affiliation(s)
- Qiao Zhan
- Department of Infectious Diseases, Peking University First Hospital, Beijing 100034, China
| | - Jing-Hang Xu
- Department of Infectious Diseases, Peking University First Hospital, Beijing 100034, China
| | - Yan-Yan Yu
- Department of Infectious Diseases, Peking University First Hospital, Beijing 100034, China
| | - Emily Lo KK
- School of Biological Sciences, University of Hong Kong, Hong Kong, China
| | - Felicianna
- School of Biological Sciences, University of Hong Kong, Hong Kong, China
| | - Hani El-Nezami
- School of Biological Sciences, University of Hong Kong, Hong Kong, China
- Institute of Public Health and Clinical Nutrition, School of Medicine, University of Eastern Finland, Kuopio FI-70211, Finland
| | - Zheng Zeng
- Department of Infectious Diseases, Peking University First Hospital, Beijing 100034, China
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5
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Hong B, Wang L, Huang C, Hong X, Liu A, Li Q, Liu Q, Su L, Wang L, Wang C, Ying T. Decrease of Clone Diversity in IgM Repertoires of HBV Chronically Infected Individuals With High Level of Viral Replication. Front Microbiol 2021; 11:615669. [PMID: 33519772 PMCID: PMC7843509 DOI: 10.3389/fmicb.2020.615669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/22/2020] [Indexed: 01/05/2023] Open
Abstract
High-throughput antibody sequencing allows in-depth insights into human antibody repertoires. To investigate the characteristics of antibody repertoires in patients with chronic HBV infection, we performed Illumina sequencing and IMGT/HighV-QUEST analysis of B lymphocytes from healthy adults and the HBV carriers with high or low level of viral replication. The comparative study revealed high levels of similarity between the IgM and IgG repertoires of the HBV carriers and the healthy adults, including the somatic mutations in V regions, the average CDR3 length, and the occurrence of junctional modifications. Nevertheless, the diversity of the unique clones decreased and some clusters of unique clones expanded in the IgM repertoire of chronic HBV carriers (CHB) compared with healthy adults (HH) and inactive HBV carriers (IHB). Such difference in clone diversity and expansion was not observed in the IgG repertoires of the three populations. More shared antibody clones were found between the IgM repertoires of IHB and HH than that found between CHB and HH (7079 clones vs. 2304 clones). Besides, the biased used IGHD genes were IGHD2-2 and IGHD3-3 in CHB library but were IGHD3-10 and IGHD3-22 in IHB and HH library. In contrast, for IgG repertories, the preferred used VDJ genes were similar in all the three populations. These results indicated that low level of serum HBV might not induce significant changes in BCR repertoires, and high level of HBV replication could have more impacts on IgM repertories than IgG repertoires. Taken together, our findings provide a better understanding of the antibody repertoires of HBV chronically infected individuals.
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Affiliation(s)
- Binbin Hong
- Central Laboratory, Second Affiliated Hospital, Fujian Medical University, Quanzhou, China
| | - Lizhi Wang
- Traditional Chinese Medicine Department, Rehabilitation Hospital, Quanzhou, China
| | - Chunlan Huang
- Traditional Chinese Medicine Department, Rehabilitation Hospital, Quanzhou, China
| | - Xiaoju Hong
- Traditional Chinese Medicine Department, Rehabilitation Hospital, Quanzhou, China
| | - Alan Liu
- Traditional Chinese Medicine Department, Rehabilitation Hospital, Quanzhou, China
| | - Qiulan Li
- Central Laboratory, Second Affiliated Hospital, Fujian Medical University, Quanzhou, China
| | - Qiaoling Liu
- Central Laboratory, Second Affiliated Hospital, Fujian Medical University, Quanzhou, China
| | - Lili Su
- Central Laboratory, Second Affiliated Hospital, Fujian Medical University, Quanzhou, China
| | - Lixing Wang
- Central Laboratory, Second Affiliated Hospital, Fujian Medical University, Quanzhou, China
| | - Chunyu Wang
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Tianlei Ying
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai, China
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6
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Fowler A, Galson JD, Trück J, Kelly DF, Lunter G. Inferring B cell specificity for vaccines using a Bayesian mixture model. BMC Genomics 2020; 21:176. [PMID: 32087698 PMCID: PMC7036227 DOI: 10.1186/s12864-020-6571-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 02/10/2020] [Indexed: 12/30/2022] Open
Abstract
Background Vaccines have greatly reduced the burden of infectious disease, ranking in their impact on global health second only after clean water. Most vaccines confer protection by the production of antibodies with binding affinity for the antigen, which is the main effector function of B cells. This results in short term changes in the B cell receptor (BCR) repertoire when an immune response is launched, and long term changes when immunity is conferred. Analysis of antibodies in serum is usually used to evaluate vaccine response, however this is limited and therefore the investigation of the BCR repertoire provides far more detail for the analysis of vaccine response. Results Here, we introduce a novel Bayesian model to describe the observed distribution of BCR sequences and the pattern of sharing across time and between individuals, with the goal to identify vaccine-specific BCRs. We use data from two studies to assess the model and estimate that we can identify vaccine-specific BCRs with 69% sensitivity. Conclusion Our results demonstrate that statistical modelling can capture patterns associated with vaccine response and identify vaccine specific B cells in a range of different data sets. Additionally, the B cells we identify as vaccine specific show greater levels of sequence similarity than expected, suggesting that there are additional signals of vaccine response, not currently considered, which could improve the identification of vaccine specific B cells.
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Affiliation(s)
- Anna Fowler
- Department of Biostatistics, University of Liverpool, Liverpool, UK.
| | - Jacob D Galson
- University Children's Hospital Zurich and the Children's Research Center, University of Zurich, Zurich, Switzerland
| | - Johannes Trück
- University Children's Hospital Zurich and the Children's Research Center, University of Zurich, Zurich, Switzerland
| | - Dominic F Kelly
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Center, Oxford, UK
| | - Gerton Lunter
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
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7
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Miho E, Roškar R, Greiff V, Reddy ST. Large-scale network analysis reveals the sequence space architecture of antibody repertoires. Nat Commun 2019; 10:1321. [PMID: 30899025 PMCID: PMC6428871 DOI: 10.1038/s41467-019-09278-8] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 03/01/2019] [Indexed: 12/23/2022] Open
Abstract
The architecture of mouse and human antibody repertoires is defined by the sequence similarity networks of the clones that compose them. The major principles that define the architecture of antibody repertoires have remained largely unknown. Here, we establish a high-performance computing platform to construct large-scale networks from comprehensive human and murine antibody repertoire sequencing datasets (>100,000 unique sequences). Leveraging a network-based statistical framework, we identify three fundamental principles of antibody repertoire architecture: reproducibility, robustness and redundancy. Antibody repertoire networks are highly reproducible across individuals despite high antibody sequence dissimilarity. The architecture of antibody repertoires is robust to the removal of up to 50-90% of randomly selected clones, but fragile to the removal of public clones shared among individuals. Finally, repertoire architecture is intrinsically redundant. Our analysis provides guidelines for the large-scale network analysis of immune repertoires and may be used in the future to define disease-associated and synthetic repertoires.
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Affiliation(s)
- Enkelejda Miho
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland.,Institute of Medical Engineering and Medical Informatics, School of Life Sciences, FHNW University of Applied Sciences and Arts Northwestern Switzerland, 4132, Muttenz, Switzerland.,aiNET GmbH, c/o Switzerland Innovation Park Basel Area AG, Hochbergstrasse 60C, 4057, Basel, Switzerland
| | - Rok Roškar
- Research Informatics, Scientific IT Services, ETH Zürich, 8001, Zürich, Switzerland
| | - Victor Greiff
- Department of Immunology, University of Oslo, 0372, Oslo, Norway.
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland.
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8
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Manso TC, Groenner-Penna M, Minozzo JC, Antunes BC, Ippolito GC, Molina F, Felicori LF. Next-generation sequencing reveals new insights about gene usage and CDR-H3 composition in the horse antibody repertoire. Mol Immunol 2018; 105:251-259. [PMID: 30562645 DOI: 10.1016/j.molimm.2018.11.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 11/11/2018] [Accepted: 11/30/2018] [Indexed: 12/26/2022]
Abstract
Horse serum antibodies have been used for greater than a century for the treatment and prophylaxis of infectious diseases and envenomations. Little is known, however, about the immunogenetic diversity that produces horse serum antibodies. Here, we employed next-generation sequencing for a first-in-kind comprehensive analysis of the equine B-cell repertoire. Nearly 45,000 and 30,000 clonotypes were obtained for the heavy-chain (IGH) and lambda light-chain (IGL) loci, respectively. We observed skewed use of the common subgroups IGHV2 (92.49%) and IGLV8 (82.50%), consistent with previous reports, but also novel use of the rare genes IGHV6S1 and IGLV4S2. CDR-H3 amino acid composition revealed different amino acid patterns at positions 106 and 116 compared to human, rabbit, and mouse, suggesting that an extended conformation predominates among horse CDR-H3 loops. Our analysis provides new insights regarding the mechanisms employed to generate antibody diversity in the horse, and could be applicable to the optimized design of synthetic antibodies intended for future therapeutic use.
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Affiliation(s)
- Taciana Conceição Manso
- Laboratory of Synthetic Biology and Biomimetics, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas - ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Michele Groenner-Penna
- Laboratory of Synthetic Biology and Biomimetics, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas - ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - João Carlos Minozzo
- Production and Research Centre of Immunobiological Products, Department of Health of the State of Paraná, Piraquara 83302-200, Brazil
| | - Bruno Cesar Antunes
- Production and Research Centre of Immunobiological Products, Department of Health of the State of Paraná, Piraquara 83302-200, Brazil
| | - Gregory C Ippolito
- Department of Molecular Biosciences, The University of Texas at Austin, 100 E. 24th Street, Stop A5000, Austin, TX, 78712, USA
| | | | - Liza F Felicori
- Laboratory of Synthetic Biology and Biomimetics, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas - ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
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9
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Christley S, Scarborough W, Salinas E, Rounds WH, Toby IT, Fonner JM, Levin MK, Kim M, Mock SA, Jordan C, Ostmeyer J, Buntzman A, Rubelt F, Davila ML, Monson NL, Scheuermann RH, Cowell LG. VDJServer: A Cloud-Based Analysis Portal and Data Commons for Immune Repertoire Sequences and Rearrangements. Front Immunol 2018; 9:976. [PMID: 29867956 PMCID: PMC5953328 DOI: 10.3389/fimmu.2018.00976] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 04/19/2018] [Indexed: 11/13/2022] Open
Abstract
Background Recent technological advances in immune repertoire sequencing have created tremendous potential for advancing our understanding of adaptive immune response dynamics in various states of health and disease. Immune repertoire sequencing produces large, highly complex data sets, however, which require specialized methods and software tools for their effective analysis and interpretation. Results VDJServer is a cloud-based analysis portal for immune repertoire sequence data that provide access to a suite of tools for a complete analysis workflow, including modules for preprocessing and quality control of sequence reads, V(D)J gene segment assignment, repertoire characterization, and repertoire comparison. VDJServer also provides sophisticated visualizations for exploratory analysis. It is accessible through a standard web browser via a graphical user interface designed for use by immunologists, clinicians, and bioinformatics researchers. VDJServer provides a data commons for public sharing of repertoire sequencing data, as well as private sharing of data between users. We describe the main functionality and architecture of VDJServer and demonstrate its capabilities with use cases from cancer immunology and autoimmunity. Conclusion VDJServer provides a complete analysis suite for human and mouse T-cell and B-cell receptor repertoire sequencing data. The combination of its user-friendly interface and high-performance computing allows large immune repertoire sequencing projects to be analyzed with no programming or software installation required. VDJServer is a web-accessible cloud platform that provides access through a graphical user interface to a data management infrastructure, a collection of analysis tools covering all steps in an analysis, and an infrastructure for sharing data along with workflows, results, and computational provenance. VDJServer is a free, publicly available, and open-source licensed resource.
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Affiliation(s)
- Scott Christley
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Walter Scarborough
- Texas Advanced Computing Center, University of Texas at Austin, Austin, TX, United States
| | - Eddie Salinas
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - William H. Rounds
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Inimary T. Toby
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - John M. Fonner
- Texas Advanced Computing Center, University of Texas at Austin, Austin, TX, United States
| | | | - Min Kim
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Stephen A. Mock
- Texas Advanced Computing Center, University of Texas at Austin, Austin, TX, United States
| | - Christopher Jordan
- Texas Advanced Computing Center, University of Texas at Austin, Austin, TX, United States
| | - Jared Ostmeyer
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Adam Buntzman
- Bio5 Institute, University of Arizona, Tucson, AZ, United States
| | - Florian Rubelt
- Department of Microbiology and Immunology, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, United States
| | - Marco L. Davila
- H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, United States
| | - Nancy L. Monson
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX, United States,Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Richard H. Scheuermann
- J. Craig Venter Institute, La Jolla, CA, United States,Department of Pathology, University of California, San Diego, San Diego, CA, United States,La Jolla Institute for Allergy & Immunology, La Jolla, CA, United States
| | - Lindsay G. Cowell
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States,*Correspondence: Lindsay G. Cowell,
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10
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Abstract
Somatic assembly of T cell receptor and B cell receptor (BCR) genes produces a vast diversity of lymphocyte antigen recognition capacity. The advent of efficient high-throughput sequencing of lymphocyte antigen receptor genes has recently generated unprecedented opportunities for exploration of adaptive immune responses. With these opportunities have come significant challenges in understanding the analysis techniques that most accurately reflect underlying biological phenomena. In this regard, sample preparation and sequence analysis techniques, which have largely been borrowed and adapted from other fields, continue to evolve. Here, we review current methods and challenges of library preparation, sequencing and statistical analysis of lymphocyte receptor repertoire studies. We discuss the general steps in the process of immune repertoire generation including sample preparation, platforms available for sequencing, processing of sequencing data, measurable features of the immune repertoire, and the statistical tools that can be used for analysis and interpretation of the data. Because BCR analysis harbors additional complexities, such as immunoglobulin (Ig) (i.e., antibody) gene somatic hypermutation and class switch recombination, the emphasis of this review is on Ig/BCR sequence analysis.
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Affiliation(s)
- Neha Chaudhary
- Division of Rheumatology, Department of Medicine, Immunology and Allergy, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Duane R. Wesemann
- Division of Rheumatology, Department of Medicine, Immunology and Allergy, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
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11
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Miho E, Yermanos A, Weber CR, Berger CT, Reddy ST, Greiff V. Computational Strategies for Dissecting the High-Dimensional Complexity of Adaptive Immune Repertoires. Front Immunol 2018; 9:224. [PMID: 29515569 PMCID: PMC5826328 DOI: 10.3389/fimmu.2018.00224] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 01/26/2018] [Indexed: 12/21/2022] Open
Abstract
The adaptive immune system recognizes antigens via an immense array of antigen-binding antibodies and T-cell receptors, the immune repertoire. The interrogation of immune repertoires is of high relevance for understanding the adaptive immune response in disease and infection (e.g., autoimmunity, cancer, HIV). Adaptive immune receptor repertoire sequencing (AIRR-seq) has driven the quantitative and molecular-level profiling of immune repertoires, thereby revealing the high-dimensional complexity of the immune receptor sequence landscape. Several methods for the computational and statistical analysis of large-scale AIRR-seq data have been developed to resolve immune repertoire complexity and to understand the dynamics of adaptive immunity. Here, we review the current research on (i) diversity, (ii) clustering and network, (iii) phylogenetic, and (iv) machine learning methods applied to dissect, quantify, and compare the architecture, evolution, and specificity of immune repertoires. We summarize outstanding questions in computational immunology and propose future directions for systems immunology toward coupling AIRR-seq with the computational discovery of immunotherapeutics, vaccines, and immunodiagnostics.
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Affiliation(s)
- Enkelejda Miho
- Department for Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- aiNET GmbH, ETH Zürich, Basel, Switzerland
| | - Alexander Yermanos
- Department for Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Cédric R. Weber
- Department for Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Christoph T. Berger
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland
- Department of Internal Medicine, Clinical Immunology, University Hospital Basel, Basel, Switzerland
| | - Sai T. Reddy
- Department for Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Victor Greiff
- Department for Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Department of Immunology, University of Oslo, Oslo, Norway
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12
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Huang CH, Chang YH, Lin CY, Wang WH, Kuan HC, Hsieh YJ, Wang YW, Yang CH, Chiu JY, Tsai SF, Chen YH, Liu HH. Shared IgG Infection Signatures vs. Hemorrhage-Restricted IgA Clusters in Human Dengue: A Phenotype of Differential Class-Switch via TGFβ1. Front Immunol 2017; 8:1726. [PMID: 29255469 PMCID: PMC5723002 DOI: 10.3389/fimmu.2017.01726] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 11/22/2017] [Indexed: 01/08/2023] Open
Abstract
Phenotypic manifestations of infectious diseases are closely related to individual immune responses. Methods to extract information from patients' own immune reactions would be of great use for both diagnosis and treatment. Dengue fever is one of the diseases that clinical aggravations could occur paradoxically after humoral immunity appears. This property makes dengue fever an excellent disease model to explore. A principal component analyses (PCAs)-based framework derived from a prior vaccination study was developed. The framework was verified by successful demonstrations of known IgG signatures from a Mexico Dengue data set. Afterward the pipeline was tested upon de novo IgG and IgA libraries of Dengue patients from southern Taiwan. We discovered four infection signatures within IgG repertoires, two of which were identical to previous reports. However, it was IgA but not IgG that could differentiate hemorrhagic from non-hemorrhagic patients. IgA repertoires were found more diversified among bleeders, from whom seven signature clusters were characterized. The expressions of transforming growth factor beta 1 (TGFβ1) and accordingly mediated class-switch activity of IgA were distinct only among the PCA-segregated bleeding group. In sum, intercontinental sharing of IgG signatures in dengue fever was demonstrated via a unified working flow. Differential regulation of IgA class-switch with associated diversity expansion plus existences of hemorrhage-restricted clusters were shown. The ability of the framework to find common IgG signatures would implicate applications to infections even from unknown pathogens. The clusters within IgA repertoires could offer perspectives to other IgA-related bleeding disorders such as Henoch-Schönlein purpura or IgA nephropathy. Substantiated grounds for IgA-specific effector function via TGFβ1-mediated class-switch would be a new factor to consider for infectious diseases.
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Affiliation(s)
- Chung-Hao Huang
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,School of Medicine, Graduate Institute of Medicine, Sepsis Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ya-Hui Chang
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Taiwan
| | - Chun-Yu Lin
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,School of Medicine, Graduate Institute of Medicine, Sepsis Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wen-Hung Wang
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | | | | | | | - Chung-Hsiang Yang
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Taiwan
| | | | - Shih-Feng Tsai
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Taiwan
| | - Yen-Hsu Chen
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,School of Medicine, Graduate Institute of Medicine, Sepsis Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Biological Science and Technology, College of Biological Science and Technology, National Chiao Tung University, HsinChu, Taiwan
| | - Hong-Hsing Liu
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Taiwan.,Pediatrics, En Chu Kong Hospital, Sanxia, Taiwan
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Characteristics Peripheral Blood IgG and IgM Heavy Chain Complementarity Determining Region 3 Repertoire before and after Immunization with Recombinant HBV Vaccine. PLoS One 2017; 12:e0170479. [PMID: 28114326 PMCID: PMC5256919 DOI: 10.1371/journal.pone.0170479] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 01/05/2017] [Indexed: 02/05/2023] Open
Abstract
Immunization with recombinant HBV vaccine induces specific immune responses in human causing B lymphocytes to produce protective HBsAb, and to form memory B lymphocytes, thereby facilitating HBV immunity in the body. However, B lymphocytes heterogeneity and characteristics are not fully elucidated. In this study, we conducted high-throughput sequencing of BCR heavy chain CDR3 repertoires in 3 healthy volunteers before and after the third immunization with recombinant HBV vaccine. We used Roche 454 Genome Sequencer FLX system to perform a comparative analysis of IgM and IgG H chain CDR3 repertoires. First, we found that the diversity of IgG H chain CDR3 repertoires was 1/6 of IgM on average. Moreover, after the third immunization with HBV vaccine, the diversity of IgG H chain CDR3 repertoires was 1/26 of IgM on average. Second, we detected relatively high levels of HBsAbs in all the healthy volunteers after immunization with HBV vaccine. The volunteers shared a small number of CDR3 sequences before and after immunization, and among each other. However, we did not find completely identical BCR H chain CDR3 amino acid sequences in these volunteers. Lastly, after immunization with recombinant HBV vaccine, the volunteers showed high frequency of IgG H chain CDR3 amino acid sequences mostly resulting from rearrangements of IGHV, IGHD and IGHJ, suggesting that the mechanism of high frequency CDR3 generation might be associated with the maturation of IgG affinity (somatic hypermutation) during the recombinant HBV vaccine-induced B lymphocyte responses. This study identified the characteristics and changes of BCR CDR3 repertoires before and after immunization with HBV vaccine, and evaluated the performance of the sequencing technology for this application. Our findings provide a basis for further research in B lymphocyte generated HBsAb heterogeneity and monitoring the maintenance of memory B lymphocytes.
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