1
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Wang Q, Feng D, Jia S, Lu Q, Zhao M. B-Cell Receptor Repertoire: Recent Advances in Autoimmune Diseases. Clin Rev Allergy Immunol 2024; 66:76-98. [PMID: 38459209 DOI: 10.1007/s12016-024-08984-6] [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] [Accepted: 02/27/2024] [Indexed: 03/10/2024]
Abstract
In the field of contemporary medicine, autoimmune diseases (AIDs) are a prevalent and debilitating group of illnesses. However, they present extensive and profound challenges in terms of etiology, pathogenesis, and treatment. A major reason for this is the elusive pathophysiological mechanisms driving disease onset. Increasing evidence suggests the indispensable role of B cells in the pathogenesis of autoimmune diseases. Interestingly, B-cell receptor (BCR) repertoires in autoimmune diseases display a distinct skewing that can provide insights into disease pathogenesis. Over the past few years, advances in high-throughput sequencing have provided powerful tools for analyzing B-cell repertoire to understand the mechanisms during the period of B-cell immune response. In this paper, we have provided an overview of the mechanisms and analytical methods for generating BCR repertoire diversity and summarize the latest research progress on BCR repertoire in autoimmune diseases, including systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), primary Sjögren's syndrome (pSS), multiple sclerosis (MS), and type 1 diabetes (T1D). Overall, B-cell repertoire analysis is a potent tool to understand the involvement of B cells in autoimmune diseases, facilitating the creation of innovative therapeutic strategies targeting specific B-cell clones or subsets.
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Affiliation(s)
- Qian Wang
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, the Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Clinical Medical Research Center of Major Skin Diseases and Skin Health of Hunan Province, Changsha, China
| | - Delong Feng
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, the Second Xiangya Hospital of Central South University, Changsha, Hunan, China
- Clinical Medical Research Center of Major Skin Diseases and Skin Health of Hunan Province, Changsha, China
| | - Sujie Jia
- Department of Pharmacy, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, 210042, China
| | - Qianjin Lu
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, 210042, China.
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing, China.
| | - Ming Zhao
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, the Second Xiangya Hospital of Central South University, Changsha, Hunan, China.
- Clinical Medical Research Center of Major Skin Diseases and Skin Health of Hunan Province, Changsha, China.
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, 210042, China.
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing, China.
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2
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Sanromán ÁF, Joshi K, Au L, Chain B, Turajlic S. TCR sequencing: applications in immuno-oncology research. IMMUNO-ONCOLOGY TECHNOLOGY 2023; 17:100373. [PMID: 36908996 PMCID: PMC9996383 DOI: 10.1016/j.iotech.2023.100373] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
•T-cell receptor (TCR) interaction with major histocompatibility complex-antigen complexes leads to antitumour responses.•TCR sequencing analysis allows characterisation of T cells that recognise tumour neoantigens.•T-cell clonal revival and clonal replacement potentially underpin immunotherapy responses.
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Affiliation(s)
- Á F Sanromán
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - K Joshi
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK.,Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - L Au
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK.,Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia.,Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Australia
| | - B Chain
- Division of Infection and Immunity, University College London, London, UK.,Department of Computer Science, University College London, London, UK
| | - S Turajlic
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London, UK.,Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London, UK
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3
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Xu Z, Ismanto HS, Zhou H, Saputri DS, Sugihara F, Standley DM. Advances in antibody discovery from human BCR repertoires. FRONTIERS IN BIOINFORMATICS 2022; 2:1044975. [PMID: 36338807 PMCID: PMC9631452 DOI: 10.3389/fbinf.2022.1044975] [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: 09/15/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
Antibodies make up an important and growing class of compounds used for the diagnosis or treatment of disease. While traditional antibody discovery utilized immunization of animals to generate lead compounds, technological innovations have made it possible to search for antibodies targeting a given antigen within the repertoires of B cells in humans. Here we group these innovations into four broad categories: cell sorting allows the collection of cells enriched in specificity to one or more antigens; BCR sequencing can be performed on bulk mRNA, genomic DNA or on paired (heavy-light) mRNA; BCR repertoire analysis generally involves clustering BCRs into specificity groups or more in-depth modeling of antibody-antigen interactions, such as antibody-specific epitope predictions; validation of antibody-antigen interactions requires expression of antibodies, followed by antigen binding assays or epitope mapping. Together with innovations in Deep learning these technologies will contribute to the future discovery of diagnostic and therapeutic antibodies directly from humans.
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Affiliation(s)
- Zichang Xu
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Hendra S. Ismanto
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Hao Zhou
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Dianita S. Saputri
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Fuminori Sugihara
- Core Instrumentation Facility, Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Daron M. Standley
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Department Systems Immunology, Immunology Frontier Research Center, Osaka University, Suita, Japan
- *Correspondence: Daron M. Standley,
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4
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Brooks BD, Beland A, Aguero G, Taylor N, Towne FD. Moving beyond Titers. Vaccines (Basel) 2022; 10:vaccines10050683. [PMID: 35632439 PMCID: PMC9144832 DOI: 10.3390/vaccines10050683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/18/2022] [Accepted: 04/20/2022] [Indexed: 01/27/2023] Open
Abstract
Vaccination to prevent and even eliminate disease is amongst the greatest achievements of modern medicine. Opportunities remain in vaccine development to improve protection across the whole population. A next step in vaccine development is the detailed molecular characterization of individual humoral immune responses against a pathogen, especially the rapidly evolving pathogens. New technologies such as sequencing the immune repertoire in response to disease, immunogenomics/vaccinomics, particularly the individual HLA variants, and high-throughput epitope characterization offer new insights into disease protection. Here, we highlight the emerging technologies that could be used to identify variation within the human population, facilitate vaccine discovery, improve vaccine safety and efficacy, and identify mechanisms of generating immunological memory. In today’s vaccine-hesitant climate, these techniques used individually or especially together have the potential to improve vaccine effectiveness and safety and thus vaccine uptake rates. We highlight the importance of using these techniques in combination to understand the humoral immune response as a whole after vaccination to move beyond neutralizing titers as the standard for immunogenicity and vaccine efficacy, especially in clinical trials.
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Affiliation(s)
- Benjamin D. Brooks
- Department of Biomedical Sciences, Rocky Vista University, Ivins, UT 84738, USA
- Inovan Inc., Fargo, ND 58103, USA
- Correspondence: ; Tel.: +1-(435)-222-1304
| | - Alexander Beland
- College of Osteopathic Medicine, Rocky Vista University, Parker, CO 80112, USA; (A.B.); (G.A.); (N.T.); (F.D.T.)
| | - Gabriel Aguero
- College of Osteopathic Medicine, Rocky Vista University, Parker, CO 80112, USA; (A.B.); (G.A.); (N.T.); (F.D.T.)
| | - Nicholas Taylor
- College of Osteopathic Medicine, Rocky Vista University, Parker, CO 80112, USA; (A.B.); (G.A.); (N.T.); (F.D.T.)
| | - Francina D. Towne
- College of Osteopathic Medicine, Rocky Vista University, Parker, CO 80112, USA; (A.B.); (G.A.); (N.T.); (F.D.T.)
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5
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Marquez S, Babrak L, Greiff V, Hoehn KB, Lees WD, Luning Prak ET, Miho E, Rosenfeld AM, Schramm CA, Stervbo U. Adaptive Immune Receptor Repertoire (AIRR) Community Guide to Repertoire Analysis. Methods Mol Biol 2022; 2453:297-316. [PMID: 35622333 PMCID: PMC9761518 DOI: 10.1007/978-1-0716-2115-8_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Adaptive immune receptor repertoires (AIRRs) are rich with information that can be mined for insights into the workings of the immune system. Gene usage, CDR3 properties, clonal lineage structure, and sequence diversity are all capable of revealing the dynamic immune response to perturbation by disease, vaccination, or other interventions. Here we focus on a conceptual introduction to the many aspects of repertoire analysis and orient the reader toward the uses and advantages of each. Along the way, we note some of the many software tools that have been developed for these investigations and link the ideas discussed to chapters on methods provided elsewhere in this volume.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Chaim A Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Ulrik Stervbo
- Center for Translational Medicine, Immunology, and Transplantation, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany. .,Immundiagnostik, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany.
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6
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Liu H, Pan W, Tang C, Tang Y, Wu H, Yoshimura A, Deng Y, He N, Li S. The methods and advances of adaptive immune receptors repertoire sequencing. Theranostics 2021; 11:8945-8963. [PMID: 34522220 PMCID: PMC8419057 DOI: 10.7150/thno.61390] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/09/2021] [Indexed: 12/13/2022] Open
Abstract
The adaptive immune response is a powerful tool, capable of recognizing, binding to, and neutralizing a vast number of internal and external threats via T or B lymphatic receptors with widespread sets of antigen specificities. The emergence of high-throughput sequencing technology and bioinformatics provides opportunities for research in the fields of life sciences and medicine. The analysis and annotation for immune repertoire data can reveal biologically meaningful information, including immune prediction, target antigens, and effective evaluation. Continuous improvements of the immunological repertoire sequencing methods and analysis tools will help to minimize the experimental and calculation errors and realize the immunological information to meet the clinical requirements. That said, the clinical application of adaptive immune repertoire sequencing requires appropriate experimental methods and standard analytical tools. At the population cell level, we can acquire the overview of cell groups, but the information about a single cell is not obtained accurately. The information that is ignored may be crucial for understanding the heterogeneity of each cell, gene expression and drug response. The combination of high-throughput sequencing and single-cell technology allows us to obtain single-cell information with low-cost and high-throughput. In this review, we summarized the current methods and progress in this area.
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Affiliation(s)
- Hongmei Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Wenjing Pan
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Congli Tang
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Yujie Tang
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Haijing Wu
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hu-nan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China
| | - Akihiko Yoshimura
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Nongyue He
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
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7
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Trück J, Eugster A, Barennes P, Tipton CM, Luning Prak ET, Bagnara D, Soto C, Sherkow JS, Payne AS, Lefranc MP, Farmer A, Bostick M, Mariotti-Ferrandiz E. Biological controls for standardization and interpretation of adaptive immune receptor repertoire profiling. eLife 2021; 10:66274. [PMID: 34037521 PMCID: PMC8154019 DOI: 10.7554/elife.66274] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/15/2021] [Indexed: 12/15/2022] Open
Abstract
Use of adaptive immune receptor repertoire sequencing (AIRR-seq) has become widespread, providing new insights into the immune system with potential broad clinical and diagnostic applications. However, like many high-throughput technologies, it comes with several problems, and the AIRR Community was established to understand and help solve them. We, the AIRR Community’s Biological Resources Working Group, have surveyed scientists about the need for standards and controls in generating and annotating AIRR-seq data. Here, we review the current status of AIRR-seq, provide the results of our survey, and based on them, offer recommendations for developing AIRR-seq standards and controls, including future work.
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Affiliation(s)
- Johannes Trück
- University Children's Hospital and the Children's Research Center, University of Zurich, Zurich, Switzerland
| | - Anne Eugster
- CRTD Center for Regenerative Therapies Dresden, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Pierre Barennes
- Sorbonne Université U959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.,AP-HP Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi), Paris, France
| | - Christopher M Tipton
- Lowance Center for Human Immunology, Emory University School of Medicine, Atlanta, United States
| | - Eline T Luning Prak
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Davide Bagnara
- University of Genoa, Department of Experimental Medicine, Genoa, Italy
| | - Cinque Soto
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, United States.,Department of Pediatrics, Vanderbilt University Medical Center, Nashville, United States
| | - Jacob S Sherkow
- College of Law, University of Illinois, Champaign, United States.,Center for Advanced Studies in Biomedical Innovation Law, University of Copenhagen Faculty of Law, Copenhagen, Denmark.,Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States
| | - Aimee S Payne
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Marie-Paule Lefranc
- IMGT, The International ImMunoGeneTics Information System (IMGT), Laboratoire d'ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), CNRS, University of Montpellier, Montpellier, France.,Laboratoire d'ImmunoGénétique Moléculaire (LIGM) CNRS, University of Montpellier, Montpellier, France.,Institut de Génétique Humaine (IGH), CNRS, University of Montpellier, Montpellier, France
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8
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Johansson G, Kaltak M, Rîmniceanu C, Singh AK, Lycke J, Malmeström C, Hühn M, Vaarala O, Cardell S, Ståhlberg A. Ultrasensitive DNA Immune Repertoire Sequencing Using Unique Molecular Identifiers. Clin Chem 2021; 66:1228-1237. [PMID: 32814950 DOI: 10.1093/clinchem/hvaa159] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 06/25/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND Immune repertoire sequencing of the T-cell receptor can identify clonotypes that have expanded as a result of antigen recognition or hematological malignancies. However, current sequencing protocols display limitations with nonuniform amplification and polymerase-induced errors during sequencing. Here, we developed a sequencing method that overcame these issues and applied it to γδ T cells, a cell type that plays a unique role in immunity, autoimmunity, homeostasis of intestine, skin, adipose tissue, and cancer biology. METHODS The ultrasensitive immune repertoire sequencing method used PCR-introduced unique molecular identifiers. We constructed a 32-panel assay that captured the full diversity of the recombined T-cell receptor delta loci in γδ T cells. The protocol was validated on synthetic reference molecules and blood samples of healthy individuals. RESULTS The 32-panel assay displayed wide dynamic range, high reproducibility, and analytical sensitivity with single-nucleotide resolution. The method corrected for sequencing-depended quantification bias and polymerase-induced errors and could be applied to both enriched and nonenriched cells. Healthy donors displayed oligoclonal expansion of γδ T cells and similar frequencies of clonotypes were detected in both enrichment and nonenriched samples. CONCLUSIONS Ultrasensitive immune repertoire sequencing strategy enables quantification of individual and specific clonotypes in a background that can be applied to clinical as well as basic application areas. Our approach is simple, flexible, and can easily be implemented in any molecular laboratory.
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Affiliation(s)
- Gustav Johansson
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.,Translational Science & Experimental Medicine, Research and Early Development, Respiratory, Inflammation and Autoimmune (RIA), Gothenburg, Sweden
| | - Melita Kaltak
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Cristiana Rîmniceanu
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Medicinaregatan 7A, University of Gothenburg, Gothenburg, Sweden
| | - Avadhesh K Singh
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Medicinaregatan 7A, University of Gothenburg, Gothenburg, Sweden
| | - Jan Lycke
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Clas Malmeström
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Michael Hühn
- Translational Science & Experimental Medicine, Research and Early Development, Respiratory, Inflammation and Autoimmune (RIA), Gothenburg, Sweden
| | - Outi Vaarala
- Respiratory Inflammation and Autoimmunity, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Susanna Cardell
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Medicinaregatan 7A, University of Gothenburg, Gothenburg, Sweden
| | - Anders Ståhlberg
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.,Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
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9
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Zhang S, Zhang S, Lin Z, Zhang X, Dou X, Zhou X, Wang X, Wang Z, Zhang Q. Deep sequencing reveals the skewed B-cell receptor repertoire in plaques and the association between pathogens and atherosclerosis. Cell Immunol 2020; 360:104256. [PMID: 33360167 DOI: 10.1016/j.cellimm.2020.104256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 11/11/2020] [Accepted: 11/21/2020] [Indexed: 12/22/2022]
Abstract
The immune/inflammatory responses regulated by B cells are the critical determinants of atherosclerosis. B-cell receptor (BCR) plays pivotal roles in regulating B cell function. However, the composition and molecular characteristics of the BCR repertoire in atherosclerotic patients have not been fully elucidated. Herein we analyzed BCR repertoire in circulation and plaques of atherosclerotic patients by sequencing the BCR heavy chain complement determining region 3 (BCRH CDR3). Our data showed that in plaques, BCR repertoire was dramatically skewed and their combinations and diversity were significantly decreased, while the frequency of public and dominant B-cell clones was markedly increased. Additionally, BCRH CDR3 in plaques had higher positive selection pressure than that in the peripheral blood of normal subjects and atherosclerotic patients. Moreover, the BCRH CDR3 of some B cell clones specifically expanded in plaques were similar to that of antibodies which recognized certain pathogens including Influenza A virus, implying the possibility of the association between pathogens and atherosclerosis. The present study contributed to understand the roles of B cells in atherosclerosis. The design of specific antibodies based on the B cell clones specifically expanded in plaques might yield useful tools to reveal the pathogenesis of atherosclerosis, assess or alleviate the progression of atherosclerosis.
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Affiliation(s)
- Shucui Zhang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Shigang Zhang
- Neurosurgical Department, Liaocheng People's Hospital, Liaocheng, China
| | - Zongwei Lin
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | | | - Xinyao Dou
- Shandong Experimental High School, Jinan, China
| | - Xiaoming Zhou
- Division of Endocrinology and Metabolism, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xiaowei Wang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Zhe Wang
- Division of Endocrinology and Metabolism, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.
| | - Qunye Zhang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.
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10
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Lee S, Song S, Yoon SS, Koh Y, Yun H. Proper Read Filtering Method to Adequately Analyze Whole-Transcriptome Sequencing and RNA Based Immune Repertoire Sequencing Data for Tumor Milieu Research. Cancers (Basel) 2020; 12:cancers12123693. [PMID: 33317041 PMCID: PMC7763492 DOI: 10.3390/cancers12123693] [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: 11/14/2020] [Revised: 12/05/2020] [Accepted: 12/07/2020] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The recent advancement in high-throughput sequencing has become indispensable for immune-genomics and profiling the T- and B-cell receptor repertoires. Immune repertoire sequencing (IR-seq) and whole transcriptome sequencing (WTS) can be implemented to investigate and quantitatively characterize the complex pattern of the CDR3 region. We conducted T-cell diversity analysis result comparisons of these sequencing methods and suggest an intuitive approach to discriminate reliable TCR sequences and clonotype patterns from capturing errors. Although bulk-RNA sequencing is commonly used for cancer analysis, we confirmed capturing highly enriched TCR transcripts with IR-seq is more reliable for accurate immune repertoire discovery, and singleton read filtering criteria should be applied to capture true clonotypes from error-prone sequencing data. The use of such well-established data and analytical methodologies can broaden understanding of antigen specificity in immunity and enabling efficient therapeutic antibody finding. Abstract Analysis of the T-cell receptor (TCR) repertoire is essential to characterize the extensive collections of T-cell populations with recognizing antigens in cancer research, and whole transcriptome sequencing (WTS) and immune repertoire sequencing (IR-seq) are commonly used for this measure. To date, no standard read filtering method for IR measurement has been presented. We assessed the diversity of the TCR repertoire results from the paired WTS and IR-seq data of 31 multiple myeloma (MM) patients. To invent an adequate read filtering strategy for IR analysis, we conducted comparisons with WTS results. First, our analyses for determining an optimal threshold for selecting clonotypes showed that the clonotypes supported by a single read largely affected the shared clonotypes and manifested distinct patterns of mapping qualities, unlike clonotypes with multiple reads. Second, although IR-seq could reflect a wider TCR region with a higher capture rate than WTS, an adequate comparison with the removal of unwanted bias from potential sequencing errors was possible only after applying our read filtering strategy. As a result, we suggest that TCR repertoire analysis be carried out through IR-seq to produce reliable and accurate results, along with the removal of single-read clonotypes, to conduct immune research in cancer using high-throughput sequencing.
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Affiliation(s)
- Sungyoung Lee
- Center for Precision Medicine, Seoul National University Hospital, Seoul 03082, Korea;
| | - Seulki Song
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea; (S.S.); (S.-S.Y.)
| | - Sung-Soo Yoon
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea; (S.S.); (S.-S.Y.)
- Department of Internal Medicine, Seoul National University Hospital, Seoul 03080, Korea
| | - Youngil Koh
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea; (S.S.); (S.-S.Y.)
- Department of Internal Medicine, Seoul National University Hospital, Seoul 03080, Korea
- Correspondence: (Y.K.); (H.Y.)
| | - Hongseok Yun
- Center for Precision Medicine, Seoul National University Hospital, Seoul 03082, Korea;
- Correspondence: (Y.K.); (H.Y.)
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11
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Ultrasensitive amplicon barcoding for next-generation sequencing facilitating sequence error and amplification-bias correction. Sci Rep 2020; 10:10570. [PMID: 32601361 PMCID: PMC7324614 DOI: 10.1038/s41598-020-67290-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 06/01/2020] [Indexed: 11/08/2022] Open
Abstract
The ability to accurately characterize DNA variant proportions using PCR amplification is key to many genetic studies, including studying tumor heterogeneity, 16S microbiome, viral and immune receptor sequencing. We develop a novel generalizable ultrasensitive amplicon barcoding approach that significantly reduces the inflation/deflation of DNA variant proportions due to PCR amplification biases and sequencing errors. This method was applied to immune receptor sequencing, where it significantly improves the quality and estimation of diversity of the resulting library.
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12
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Brochu HN, Tseng E, Smith E, Thomas MJ, Jones AM, Diveley KR, Law L, Hansen SG, Picker LJ, Gale M, Peng X. Systematic Profiling of Full-Length Ig and TCR Repertoire Diversity in Rhesus Macaque through Long Read Transcriptome Sequencing. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2020; 204:3434-3444. [PMID: 32376650 PMCID: PMC7276939 DOI: 10.4049/jimmunol.1901256] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 04/13/2020] [Indexed: 12/19/2022]
Abstract
The diversity of Ig and TCR repertoires is a focal point of immunological studies. Rhesus macaques (Macaca mulatta) are key for modeling human immune responses, placing critical importance on the accurate annotation and quantification of their Ig and TCR repertoires. However, because of incomplete reference resources, the coverage and accuracy of the traditional targeted amplification strategies for profiling rhesus Ig and TCR repertoires are largely unknown. In this study, using long read sequencing, we sequenced four Indian-origin rhesus macaque tissues and obtained high-quality, full-length sequences for over 6000 unique Ig and TCR transcripts, without the need for sequence assembly. We constructed, to our knowledge, the first complete reference set for the constant regions of all known isotypes and chain types of rhesus Ig and TCR repertoires. We show that sequence diversity exists across the entire variable regions of rhesus Ig and TCR transcripts. Consequently, existing strategies using targeted amplification of rearranged variable regions comprised of V(D)J gene segments miss a significant fraction (27-53% and 42-49%) of rhesus Ig/TCR diversity. To overcome these limitations, we designed new rhesus-specific assays that remove the need for primers conventionally targeting variable regions and allow single cell level Ig and TCR repertoire analysis. Our improved approach will enable future studies to fully capture rhesus Ig and TCR repertoire diversity and is applicable for improving annotations in any model organism.
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Affiliation(s)
- Hayden N Brochu
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC 27607
- Bioinformatics Graduate Program, North Carolina State University, Raleigh, NC 27695
| | | | - Elise Smith
- Department of Immunology, University of Washington, Seattle, WA 98109
| | - Matthew J Thomas
- Department of Immunology, University of Washington, Seattle, WA 98109
- Center for Innate Immunity and Immune Diseases, University of Washington, Seattle, WA 98109
| | - Aiden M Jones
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC 27607
- Genetics Graduate Program, North Carolina State University, Raleigh, NC 27695
| | - Kayleigh R Diveley
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC 27607
- Genetics Graduate Program, North Carolina State University, Raleigh, NC 27695
| | - Lynn Law
- Department of Immunology, University of Washington, Seattle, WA 98109
- Center for Innate Immunity and Immune Diseases, University of Washington, Seattle, WA 98109
| | - Scott G Hansen
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006
| | - Louis J Picker
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006
| | - Michael Gale
- Department of Immunology, University of Washington, Seattle, WA 98109
- Center for Innate Immunity and Immune Diseases, University of Washington, Seattle, WA 98109
- Washington National Primate Research Center, University of Washington, Seattle, WA 98121; and
| | - Xinxia Peng
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC 27607;
- Bioinformatics Graduate Program, North Carolina State University, Raleigh, NC 27695
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695
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13
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Maranhão AQ, Silva HM, da Silva WMC, França RKA, De Leo TC, Dias-Baruffi M, Burtet RT, Brigido MM. Discovering Selected Antibodies From Deep-Sequenced Phage-Display Antibody Library Using ATTILA. Bioinform Biol Insights 2020; 14:1177932220915240. [PMID: 32425512 PMCID: PMC7218273 DOI: 10.1177/1177932220915240] [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: 10/25/2019] [Accepted: 03/03/2020] [Indexed: 11/20/2022] Open
Abstract
Phage display is a powerful technique to select high-affinity antibodies for different purposes, including biopharmaceuticals. Next-generation sequencing (NGS) presented itself as a robust solution, making it possible to assess billions of sequences of the variable domains from selected sublibraries. Handling this process, a central difficulty is to find the selected clones. Here, we present the AutomaTed Tool For Immunoglobulin Analysis (ATTILA), a new tool to analyze and find the enriched variable domains throughout a biopanning experiment. The ATTILA is a workflow that combines publicly available tools and in-house programs and scripts to find the fold-change frequency of deeply sequenced amplicons generated from selected VH and VL domains. We analyzed the same human Fab library NGS data using ATTILA in 5 different experiments, as well as on 2 biopanning experiments regarding performance, accuracy, and output. These analyses proved to be suitable to assess library variability and to list the more enriched variable domains, as ATTILA provides a report with the amino acid sequence of each identified domain, along with its complementarity-determining regions (CDRs), germline classification, and fold change. Finally, the methods employed here demonstrated a suitable manner to combine amplicon generation and NGS data analysis to discover new monoclonal antibodies (mAbs).
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Affiliation(s)
- Andréa Queiroz Maranhão
- Department of Cellular Biology, Institute of Biological Science, University of Brasília, Brasília, Brazil.,Instituto de Investigação em Imunologia, Instituto Nacional de Ciência e Tecnologia (iii-INCT), São Paulo, Brazil
| | - Heidi Muniz Silva
- Department of Cellular Biology, Institute of Biological Science, University of Brasília, Brasília, Brazil
| | - Waldeyr Mendes Cordeiro da Silva
- Department of Cellular Biology, Institute of Biological Science, University of Brasília, Brasília, Brazil.,NEPBio, Federal Institute of Goiás, Formosa, Brazil
| | - Renato Kaylan Alves França
- Department of Cellular Biology, Institute of Biological Science, University of Brasília, Brasília, Brazil
| | - Thais Canassa De Leo
- School of Pharmaceutical Sciences of Ribeirão Preto, USP, Ribeirão Preto, Brazil
| | - Marcelo Dias-Baruffi
- School of Pharmaceutical Sciences of Ribeirão Preto, USP, Ribeirão Preto, Brazil
| | - Rafael Trindade Burtet
- Department of Cellular Biology, Institute of Biological Science, University of Brasília, Brasília, Brazil
| | - Marcelo Macedo Brigido
- Department of Cellular Biology, Institute of Biological Science, University of Brasília, Brasília, Brazil.,Instituto de Investigação em Imunologia, Instituto Nacional de Ciência e Tecnologia (iii-INCT), São Paulo, Brazil
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14
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Caeser R, Di Re M, Krupka JA, Gao J, Lara-Chica M, Dias JML, Cooke SL, Fenner R, Usheva Z, Runge HFP, Beer PA, Eldaly H, Pak HK, Park CS, Vassiliou GS, Huntly BJP, Mupo A, Bashford-Rogers RJM, Hodson DJ. Genetic modification of primary human B cells to model high-grade lymphoma. Nat Commun 2019; 10:4543. [PMID: 31586074 PMCID: PMC6778131 DOI: 10.1038/s41467-019-12494-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 09/11/2019] [Indexed: 12/03/2022] Open
Abstract
Sequencing studies of diffuse large B cell lymphoma (DLBCL) have identified hundreds of recurrently altered genes. However, it remains largely unknown whether and how these mutations may contribute to lymphomagenesis, either individually or in combination. Existing strategies to address this problem predominantly utilize cell lines, which are limited by their initial characteristics and subsequent adaptions to prolonged in vitro culture. Here, we describe a co-culture system that enables the ex vivo expansion and viral transduction of primary human germinal center B cells. Incorporation of CRISPR/Cas9 technology enables high-throughput functional interrogation of genes recurrently mutated in DLBCL. Using a backbone of BCL2 with either BCL6 or MYC, we identify co-operating genetic alterations that promote growth or even full transformation into synthetically engineered DLBCL models. The resulting tumors can be expanded and sequentially transplanted in vivo, providing a scalable platform to test putative cancer genes and to create mutation-directed, bespoke lymphoma models.
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Affiliation(s)
- Rebecca Caeser
- Wellcome MRC Cambridge Stem Cell Institute, Cambridge, CB2 0AW, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Miriam Di Re
- Wellcome MRC Cambridge Stem Cell Institute, Cambridge, CB2 0AW, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Joanna A Krupka
- Wellcome MRC Cambridge Stem Cell Institute, Cambridge, CB2 0AW, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, UK
| | - Jie Gao
- Wellcome MRC Cambridge Stem Cell Institute, Cambridge, CB2 0AW, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Maribel Lara-Chica
- Cancer Molecular Diagnostics Laboratory (CMDL), Department of Haematology, University of Cambridge, Cambridge, UK
| | - João M L Dias
- Cancer Molecular Diagnostics Laboratory (CMDL), Department of Haematology, University of Cambridge, Cambridge, UK
| | - Susanna L Cooke
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Glasgow, UK
| | - Rachel Fenner
- Wellcome MRC Cambridge Stem Cell Institute, Cambridge, CB2 0AW, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Zelvera Usheva
- Wellcome MRC Cambridge Stem Cell Institute, Cambridge, CB2 0AW, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Hendrik F P Runge
- Wellcome MRC Cambridge Stem Cell Institute, Cambridge, CB2 0AW, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Philip A Beer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CA, CB10 1SA, UK
| | - Hesham Eldaly
- Department of Pathology, Cambridge University Hospitals, Cambridge, UK
- Department of Clinical Pathology, Cairo University, Giza, Egypt
| | - Hyo-Kyung Pak
- Department of Pathology, University of Ulsan College of Medicine, Asan Medical Centre, Seoul, Korea
| | - Chan-Sik Park
- Department of Pathology, University of Ulsan College of Medicine, Asan Medical Centre, Seoul, Korea
| | - George S Vassiliou
- Wellcome MRC Cambridge Stem Cell Institute, Cambridge, CB2 0AW, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CA, CB10 1SA, UK
| | - Brian J P Huntly
- Wellcome MRC Cambridge Stem Cell Institute, Cambridge, CB2 0AW, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Annalisa Mupo
- Cancer Molecular Diagnostics Laboratory (CMDL), Department of Haematology, University of Cambridge, Cambridge, UK
| | | | - Daniel J Hodson
- Wellcome MRC Cambridge Stem Cell Institute, Cambridge, CB2 0AW, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
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15
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Bennett J, Moreland NJ, Oliver J, Crane J, Williamson DA, Sika-Paotonu D, Harwood M, Upton A, Smith S, Carapetis J, Baker MG. Understanding group A streptococcal pharyngitis and skin infections as causes of rheumatic fever: protocol for a prospective disease incidence study. BMC Infect Dis 2019; 19:633. [PMID: 31315580 PMCID: PMC6637506 DOI: 10.1186/s12879-019-4126-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 05/22/2019] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Group A Streptococcal (GAS) infections cause the autoimmune disease acute rheumatic fever (ARF), which can progress to chronic rheumatic heart disease (RHD). Treating pharyngitis caused by GAS with antibiotics is important in preventing ARF. However, it is difficult to distinguish these infections from GAS carriers. There is growing evidence for GAS skin infections as a cause of ARF. This study will identify the incidence of true GAS pharyngitis and serological responses to GAS skin infections. The effectiveness of antibiotics for these conditions will be explored, and modifiable risk factors. Serum antibody titres indicating the upper limits of normal (ULN for ASO/ADB antibodies) will be established alongside carriage rates in asymptomatic children. METHODS This is a prospective disease incidence study, with an associated case-control study. The study population includes 1000 children (5-14 years) from Auckland, New Zealand, 800 of whom have visited their healthcare professional, resulting in a throat or skin swab for GAS, and 200 who are asymptomatic. The conditions of interest are GAS throat swab positive pharyngitis (n = 200); GAS carriage (n = 200); GAS negative throat swab (n = 200); GAS skin infections (n = 200); and asymptomatic controls (n = 200). All participants, except asymptomatic controls, will have acute and convalescent serological testing for ASO/ADB titres (collected < 9 days, and 2-4 weeks following symptom onset, respectively), alongside viral PCR from throat swabs. Asymptomatic controls will have ASO/ADB titres measured in one blood specimen and a throat swab for microbial culture. Caregivers of children will be interviewed using a questionnaire and any GAS isolates identified will be emm typed. The persistence of GAS antibodies will also be investigated. DISCUSSION Findings from this study will fill critical gaps in scientific knowledge to better understand the pathophysiology of ARF, improve clinical management of GAS infections, and design more effective ARF prevention programmes. In particular it will measure the incidence of true, serologically confirmed GAS pharyngitis; assess the immune response to GAS skin infections and its role as a cause of ARF; examine the effectiveness of oral antibiotics for treating GAS pharyngitis and carriage; and identify whether risk factors for GAS infections might provide intervention points for reducing ARF.
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Affiliation(s)
- Julie Bennett
- Department of Public Health, University of Otago, Wellington, New Zealand
| | - Nicole J. Moreland
- School of Medical Sciences, University of Auckland, Auckland, New Zealand
| | - Jane Oliver
- Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Julian Crane
- Department of Medicine, University of Otago, Wellington, New Zealand
| | | | - Dianne Sika-Paotonu
- Deans Department and Department of Pathology and Molecular Medicine, University of Otago, Wellington, New Zealand
- Wesfarmers Centre for Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, Australia
- Faculty of Health, Victoria University of Wellington, Wellington, New Zealand
| | - Matire Harwood
- Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Arlo Upton
- Southern Community Laboratory, Dunedin, New Zealand
| | | | - Jonathan Carapetis
- Telethon Kids Institute, University ofWestern Australia, Perth, Australia
| | - Michael G. Baker
- Department of Public Health, University of Otago, Wellington, New Zealand
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16
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Zhuang Y, Zhang C, Wu Q, Zhang J, Ye Z, Qian Q. Application of immune repertoire sequencing in cancer immunotherapy. Int Immunopharmacol 2019; 74:105688. [PMID: 31276974 DOI: 10.1016/j.intimp.2019.105688] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 05/05/2019] [Accepted: 06/05/2019] [Indexed: 12/21/2022]
Abstract
With the prominent breakthrough in the field of tumor immunology, diverse cancer immunotherapies have attracted great attention in the last decade. The immune checkpoint inhibitors, adoptive cell therapies, and therapeutic cancer vaccines have already achieved impressive clinical success. However, the fact that only a small subset of patients with specific tumor types can benefit from these treatments limits the application of cancer immunotherapy. To seek out the molecular mechanisms behind this challenge and to select cancer precision medicine for different individuals, researchers apply the immune repertoire sequencing (IRS) to evaluate genetic responses of each patient to current immunotherapies. This review summarizes the technical advances and recent applications of IRS in cancer immunotherapy, indicates the limitations of this technique, and predicts future perspectives both in basic studies and clinical trials.
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Affiliation(s)
- Yuan Zhuang
- Shanghai Baize Medical Laboratory, Shanghai, China
| | - Changzheng Zhang
- Shanghai Baize Medical Laboratory, Shanghai, China; Shanghai Engineering Research Center for Cell Therapy, Shanghai, China
| | - Qiong Wu
- Shanghai Baize Medical Laboratory, Shanghai, China
| | - Jing Zhang
- Shanghai Baize Medical Laboratory, Shanghai, China
| | - Zhenlong Ye
- Shanghai Baize Medical Laboratory, Shanghai, China; Shanghai Cell Therapy Research Institute, Shanghai, China; Shanghai Engineering Research Center for Cell Therapy, Shanghai, China.
| | - Qijun Qian
- Shanghai Baize Medical Laboratory, Shanghai, China; Shanghai Cell Therapy Research Institute, Shanghai, China; Shanghai Engineering Research Center for Cell Therapy, Shanghai, China.
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17
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Lanz TV, Pröbstel AK, Mildenberger I, Platten M, Schirmer L. Single-Cell High-Throughput Technologies in Cerebrospinal Fluid Research and Diagnostics. Front Immunol 2019; 10:1302. [PMID: 31244848 PMCID: PMC6579921 DOI: 10.3389/fimmu.2019.01302] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 05/22/2019] [Indexed: 01/08/2023] Open
Abstract
High-throughput single-cell technologies have recently emerged as essential tools in biomedical research with great potential for clinical pathology when studying liquid and solid biopsies. We provide an update on current single-cell methods in cerebrospinal fluid research and diagnostics, focusing on high-throughput cell-type specific proteomic and genomic technologies. Proteomic methods comprising flow cytometry and mass cytometry as well as genomic approaches including immune cell repertoire and single-cell transcriptomic studies are critically reviewed and future directions discussed.
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Affiliation(s)
- Tobias V. Lanz
- Department of Neurology, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Anne-Katrin Pröbstel
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, United States
- Departments of Medicine and Biomedicine, Neurologic Clinic and Policlinic, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Iris Mildenberger
- Department of Neurology, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Michael Platten
- Department of Neurology, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
- DKTK Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lucas Schirmer
- Department of Neurology, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
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18
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López-Santibáñez-Jácome L, Avendaño-Vázquez SE, Flores-Jasso CF. The Pipeline Repertoire for Ig-Seq Analysis. Front Immunol 2019; 10:899. [PMID: 31114573 PMCID: PMC6503734 DOI: 10.3389/fimmu.2019.00899] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 04/08/2019] [Indexed: 11/22/2022] Open
Abstract
With the advent of high-throughput sequencing of immunoglobulin genes (Ig-Seq), the understanding of antibody repertoires and their dynamics among individuals and populations has become an exciting area of research. There is an increasing number of computational tools that aid in every step of the immune repertoire characterization. However, since not all tools function identically, every pipeline has its unique rationale and capabilities, creating a rich blend of useful features that may appear intimidating for newcomer laboratories with the desire to plunge into immune repertoire analysis to expand and improve their research; hence, all pipeline strengths and differences may not seem evident. In this review we provide a practical and organized list of the current set of computational tools, focusing on their most attractive features and differences in order to carry out the characterization of antibody repertoires so that the reader better decides a strategic approach for the experimental design, and computational pathways for the analyses of immune repertoires.
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Affiliation(s)
- Laura López-Santibáñez-Jácome
- Consorcio de Metabolismo de RNA, Instituto Nacional de Medicina Genómica, Mexico City, Mexico.,Maestría en Ciencia de Datos, Instituto Tecnológico Autónomo de México, Mexico City, Mexico
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19
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Rettig TA, Pecaut MJ, Chapes SK. A comparison of unamplified and massively multiplexed PCR amplification for murine antibody repertoire sequencing. FASEB Bioadv 2019; 1:6-17. [PMID: 30740592 PMCID: PMC6366624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023] Open
Abstract
Sequencing antibody repertoires has steadily become cheaper and easier. Sequencing methods usually rely on some form of amplification, often a massively multiplexed PCR prior to sequencing. To eliminate potential biases and create a data set that could be used for other studies, our lab compared unamplified sequencing results from the splenic heavy-chain repertoire in the mouse to those processed through two commercial applications. We also compared the use of mRNA vs total RNA, reverse transcriptase, and primer usage for cDNA synthesis and submission. The use of mRNA for cDNA synthesis resulted in higher read counts but reverse transcriptase and primer usage had no statistical effects on read count. Although most of the amplified data sets contained more antibody reads than the unamplified data set, we detected more unique V-gene segments in the unamplified data set. Although unique CDR3 detection was much lower in the unamplified data set, RNASeq detected 98% of the high frequency CDR3s. We have shown that unamplified profiling of the antibody repertoire is possible, detects more V-gene segments, and detects high frequency clones in the repertoire.
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Affiliation(s)
- Trisha A. Rettig
- Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Michael J. Pecaut
- Division of Radiation Research, Loma Linda University, Loma Linda, CA, USA
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20
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Lindeman I, Stubbington MJT. Antigen Receptor Sequence Reconstruction and Clonality Inference from scRNA-Seq Data. Methods Mol Biol 2019; 1935:223-249. [PMID: 30758830 DOI: 10.1007/978-1-4939-9057-3_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In this chapter, we describe TraCeR and BraCeR, our computational tools for reconstruction of paired full-length antigen receptor sequences and clonality inference from single-cell RNA-seq (scRNA-seq) data. In brief, TraCeR reconstructs T-cell receptor (TCR) sequences from scRNA-seq data by extracting sequencing reads derived from TCRs by aligning the reads from each cell against synthetic TCR sequences. TCR-derived reads are then assembled into full-length recombined TCR sequences. BraCeR builds on the TraCeR pipeline and accounts for somatic hypermutations (SHM) and isotype switching. Here we discuss experimental design, use of the tools, and interpretation of the results.
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Affiliation(s)
- Ida Lindeman
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
- KG Jebsen Coeliac Disease Research Centre and Department of Immunology, University of Oslo, Oslo, Norway
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21
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Eliyahu S, Sharabi O, Elmedvi S, Timor R, Davidovich A, Vigneault F, Clouser C, Hope R, Nimer A, Braun M, Weiss YY, Polak P, Yaari G, Gal-Tanamy M. Antibody Repertoire Analysis of Hepatitis C Virus Infections Identifies Immune Signatures Associated With Spontaneous Clearance. Front Immunol 2018; 9:3004. [PMID: 30622532 PMCID: PMC6308210 DOI: 10.3389/fimmu.2018.03004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 12/05/2018] [Indexed: 12/13/2022] Open
Abstract
Hepatitis C virus (HCV) is a major public health concern, with over 70 million people infected worldwide, who are at risk for developing life-threatening liver disease. No vaccine is available, and immunity against the virus is not well-understood. Following the acute stage, HCV usually causes chronic infections. However, ~30% of infected individuals spontaneously clear the virus. Therefore, using HCV as a model for comparing immune responses between spontaneous clearer (SC) and chronically infected (CI) individuals may empower the identification of mechanisms governing viral infection outcomes. Here, we provide the first in-depth analysis of adaptive immune receptor repertoires in individuals with current or past HCV infection. We demonstrate that SC individuals, in contrast to CI patients, develop clusters of antibodies with distinct properties. These antibodies' characteristics were used in a machine learning framework to accurately predict infection outcome. Using combinatorial antibody phage display library technology, we identified HCV-specific antibody sequences. By integrating these data with the repertoire analysis, we constructed two antibodies characterized by high neutralization breadth, which are associated with clearance. This study provides insight into the nature of effective immune response against HCV and demonstrates an innovative approach for constructing antibodies correlating with successful infection clearance. It may have clinical implications for prognosis of the future status of infection, and the design of effective immunotherapies and a vaccine for HCV.
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Affiliation(s)
- Sivan Eliyahu
- Molecular Virology Lab, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Oz Sharabi
- Bioengineering, Faculty of Engineering, Bar-Ilan University, Ramat-Gan, Israel
| | - Shiri Elmedvi
- Molecular Virology Lab, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Reut Timor
- Bioengineering, Faculty of Engineering, Bar-Ilan University, Ramat-Gan, Israel
| | - Ateret Davidovich
- Molecular Virology Lab, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | | | | | - Ronen Hope
- Bioengineering, Faculty of Engineering, Bar-Ilan University, Ramat-Gan, Israel
| | - Assy Nimer
- Internal Medicine Department A, Western Galilee Medical Center, Naharyia and Faculty of Medicine in the Galilee, Bar-Ilan University, Safed, Israel
| | - Marius Braun
- Liver Institute, Rabin Medical Center, Sackler School of Medicine, Tel-Aviv University, Tel Aviv-Yafo, Israel
| | - Yaacov Y Weiss
- Bioengineering, Faculty of Engineering, Bar-Ilan University, Ramat-Gan, Israel
| | - Pazit Polak
- Bioengineering, Faculty of Engineering, Bar-Ilan University, Ramat-Gan, Israel
| | - Gur Yaari
- Bioengineering, Faculty of Engineering, Bar-Ilan University, Ramat-Gan, Israel
| | - Meital Gal-Tanamy
- Molecular Virology Lab, The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
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22
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Rettig TA, Pecaut MJ, Chapes SK. A comparison of unamplified and massively multiplexed PCR amplification for murine antibody repertoire sequencing. FASEB Bioadv 2018; 1:6-17. [PMID: 32123808 PMCID: PMC6996338 DOI: 10.1096/fba.1017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/09/2018] [Accepted: 08/17/2018] [Indexed: 11/26/2022] Open
Abstract
Sequencing antibody repertoires has steadily become cheaper and easier. Sequencing methods usually rely on some form of amplification, often a massively multiplexed PCR prior to sequencing. To eliminate potential biases and create a data set that could be used for other studies, our laboratory compared unamplified sequencing results from the splenic heavy‐chain repertoire in the mouse to those processed through two commercial applications. We also compared the use of mRNA vs total RNA, reverse transcriptase, and primer usage for cDNA synthesis and submission. The use of mRNA for cDNA synthesis resulted in higher read counts but reverse transcriptase and primer usage had no statistical effects on read count. Although most of the amplified data sets contained more antibody reads than the unamplified data set, we detected more unique variable (V)‐gene segments in the unamplified data set. Although unique CDR3 detection was much lower in the unamplified data set, RNASeq detected 98% of the high‐frequency CDR3s. We have shown that unamplified profiling of the antibody repertoire is possible, detects more V‐gene segments, and detects high‐frequency clones in the repertoire.
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Affiliation(s)
- Trisha A Rettig
- Division of Biology Kansas State University Manhattan Kansas
| | - Michael J Pecaut
- Division of Biomedical Engineering Sciences (BMES) Loma Linda University Loma Linda California
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23
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Simon JS, Botero S, Simon SM. Sequencing the peripheral blood B and T cell repertoire - Quantifying robustness and limitations. J Immunol Methods 2018; 463:137-147. [PMID: 30312601 DOI: 10.1016/j.jim.2018.10.003] [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: 08/21/2018] [Revised: 10/04/2018] [Accepted: 10/04/2018] [Indexed: 12/27/2022]
Abstract
The adaptive immune response generates a large repertoire of T cells with T-cell receptors (TCRalpha and TCRbeta) and B cells with immunoglobulins (Ig). The repertoire changes in response to antigen stimulation both through amplification of specific cells (clonal expansion) as well as somatic hypermutation of immunoglobulins. Alterations of the immune repertoire have been observed in response to acute disease, such as external pathogens, or chronic diseases, such as autoimmunity and cancer. Here we establish experimental and analytical protocols for quantifying the peripheral blood of healthy human individuals by profiling the immune repertoire for the Complementarity determining region 3 (CDR3) of the variable regions of TCRbeta (CDRβ3) and the IgG heavy chain (CDRH1, CDRH2, CDRH3). The results demonstrate that 40 ml of blood are sufficient to reliably capture the 10,000 most common TCRbeta and 1000 most common IgG and determine their relative frequency in the circulation. We conclude that by using an accessible sample size of human PBMC one is able to robustly monitor alterations in the immune repertoire.
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Affiliation(s)
- Joel S Simon
- Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, United States
| | - Sergio Botero
- Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, United States
| | - Sanford M Simon
- Laboratory of Cellular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, United States.
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24
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Chaara W, Gonzalez-Tort A, Florez LM, Klatzmann D, Mariotti-Ferrandiz E, Six A. RepSeq Data Representativeness and Robustness Assessment by Shannon Entropy. Front Immunol 2018; 9:1038. [PMID: 29868003 PMCID: PMC5962720 DOI: 10.3389/fimmu.2018.01038] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 04/25/2018] [Indexed: 12/30/2022] Open
Abstract
High-throughput sequencing (HTS) has the potential to decipher the diversity of T cell repertoires and their dynamics during immune responses. Applied to T cell subsets such as T effector and T regulatory cells, it should help identify novel biomarkers of diseases. However, given the extreme diversity of TCR repertoires, understanding how the sequencing conditions, including cell numbers, biological and technical sampling and sequencing depth, impact the experimental outcome is critical to proper use of these data. Here, we assessed the representativeness and robustness of TCR repertoire diversity assessment according to experimental conditions. By comparative analyses of experimental datasets and computer simulations, we found that (i) for small samples, the number of clonotypes recovered is often higher than the number of cells per sample, even after removing the singletons; (ii) high-sequencing depth for small samples alters the clonotype distributions, which can be corrected by filtering the datasets using Shannon entropy as a threshold; and (iii) a single sequencing run at high depth does not ensure a good coverage of the clonotype richness in highly polyclonal populations, which can be better covered using multiple sequencing. Altogether, our results warrant better understanding and awareness of the limitation of TCR diversity analyses by HTS and justify the development of novel computational tools for improved modeling of the highly complex nature of TCR repertoires.
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Affiliation(s)
- Wahiba Chaara
- Sorbonne Université, INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.,AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France
| | - Ariadna Gonzalez-Tort
- Sorbonne Université, INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France
| | - Laura-Maria Florez
- Sorbonne Université, INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France
| | - David Klatzmann
- Sorbonne Université, INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.,AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France
| | - Encarnita Mariotti-Ferrandiz
- Sorbonne Université, INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.,AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France
| | - Adrien Six
- Sorbonne Université, INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (i3), Paris, France.,AP-HP, Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), Paris, France
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25
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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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26
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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: 46] [Impact Index Per Article: 7.7] [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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27
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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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28
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Bürckert JP, Dubois ARSX, Faison WJ, Farinelle S, Charpentier E, Sinner R, Wienecke-Baldacchino A, Muller CP. Functionally Convergent B Cell Receptor Sequences in Transgenic Rats Expressing a Human B Cell Repertoire in Response to Tetanus Toxoid and Measles Antigens. Front Immunol 2017; 8:1834. [PMID: 29312330 PMCID: PMC5743747 DOI: 10.3389/fimmu.2017.01834] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 12/05/2017] [Indexed: 11/13/2022] Open
Abstract
The identification and tracking of antigen-specific immunoglobulin (Ig) sequences within total Ig repertoires is central to high-throughput sequencing (HTS) studies of infections or vaccinations. In this context, public Ig sequences shared by different individuals exposed to the same antigen could be valuable markers for tracing back infections, measuring vaccine immunogenicity, and perhaps ultimately allow the reconstruction of the immunological history of an individual. Here, we immunized groups of transgenic rats expressing human Ig against tetanus toxoid (TT), Modified Vaccinia virus Ankara (MVA), measles virus hemagglutinin and fusion proteins expressed on MVA, and the environmental carcinogen benzo[a]pyrene, coupled to TT. We showed that these antigens impose a selective pressure causing the Ig heavy chain (IgH) repertoires of the rats to converge toward the expression of antibodies with highly similar IgH CDR3 amino acid sequences. We present a computational approach, similar to differential gene expression analysis, that selects for clusters of CDR3s with 80% similarity, significantly overrepresented within the different groups of immunized rats. These IgH clusters represent antigen-induced IgH signatures exhibiting stereotypic amino acid patterns including previously described TT- and measles-specific IgH sequences. Our data suggest that with the presented methodology, transgenic Ig rats can be utilized as a model to identify antigen-induced, human IgH signatures to a variety of different antigens.
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Affiliation(s)
- Jean-Philippe Bürckert
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Axel R S X Dubois
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - William J Faison
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Sophie Farinelle
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Emilie Charpentier
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Regina Sinner
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | | | - Claude P Muller
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
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29
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Bashford-Rogers RJM, Nicolaou KA, Bartram J, Goulden NJ, Loizou L, Koumas L, Chi J, Hubank M, Kellam P, Costeas PA, Vassiliou GS. Eye on the B-ALL: B-cell receptor repertoires reveal persistence of numerous B-lymphoblastic leukemia subclones from diagnosis to relapse. Leukemia 2016; 30:2312-2321. [PMID: 27211266 PMCID: PMC5155029 DOI: 10.1038/leu.2016.142] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 05/02/2016] [Accepted: 05/12/2016] [Indexed: 02/08/2023]
Abstract
The strongest predictor of relapse in B-cell acute lymphoblastic leukemia (B-ALL) is the level of persistence of tumor cells after initial therapy. The high mutation rate of the B-cell receptor (BCR) locus allows high-resolution tracking of the architecture, evolution and clonal dynamics of B-ALL. Using longitudinal BCR repertoire sequencing, we find that the BCR undergoes an unexpectedly high level of clonal diversification in B-ALL cells through both somatic hypermutation and secondary rearrangements, which can be used for tracking the subclonal composition of the disease and detect minimal residual disease with unprecedented sensitivity. We go on to investigate clonal dynamics of B-ALL using BCR phylogenetic analyses of paired diagnosis-relapse samples and find that large numbers of small leukemic subclones present at diagnosis re-emerge at relapse alongside a dominant clone. Our findings suggest that in all informative relapsed patients, the survival of large numbers of clonogenic cells beyond initial chemotherapy is a surrogate for inherent partial chemoresistance or inadequate therapy, providing an increased opportunity for subsequent emergence of fully resistant clones. These results frame early cytoreduction as an important determinant of long-term outcome.
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Affiliation(s)
- R J M Bashford-Rogers
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.,Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - K A Nicolaou
- The Center for the Study of Hematological Malignancies, Nicosia, Cyprus
| | - J Bartram
- Department of Haematology, Great Ormond Street Hospital for Children, London, UK.,Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK
| | - N J Goulden
- Department of Haematology, Great Ormond Street Hospital for Children, London, UK
| | - L Loizou
- Pediatric Oncology/Hematology Clinic, Nicosia, Cyprus
| | - L Koumas
- The Center for the Study of Hematological Malignancies, Nicosia, Cyprus
| | - J Chi
- The Center for the Study of Hematological Malignancies, Nicosia, Cyprus
| | - M Hubank
- Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK
| | - P Kellam
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.,Division of Infection and Immunity, Research Department of Infection, University College London, London, UK
| | - P A Costeas
- The Center for the Study of Hematological Malignancies, Nicosia, Cyprus
| | - G S Vassiliou
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.,The Center for the Study of Hematological Malignancies, Nicosia, Cyprus.,Cambridge Blood and Stem Cell Biobank and Cancer Molecular Diagnosis Laboratory, Cambridge Biomedical Research Centre, Cambridge, UK
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30
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Hoehn KB, Gall A, Bashford-Rogers R, Fidler SJ, Kaye S, Weber JN, McClure MO, Kellam P, Pybus OG. Dynamics of immunoglobulin sequence diversity in HIV-1 infected individuals. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0241. [PMID: 26194755 PMCID: PMC4528418 DOI: 10.1098/rstb.2014.0241] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Advances in immunoglobulin (Ig) sequencing technology are leading to new perspectives on immune system dynamics. Much research in this nascent field has focused on resolving immune responses to viral infection. However, the dynamics of B-cell diversity in early HIV infection, and in response to anti-retroviral therapy, are still poorly understood. Here, we investigate these dynamics through bulk Ig sequencing of samples collected over 2 years from a group of eight HIV-1 infected patients, five of whom received anti-retroviral therapy during the first half of the study period. We applied previously published methods for visualizing and quantifying B-cell sequence diversity, including the Gini index, and compared their efficacy to alternative measures. While we found significantly greater clonal structure in HIV-infected patients versus healthy controls, within HIV patients, we observed no significant relationships between statistics of B-cell clonal expansion and clinical variables such as viral load and CD4+ count. Although there are many potential explanations for this, we suggest that important factors include poor sampling resolution and complex B-cell dynamics that are difficult to summarize using simple summary statistics. Importantly, we find a significant association between observed Gini indices and sequencing read depth, and we conclude that more robust analytical methods and a closer integration of experimental and theoretical work is needed to further our understanding of B-cell repertoire diversity during viral infection.
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Affiliation(s)
| | - Astrid Gall
- Wellcome Trust Sanger Institute, Cambridge, UK
| | - Rachael Bashford-Rogers
- Wellcome Trust Sanger Institute, Cambridge, UK Cambridge Institute of Medical Research, University of Cambridge, Cambridge, UK
| | - S J Fidler
- Faculty of Medicine, Imperial College, London, UK
| | - S Kaye
- Faculty of Medicine, Imperial College, London, UK
| | - J N Weber
- Faculty of Medicine, Imperial College, London, UK
| | - M O McClure
- Faculty of Medicine, Imperial College, London, UK
| | | | - Paul Kellam
- Wellcome Trust Sanger Institute, Cambridge, UK MRC/UCL Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, London, UK
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31
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Rhesus Macaque B-Cell Responses to an HIV-1 Trimer Vaccine Revealed by Unbiased Longitudinal Repertoire Analysis. mBio 2015; 6:e01375-15. [PMID: 26530382 PMCID: PMC4631801 DOI: 10.1128/mbio.01375-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Next-generation sequencing (NGS) has been used to investigate the diversity and maturation of broadly neutralizing antibodies (bNAbs) in HIV-1-infected individuals. However, the application of NGS to the preclinical assessment of human vaccines, particularly the monitoring of vaccine-induced B-cell responses in a nonhuman primate (NHP) model, has not been reported. Here, we present a longitudinal NGS analysis of memory B-cell responses to an HIV-1 trimer vaccine in a macaque that has been extensively studied by single B-cell sorting and antibody characterization. We first established an NHP antibodyomics pipeline using the available 454 pyrosequencing data from this macaque and developed a protocol to sequence the NHP antibody repertoire in an unbiased manner. Using these methods, we then analyzed memory B-cell repertoires at four time points of NHP immunization and traced the lineages of seven CD4-binding site (CD4bs)-directed monoclonal antibodies previously isolated from this macaque. Longitudinal analysis revealed distinct patterns of B-cell lineage development in response to an HIV-1 trimer vaccine. While the temporal B-cell repertoire profiles and lineage patterns provide a baseline for comparison with forthcoming HIV-1 trimer vaccines, the newly developed NHP antibody NGS technologies and antibodyomics tools will facilitate future evaluation of human vaccine candidates. The nonhuman primate model has been widely used in the preclinical assessment of human vaccines. Next-generation sequencing of B-cell repertoires provides a quantitative tool to analyze B-cell responses to a vaccine. In this study, the longitudinal B-cell repertoire analysis of a rhesus macaque immunized with an HIV-1 trimer vaccine revealed complex B-cell lineage patterns and showed the potential to facilitate the evaluation of future HIV-1 vaccines. The repertoire sequencing technologies and antibodyomics methods reported here can be extended to vaccine development for other human pathogens utilizing the nonhuman primate model.
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32
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Bioinformatic and Statistical Analysis of Adaptive Immune Repertoires. Trends Immunol 2015; 36:738-749. [DOI: 10.1016/j.it.2015.09.006] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 09/15/2015] [Accepted: 09/15/2015] [Indexed: 01/16/2023]
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33
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Galson JD, Trück J, Fowler A, Münz M, Cerundolo V, Pollard AJ, Lunter G, Kelly DF. In-Depth Assessment of Within-Individual and Inter-Individual Variation in the B Cell Receptor Repertoire. Front Immunol 2015; 6:531. [PMID: 26528292 PMCID: PMC4601265 DOI: 10.3389/fimmu.2015.00531] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/28/2015] [Indexed: 11/24/2022] Open
Abstract
High-throughput sequencing of the B cell receptor (BCR) repertoire can provide rapid characterization of the B cell response in a wide variety of applications in health, after vaccination and in infectious, inflammatory and immune-driven disease, and is starting to yield clinical applications. However, the interpretation of repertoire data is compromised by a lack of studies to assess the intra and inter-individual variation in the BCR repertoire over time in healthy individuals. We applied a standardized isotype-specific BCR repertoire deep sequencing protocol to a single highly sampled participant, and then evaluated the method in 9 further participants to comprehensively describe such variation. We assessed total repertoire metrics of mutation, diversity, VJ gene usage and isotype subclass usage as well as tracking specific BCR sequence clusters. There was good assay reproducibility (both in PCR amplification and biological replicates), but we detected striking fluctuations in the repertoire over time that we hypothesize may be due to subclinical immune activation. Repertoire properties were unique for each individual, which could partly be explained by a decrease in IgG2 with age, and genetic differences at the immunoglobulin locus. There was a small repertoire of public clusters (0.5, 0.3, and 1.4% of total IgA, IgG, and IgM clusters, respectively), which was enriched for expanded clusters containing sequences with suspected specificity toward antigens that should have been historically encountered by all participants through prior immunization or infection. We thus provide baseline BCR repertoire information that can be used to inform future study design, and aid in interpretation of results from these studies. Furthermore, our results indicate that BCR repertoire studies could be used to track changes in the public repertoire in and between populations that might relate to population immunity against infectious diseases, and identify the characteristics of inflammatory and immunological diseases.
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Affiliation(s)
- Jacob D. Galson
- Oxford Vaccine Group, Department of Paediatrics, The NIHR Oxford Biomedical Research Center, University of Oxford, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Johannes Trück
- Oxford Vaccine Group, Department of Paediatrics, The NIHR Oxford Biomedical Research Center, University of Oxford, Oxford, UK
- Paediatric Immunology, University Children’s Hospital, Zürich, Switzerland
| | - Anna Fowler
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Márton Münz
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Vincenzo Cerundolo
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Andrew J. Pollard
- Oxford Vaccine Group, Department of Paediatrics, The NIHR Oxford Biomedical Research Center, University of Oxford, Oxford, UK
| | - Gerton Lunter
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Dominic F. Kelly
- Oxford Vaccine Group, Department of Paediatrics, The NIHR Oxford Biomedical Research Center, University of Oxford, Oxford, UK
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34
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Thapa DR, Tonikian R, Sun C, Liu M, Dearth A, Petri M, Pepin F, Emerson RO, Ranger A. Longitudinal analysis of peripheral blood T cell receptor diversity in patients with systemic lupus erythematosus by next-generation sequencing. Arthritis Res Ther 2015; 17:132. [PMID: 26001779 PMCID: PMC4458014 DOI: 10.1186/s13075-015-0655-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 05/14/2015] [Indexed: 11/10/2022] Open
Abstract
INTRODUCTION T cells play an important role in the pathogenesis of systemic lupus erythematosus (SLE). Clonal expansion of T cells correlating with disease activity has been observed in peripheral blood (PB) of SLE subjects. Recently, next-generation sequencing (NGS) of the T cell receptor (TCR) β loci has emerged as a sensitive way to measure the T cell repertoire. In this study, we utilized NGS to assess whether changes in T cell repertoire diversity in PB of SLE patients correlate with or predict changes in disease activity. METHODS Total RNA was isolated from the PB of 11 SLE patients. Each subject had three samples, collected at periods of clinical quiescence and at a flare. Twelve age-matched healthy controls (HC) were used for reference. NGS was used to profile the complementarity-determining region 3 (CDR3) of the rearranged TCR β loci. RESULTS Relative to the HC, SLE patients (at quiescence) demonstrated a 2.2-fold reduction in repertoire diversity in a given PB volume (P <0.0002), a more uneven distribution of the repertoire (Gini coefficient, HC vs SLE, P = 0.015), and a trend toward increased percentage of expanded clones in the repertoire (clone size >1.0%, HC vs SLE, P = 0.078). No significant correlation between the overall repertoire diversity and clinical disease activity was observed for most SLE patients with only two of eleven SLE patients showing a decreasing trend in repertoire diversity approaching the flare time point. We did not observe any overlap of CDR3 amino acid sequences or a preferential Vβ or Jβ gene usage among the top 100 expanded clones from all SLE patients. In both HC and SLE, the majority of the expanded clones were remarkably stable over time (HC = 5.5 ±0.5 months, SLE = 7.2 ±2.4 months). CONCLUSIONS A significant decrease in T cell repertoire diversity was observed in PB of SLE patients compared to HC. However, in most SLE patients, repertoire diversity did not change significantly with increases in disease activity to a flare. Thus, without a priori knowledge of disease-specific clones, monitoring TCR repertoire in PB from SLE patients is not likely to be useful to predict changes in disease activity.
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Affiliation(s)
| | - Raffi Tonikian
- Biogen, 250 Binney Street, Cambridge, MA, 02142, USA. .,Novartis Pharmaceuticals Canada Inc, 385 Bouchard Boulevard, Dorval, QC, H9S 1A9, Canada.
| | - Chao Sun
- Biogen, 250 Binney Street, Cambridge, MA, 02142, USA.
| | - Mei Liu
- Biogen, 250 Binney Street, Cambridge, MA, 02142, USA.
| | - Andrea Dearth
- Biogen, 250 Binney Street, Cambridge, MA, 02142, USA.
| | - Michelle Petri
- Johns Hopkins University School of Medicine, 1830 East Monument Street, Baltimore, MD, 21205, USA.
| | - Francois Pepin
- Adaptive Biotechnologies, 1551 Eastlake Avenue East, Seattle, WA, 98102, USA.
| | - Ryan O Emerson
- Adaptive Biotechnologies, 1551 Eastlake Avenue East, Seattle, WA, 98102, USA.
| | - Ann Ranger
- Biogen, 250 Binney Street, Cambridge, MA, 02142, USA.
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35
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Colman RE, Schupp JM, Hicks ND, Smith DE, Buchhagen JL, Valafar F, Crudu V, Romancenco E, Noroc E, Jackson L, Catanzaro DG, Rodwell TC, Catanzaro A, Keim P, Engelthaler DM. Detection of Low-Level Mixed-Population Drug Resistance in Mycobacterium tuberculosis Using High Fidelity Amplicon Sequencing. PLoS One 2015; 10:e0126626. [PMID: 25970423 PMCID: PMC4430321 DOI: 10.1371/journal.pone.0126626] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 04/03/2015] [Indexed: 12/20/2022] Open
Abstract
Undetected and untreated, low-levels of drug resistant (DR) subpopulations in clinical Mycobacterium tuberculosis (Mtb) infections may lead to development of DR-tuberculosis, potentially resulting in treatment failure. Current phenotypic DR susceptibility testing has a theoretical potential for 1% sensitivity, is not quantitative, and requires several weeks to complete. The use of "single molecule-overlapping reads" (SMOR) analysis with next generation DNA sequencing for determination of ultra-rare target alleles in complex mixtures provides increased sensitivity over standard DNA sequencing. Ligation free amplicon sequencing with SMOR analysis enables the detection of resistant allele subpopulations at ≥0.1% of the total Mtb population in near real-time analysis. We describe the method using standardized mixtures of DNA from resistant and susceptible Mtb isolates and the assay's performance for detecting ultra-rare DR subpopulations in DNA extracted directly from clinical sputum samples. SMOR analysis enables rapid near real-time detection and tracking of previously undetectable DR sub-populations in clinical samples allowing for the evaluation of the clinical relevance of low-level DR subpopulations. This will provide insights into interventions aimed at suppressing minor DR subpopulations before they become clinically significant.
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MESH Headings
- Antitubercular Agents/pharmacology
- Antitubercular Agents/therapeutic use
- DNA, Bacterial/genetics
- DNA, Bacterial/isolation & purification
- Drug Resistance, Multiple, Bacterial/genetics
- Gene Frequency
- Genetic Loci
- High-Throughput Nucleotide Sequencing
- Humans
- Microbial Sensitivity Tests
- Molecular Diagnostic Techniques
- Mycobacterium tuberculosis/genetics
- Polymorphism, Single Nucleotide
- Sequence Analysis, DNA
- Sputum/microbiology
- Tuberculosis, Multidrug-Resistant/diagnosis
- Tuberculosis, Multidrug-Resistant/drug therapy
- Tuberculosis, Multidrug-Resistant/microbiology
- Tuberculosis, Pulmonary/diagnosis
- Tuberculosis, Pulmonary/drug therapy
- Tuberculosis, Pulmonary/microbiology
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Affiliation(s)
- Rebecca E. Colman
- Translational Genomics Research Institute, Flagstaff, AZ, United States of America
| | - James M. Schupp
- Translational Genomics Research Institute, Flagstaff, AZ, United States of America
| | - Nathan D. Hicks
- Translational Genomics Research Institute, Flagstaff, AZ, United States of America
| | - David E. Smith
- Translational Genomics Research Institute, Flagstaff, AZ, United States of America
| | - Jordan L. Buchhagen
- Translational Genomics Research Institute, Flagstaff, AZ, United States of America
| | - Faramarz Valafar
- San Diego State University, San Diego, CA, United States of America
| | - Valeriu Crudu
- Phthisiopneumology Institute (PPI), Chisinau, Republic of Moldova
| | - Elena Romancenco
- University of California San Diego, San Diego, CA, United States of America
| | - Ecaterina Noroc
- Phthisiopneumology Institute (PPI), Chisinau, Republic of Moldova
| | - Lynn Jackson
- University of California San Diego, San Diego, CA, United States of America
| | - Donald G. Catanzaro
- University of Arkansas College of Education and Health Professions, Fayetteville, AR, United States of America
| | - Timothy C. Rodwell
- University of California San Diego, San Diego, CA, United States of America
| | - Antonino Catanzaro
- University of California San Diego, San Diego, CA, United States of America
| | - Paul Keim
- Translational Genomics Research Institute, Flagstaff, AZ, United States of America
- Center for Microbial Genetics & Genomics, Northern Arizona University, Flagstaff, AZ, United States of America
| | - David M. Engelthaler
- Translational Genomics Research Institute, Flagstaff, AZ, United States of America
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Castiblanco J, Anaya JM. Genetics and vaccines in the era of personalized medicine. Curr Genomics 2015; 16:47-59. [PMID: 25937813 PMCID: PMC4412964 DOI: 10.2174/1389202916666141223220551] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 12/22/2014] [Accepted: 12/23/2014] [Indexed: 12/17/2022] Open
Abstract
Vaccines represent the most successful and sustainable tactic to prevent and counteract infection. A vaccine generally improves immunity to a particular disease upon administration by inducing specific protective and efficient immune responses in all of the receiving population. The main known factors influencing the observed heterogeneity for immune re-sponses induced by vaccines are gender, age, co-morbidity, immune system, and genetic background. This review is mainly focused on the genetic status effect to vaccine immune responses and how this could contribute to the development of novel vaccine candidates that could be better directed and predicted relative to the genetic history of an individual and/or population. The text offers a brief history of vaccinology as a field, a description of the genetic status of the most relevant and studied genes and their functionality and correlation with exposure to specific vaccines; followed by an inside look into autoimmunity as a concern when designing vaccines as well as perspectives and conclusions looking towards an era of personalized and predictive vaccinology instead of a one size fits all approach.
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Affiliation(s)
- John Castiblanco
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Carrera 24 #63-C-69, Bogota, Colombia ; Doctoral Program in Biomedical Sciences, Universidad del Rosario, Bogotá,Colombia
| | - Juan-Manuel Anaya
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Carrera 24 #63-C-69, Bogota, Colombia
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Greiff V, Menzel U, Haessler U, Cook SC, Friedensohn S, Khan TA, Pogson M, Hellmann I, Reddy ST. Quantitative assessment of the robustness of next-generation sequencing of antibody variable gene repertoires from immunized mice. BMC Immunol 2014; 15:40. [PMID: 25318652 PMCID: PMC4233042 DOI: 10.1186/s12865-014-0040-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 09/15/2014] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) of antibody variable regions has emerged as a powerful tool in systems immunology by providing quantitative molecular information on polyclonal humoral immune responses. Reproducible and robust information on antibody repertoires is valuable for basic and applied immunology studies: thus, it is essential to establish the reliability of antibody NGS data. RESULTS We isolated RNA from antibody-secreting cells (ASCs) from either 1 mouse or a pool of 9 immunized mice in order to simulate both normal and high diversity populations. Next, we prepared three technical replicates of antibody libraries by RT-PCR from each diversity scenario, which were sequenced using the Illumina MiSeq platform resulting in >106 250 bp paired-end reads per replicate. We then assessed the robustness of antibody repertoire data based on clonal identification defined by amino acid sequence of either full-length VDJ region or the complementarity determining region 3 (CDR3). Leveraging modeling approaches adapted from mathematical ecology, we found that in either diversity scenario both CDR3 and VDJ detection nears completeness indicating deep coverage of ASC repertoires. Additionally, we defined reliability thresholds for accurate quantification and ranking of CDR3s and VDJs. Importantly, we show that both factors-(i) replicate sequencing and (ii) sequencing depth-are crucial for robust CDR3 and VDJ detection and ranking. CONCLUSIONS In summary, we established widely applicable experimental and computational guidelines for robust antibody NGS and analysis, which will help advance systems immunology studies related to the quantitative profiling of antibody responses following infection and vaccination.
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Affiliation(s)
- Victor Greiff
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Ulrike Menzel
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Ulrike Haessler
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Skylar C Cook
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Simon Friedensohn
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Tarik A Khan
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Mark Pogson
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Ina Hellmann
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
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