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Lê Quý K, Chernigovskaya M, Stensland M, Singh S, Leem J, Revale S, Yadin DA, Nice FL, Povall C, Minns DH, Galson JD, Nyman TA, Snapkow I, Greiff V. Benchmarking and integrating human B-cell receptor genomic and antibody proteomic profiling. NPJ Syst Biol Appl 2024; 10:73. [PMID: 38997321 PMCID: PMC11245537 DOI: 10.1038/s41540-024-00402-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 07/01/2024] [Indexed: 07/14/2024] Open
Abstract
Immunoglobulins (Ig), which exist either as B-cell receptors (BCR) on the surface of B cells or as antibodies when secreted, play a key role in the recognition and response to antigenic threats. The capability to jointly characterize the BCR and antibody repertoire is crucial for understanding human adaptive immunity. From peripheral blood, bulk BCR sequencing (bulkBCR-seq) currently provides the highest sampling depth, single-cell BCR sequencing (scBCR-seq) allows for paired chain characterization, and antibody peptide sequencing by tandem mass spectrometry (Ab-seq) provides information on the composition of secreted antibodies in the serum. Yet, it has not been benchmarked to what extent the datasets generated by these three technologies overlap and complement each other. To address this question, we isolated peripheral blood B cells from healthy human donors and sequenced BCRs at bulk and single-cell levels, in addition to utilizing publicly available sequencing data. Integrated analysis was performed on these datasets, resolved by replicates and across individuals. Simultaneously, serum antibodies were isolated, digested with multiple proteases, and analyzed with Ab-seq. Systems immunology analysis showed high concordance in repertoire features between bulk and scBCR-seq within individuals, especially when replicates were utilized. In addition, Ab-seq identified clonotype-specific peptides using both bulk and scBCR-seq library references, demonstrating the feasibility of combining scBCR-seq and Ab-seq for reconstructing paired-chain Ig sequences from the serum antibody repertoire. Collectively, our work serves as a proof-of-principle for combining bulk sequencing, single-cell sequencing, and mass spectrometry as complementary methods towards capturing humoral immunity in its entirety.
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Grants
- The Leona M. and Harry B. Helmsley Charitable Trust (#2019PG-T1D011, to VG), UiO World-Leading Research Community (to VG), UiO: LifeScience Convergence Environment Immunolingo (to VG), EU Horizon 2020 iReceptorplus (#825821) (to VG), a Norwegian Cancer Society Grant (#215817, to VG), Research Council of Norway projects (#300740, (#311341, #331890 to VG), a Research Council of Norway IKTPLUSS project (#311341, to VG). This project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement No 101007799 (Inno4Vac). This Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation programme and EFPIA (to VG).
- Mass spectrometry-based proteomic analyses were performed by the Proteomics Core Facility, Department of Immunology, University of Oslo/Oslo University Hospital, which is supported by the Core Facilities program of the South-Eastern Norway Regional Health Authority. This core facility is also a member of the National Network of Advanced Proteomics Infrastructure (NAPI), which is funded by the Research Council of Norway INFRASTRUKTUR-program (project number: 295910).
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Affiliation(s)
- Khang Lê Quý
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Maria Chernigovskaya
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Maria Stensland
- Proteomics Core Facility, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Sachin Singh
- Proteomics Core Facility, University of Oslo and Oslo University Hospital, Oslo, Norway
| | | | | | | | | | | | | | | | - Tuula A Nyman
- Proteomics Core Facility, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Igor Snapkow
- Department of Chemical Toxicology, Norwegian Institute of Public Health, Oslo, Norway
| | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway.
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2
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Ramirez Valdez K, Nzau B, Dorey-Robinson D, Jarman M, Nyagwange J, Schwartz JC, Freimanis G, Steyn AW, Warimwe GM, Morrison LJ, Mwangi W, Charleston B, Bonnet-Di Placido M, Hammond JA. A Customizable Suite of Methods to Sequence and Annotate Cattle Antibodies. Vaccines (Basel) 2023; 11:1099. [PMID: 37376488 PMCID: PMC10302312 DOI: 10.3390/vaccines11061099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/07/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Studying the antibody response to infection or vaccination is essential for developing more effective vaccines and therapeutics. Advances in high-throughput antibody sequencing technologies and immunoinformatic tools now allow the fast and comprehensive analysis of antibody repertoires at high resolution in any species. Here, we detail a flexible and customizable suite of methods from flow cytometry, single cell sorting, heavy and light chain amplification to antibody sequencing in cattle. These methods were used successfully, including adaptation to the 10x Genomics platform, to isolate native heavy-light chain pairs. When combined with the Ig-Sequence Multi-Species Annotation Tool, this suite represents a powerful toolkit for studying the cattle antibody response with high resolution and precision. Using three workflows, we processed 84, 96, and 8313 cattle B cells from which we sequenced 24, 31, and 4756 antibody heavy-light chain pairs, respectively. Each method has strengths and limitations in terms of the throughput, timeline, specialist equipment, and cost that are each discussed. Moreover, the principles outlined here can be applied to study antibody responses in other mammalian species.
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Affiliation(s)
| | - Benjamin Nzau
- The Pirbright Institute, Pirbright GU24 0NF, UK
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
| | | | | | - James Nyagwange
- The Pirbright Institute, Pirbright GU24 0NF, UK
- KEMRI-Wellcome Trust Research Programme CGMRC, Kilifi P.O. Box 230-80108, Kenya
| | | | | | | | - George M Warimwe
- KEMRI-Wellcome Trust Research Programme CGMRC, Kilifi P.O. Box 230-80108, Kenya
| | - Liam J Morrison
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
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3
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Cohn H, Bloom N, Cai G, Clark J, Tarke A, Bermúdez-González MC, Altman D, Lugo LA, Lobo FP, Marquez S, Chen JQ, Ren W, Qin L, Crotty S, Krammer F, Grifoni A, Sette A, Simon V, Coelho CH. Mpox vaccine and infection-driven human immune signatures. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.07.23286701. [PMID: 36945651 PMCID: PMC10029032 DOI: 10.1101/2023.03.07.23286701] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Background Mpox (formerly known as monkeypox) outbreaks outside endemic areas peaked in July 2022, infecting > 85,000 people and raising concerns about our preparedness against this emerging viral pathogen. Licensed and approved for mpox, the JYNNEOS vaccine has fewer side effects than previous smallpox vaccines and demonstrated efficacy against mpox infection in humans. Comparing JYNNEOS vaccine- and mpox-induced immunity is imperative to evaluate JYNNEOS' immunogenicity and inform vaccine administration and design. Methods We examined the polyclonal serum (ELISA) and single B cell (heavy chain gene and transcriptome data) antibody repertoires and T cells (AIM and ICS assays) induced by the JYNNEOS vaccine as well as mpox infection. Findings Gene-level plasmablast and antibody responses were negligible and JYNNEOS vaccinee sera displayed minimal binding to recombinant mpox proteins and native proteins from the 2022 outbreak strain. In contrast, recent mpox infection (within 20-102 days) induced robust serum antibody responses to A29L, A35R, A33R, B18R, and A30L, and to native mpox proteins, compared to vaccinees. JYNNEOS vaccine recipients presented comparable CD4 and CD8 T cell responses against orthopox peptides to those observed after mpox infection. Interpretation JYNNEOS immunization does not elicit a robust B cell response, and its immunogenicity may be mediated by T cells. Funding Research reported in this publication was supported, in part, by the National Cancer Institute of the National Institutes of Health under Award Number U54CA267776, U19AI168631(VS), as well as institutional funds from the Icahn School of Medicine.
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4
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Pennell M, Rodriguez OL, Watson CT, Greiff V. The evolutionary and functional significance of germline immunoglobulin gene variation. Trends Immunol 2023; 44:7-21. [PMID: 36470826 DOI: 10.1016/j.it.2022.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 11/07/2022] [Indexed: 12/04/2022]
Abstract
The recombination between immunoglobulin (IG) gene segments determines an individual's naïve antibody repertoire and, consequently, (auto)antigen recognition. Emerging evidence suggests that mammalian IG germline variation impacts humoral immune responses associated with vaccination, infection, and autoimmunity - from the molecular level of epitope specificity, up to profound changes in the architecture of antibody repertoires. These links between IG germline variants and immunophenotype raise the question on the evolutionary causes and consequences of diversity within IG loci. We discuss why the extreme diversity in IG loci remains a mystery, why resolving this is important for the design of more effective vaccines and therapeutics, and how recent evidence from multiple lines of inquiry may help us do so.
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Affiliation(s)
- Matt Pennell
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA; Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
| | - Oscar L Rodriguez
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway.
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5
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The major role of junctional diversity in the horse antibody repertoire. Mol Immunol 2022; 151:231-241. [PMID: 36179605 DOI: 10.1016/j.molimm.2022.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 11/20/2022]
Abstract
The antibody repertoire (Rep-seq) sequencing revolutionized the diversity of antigen B cell receptor studies, allowing deep and quantitative analysis to decipher the role of adaptive immunity in health and disease. Particularly, horse (Equus caballus) polyclonal antibodies have been produced and used since the century XIX to treat and prophylaxis diphtheria, tuberculosis, tetanus, pneumonia, and, more recently, COVID-19. However, our knowledge about the horse B cell receptors repertories is minimal. We present a deep horse antibody heavy chain repertoire (IGH) characterization of non-infected horses using NGS (Next generation sequencing). This study obtained a mean of 248,169 unique IgM clones and 66,141 unique IgG clones from four domestic adult horses. Rarefaction analysis showed sequence coverage was between 52 % and 82 % in IgM and IgG isotypes. We observed that besides horses antibody can use all functional IGHV genes, around 80 % of their antibodies use only three IGHV gene segments, and around 55 % use only one IGHJ gene segment. This limited VJ diversity seems to be compensated by the junctional diversity of these antibodies. We observed that the junctional diversity in horse antibodies is widespread, present in more than 90 % of horse antibodies. Besides this, the length of this region seems to be higher in horse antibodies than in other species. N1 and N2 nucleotides addition range from 0 to 111 nucleotides. In addition, around 45 % of the antibody clones have more than ten nucleotides in both the N1 and N2 junction regions. This diversity mechanism may be one of the most important in providing variability to the equine antibody repertoire. This study provides new insights regarding horse antibody composition, diversity generation, and particularities compared to other species, such as the frequency and length of N nucleotide addition. This study also points out the urgent need to better characterize TdT in horses and other species to better understand antibody repertoire characteristics.
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6
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Rosenfeld R, Alcalay R, Zvi A, Ben-David A, Noy-Porat T, Chitlaru T, Epstein E, Israeli O, Lazar S, Caspi N, Barnea A, Dor E, Chomsky I, Pitel S, Makdasi E, Zichel R, Mazor O. Centaur antibodies: Engineered chimeric equine-human recombinant antibodies. Front Immunol 2022; 13:942317. [PMID: 36059507 PMCID: PMC9437483 DOI: 10.3389/fimmu.2022.942317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/28/2022] [Indexed: 11/27/2022] Open
Abstract
Hyper-immune antisera from large mammals, in particular horses, are routinely used for life-saving anti-intoxication intervention. While highly efficient, the use of these immunotherapeutics is complicated by possible recipient reactogenicity and limited availability. Accordingly, there is an urgent need for alternative improved next-generation immunotherapies to respond to this issue of high public health priority. Here, we document the development of previously unavailable tools for equine antibody engineering. A novel primer set, EquPD v2020, based on equine V-gene data, was designed for efficient and accurate amplification of rearranged horse antibody V-segments. The primer set served for generation of immune phage display libraries, representing highly diverse V-gene repertoires of horses immunized against botulinum A or B neurotoxins. Highly specific scFv clones were selected and expressed as full-length antibodies, carrying equine V-genes and human Gamma1/Lambda constant genes, to be referred as “Centaur antibodies”. Preliminary assessment in a murine model of botulism established their therapeutic potential. The experimental approach detailed in the current report, represents a valuable tool for isolation and engineering of therapeutic equine antibodies.
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Affiliation(s)
- Ronit Rosenfeld
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
- *Correspondence: Ronit Rosenfeld, ; Ohad Mazor,
| | - Ron Alcalay
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Anat Zvi
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Alon Ben-David
- Department of Biotechnology, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Tal Noy-Porat
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Theodor Chitlaru
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Eyal Epstein
- Department of Biotechnology, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ofir Israeli
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Shirley Lazar
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Noa Caspi
- Veterinary Center for Preclinical Research, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ada Barnea
- Department of Biotechnology, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Eyal Dor
- Department of Biotechnology, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Inbar Chomsky
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Shani Pitel
- Department of Biotechnology, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Efi Makdasi
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ran Zichel
- Department of Biotechnology, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ohad Mazor
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
- *Correspondence: Ronit Rosenfeld, ; Ohad Mazor,
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7
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O'Connor D. The omics strategy: the use of systems vaccinology to characterise immune responses to childhood immunisation. Expert Rev Vaccines 2022; 21:1205-1214. [PMID: 35786291 DOI: 10.1080/14760584.2022.2093193] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Vaccines have had a transformative impact on child health. Despite this impact the immunological processes involved in protective responses are not entirely understood and vaccine development has been largely empirical. Recent technological advances offer the opportunity to reveal the immunology underlying vaccine response at an unprecedented resolution. These data could revolutionise the way vaccines are developed and tested and further augment their role in securing the health of children around the world. AREAS COVERED Systems level information and the tools are now being deployed by vaccinologists at all stages of the vaccine development pathway; however, this review will specifically describe some of the key findings that have be gleaned from multi-omics datasets collected in the context of childhood immunisation. EXPERT OPINION Despite the success of vaccines there remains hard-to-target pathogens, refractory to current vaccination strategies. Moreover, zoonotic diseases with pandemic potential are a threat to global health, as recently illustrated by COVID-19. Systems vaccinology holds a great deal of promise in revealing a greater understanding of vaccine responses and consequently modernising vaccinology. However, there is a need for future studies -particularly in vulnerable populations that are targets for vaccination programmes - if this potential is to be fulfilled.
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Affiliation(s)
- Daniel O'Connor
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.,NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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8
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Prabhu PR, Carter JJ, Galloway DA. B Cell Responses upon Human Papillomavirus (HPV) Infection and Vaccination. Vaccines (Basel) 2022; 10:vaccines10060837. [PMID: 35746445 PMCID: PMC9229470 DOI: 10.3390/vaccines10060837] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/20/2022] [Accepted: 05/23/2022] [Indexed: 02/01/2023] Open
Abstract
Infection with human papillomavirus (HPV) is the necessary cause of cervical cancer. Availability of vaccines against HPV makes it a highly preventable disease. HPV vaccines act through type-specific neutralizing antibodies produced by antigen-specific plasma cells known as long-lived plasma cells (LLPC). However, just as any other vaccine, success of HPV vaccine is attributed to the immunologic memory that it builds, which is largely attained through generation and maintenance of a class of B cells named memory B cells (Bmem). Both LLPCs and Bmems are important in inducing and maintaining immune memory and it is therefore necessary to understand their role after HPV vaccination to better predict outcomes. This review summarizes current knowledge of B-cell responses following HPV vaccination and natural infection, including molecular signatures associated with these responses.
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9
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Characterization of human IgM and IgG repertoires in individuals with chronic HIV-1 infection. Virol Sin 2022; 37:370-379. [PMID: 35247647 PMCID: PMC9243603 DOI: 10.1016/j.virs.2022.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 02/24/2022] [Indexed: 11/23/2022] Open
Abstract
Advancements in high-throughput sequencing (HTS) of antibody repertoires (Ig-Seq) have unprecedentedly improved our ability to characterize the antibody repertoires on a large scale. However, currently, only a few studies explored the influence of chronic HIV-1 infection on human antibody repertoires and many of them reached contradictory conclusions, possibly limited by inadequate sequencing depth and throughput. To better understand how HIV-1 infection would impact humoral immune system, in this study, we systematically analyzed the differences between the IgM (HIV-IgM) and IgG (HIV-IgG) heavy chain repertoires of HIV-1 infected patients, as well as between antibody repertoires of HIV-1 patients and healthy donors (HH). Notably, the public unique clones accounted for only a negligible proportion between the HIV-IgM and HIV-IgG repertoires libraries, and the diversity of unique clones in HIV-IgG remarkably reduced. In aspect of somatic mutation rates of CDR1 and CDR2, the HIV-IgG repertoire was higher than HIV-IgM. Besides, the average length of CDR3 region in HIV-IgM was significant longer than that in the HH repertoire, presumably caused by the great number of novel VDJ rearrangement patterns, especially a massive use of IGHJ6. Moreover, some of the B cell clonotypes had numerous clones, and somatic variants were detected within the clonotype lineage in HIV-IgG, indicating HIV-1 neutralizing activities. The in-depth characterization of HIV-IgG and HIV-IgM repertoires enriches our knowledge in the profound effect of HIV-1 infection on human antibody repertoires and may have practical value for the discovery of therapeutic antibodies. Ultra-deep sequencing of both IgM and IgG repertoires in chronic HIV-1 infection. VDJ gene rearrangement patterns can be dramatically changed by HIV-1 infection. Multiple mechanisms cause the high complexity of HIV-1-experienced antibodies. Discovery of promising neutralizing HIV-1 antibodies from antibody repertoires.
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10
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Khetan R, Curtis R, Deane CM, Hadsund JT, Kar U, Krawczyk K, Kuroda D, Robinson SA, Sormanni P, Tsumoto K, Warwicker J, Martin ACR. Current advances in biopharmaceutical informatics: guidelines, impact and challenges in the computational developability assessment of antibody therapeutics. MAbs 2022; 14:2020082. [PMID: 35104168 PMCID: PMC8812776 DOI: 10.1080/19420862.2021.2020082] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Therapeutic monoclonal antibodies and their derivatives are key components of clinical pipelines in the global biopharmaceutical industry. The availability of large datasets of antibody sequences, structures, and biophysical properties is increasingly enabling the development of predictive models and computational tools for the "developability assessment" of antibody drug candidates. Here, we provide an overview of the antibody informatics tools applicable to the prediction of developability issues such as stability, aggregation, immunogenicity, and chemical degradation. We further evaluate the opportunities and challenges of using biopharmaceutical informatics for drug discovery and optimization. Finally, we discuss the potential of developability guidelines based on in silico metrics that can be used for the assessment of antibody stability and manufacturability.
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Affiliation(s)
- Rahul Khetan
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Robin Curtis
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | | | | | - Uddipan Kar
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | | | - Daisuke Kuroda
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.,Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, Japan.,Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan
| | | | - Pietro Sormanni
- Chemistry of Health, Yusuf Hamied Department of Chemistry, University of Cambridge
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.,Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, Japan.,Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.,The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Jim Warwicker
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Andrew C R Martin
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
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11
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Akbar R, Bashour H, Rawat P, Robert PA, Smorodina E, Cotet TS, Flem-Karlsen K, Frank R, Mehta BB, Vu MH, Zengin T, Gutierrez-Marcos J, Lund-Johansen F, Andersen JT, Greiff V. Progress and challenges for the machine learning-based design of fit-for-purpose monoclonal antibodies. MAbs 2022; 14:2008790. [PMID: 35293269 PMCID: PMC8928824 DOI: 10.1080/19420862.2021.2008790] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 11/04/2021] [Accepted: 11/17/2021] [Indexed: 12/15/2022] Open
Abstract
Although the therapeutic efficacy and commercial success of monoclonal antibodies (mAbs) are tremendous, the design and discovery of new candidates remain a time and cost-intensive endeavor. In this regard, progress in the generation of data describing antigen binding and developability, computational methodology, and artificial intelligence may pave the way for a new era of in silico on-demand immunotherapeutics design and discovery. Here, we argue that the main necessary machine learning (ML) components for an in silico mAb sequence generator are: understanding of the rules of mAb-antigen binding, capacity to modularly combine mAb design parameters, and algorithms for unconstrained parameter-driven in silico mAb sequence synthesis. We review the current progress toward the realization of these necessary components and discuss the challenges that must be overcome to allow the on-demand ML-based discovery and design of fit-for-purpose mAb therapeutic candidates.
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Affiliation(s)
- Rahmad Akbar
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Habib Bashour
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Puneet Rawat
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - Philippe A. Robert
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Eva Smorodina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russia
| | | | - Karine Flem-Karlsen
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Department of Pharmacology, University of Oslo and Oslo University Hospital, Norway
| | - Robert Frank
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Brij Bhushan Mehta
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Mai Ha Vu
- Department of Linguistics and Scandinavian Studies, University of Oslo, Norway
| | - Talip Zengin
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
- Department of Bioinformatics, Mugla Sitki Kocman University, Turkey
| | | | | | - Jan Terje Andersen
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Department of Pharmacology, University of Oslo and Oslo University Hospital, Norway
| | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
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12
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Wang Q, Zeng H, Zhu Y, Wang M, Zhang Y, Yang X, Tang H, Li H, Chen Y, Ma C, Lan C, Liu B, Yang W, Yu X, Zhang Z. Dual UMIs and Dual Barcodes With Minimal PCR Amplification Removes Artifacts and Acquires Accurate Antibody Repertoire. Front Immunol 2021; 12:778298. [PMID: 35003093 PMCID: PMC8727365 DOI: 10.3389/fimmu.2021.778298] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/25/2021] [Indexed: 12/03/2022] Open
Abstract
Antibody repertoire sequencing (Rep-seq) has been widely used to reveal repertoire dynamics and to interrogate antibodies of interest at single nucleotide-level resolution. However, polymerase chain reaction (PCR) amplification introduces extensive artifacts including chimeras and nucleotide errors, leading to false discovery of antibodies and incorrect assessment of somatic hypermutations (SHMs) which subsequently mislead downstream investigations. Here, a novel approach named DUMPArts, which improves the accuracy of antibody repertoires by labeling each sample with dual barcodes and each molecule with dual unique molecular identifiers (UMIs) via minimal PCR amplification to remove artifacts, is developed. Tested by ultra-deep Rep-seq data, DUMPArts removed inter-sample chimeras, which cause artifactual shared clones and constitute approximately 15% of reads in the library, as well as intra-sample chimeras with erroneous SHMs and constituting approximately 20% of the reads, and corrected base errors and amplification biases by consensus building. The removal of these artifacts will provide an accurate assessment of antibody repertoires and benefit related studies, especially mAb discovery and antibody-guided vaccine design.
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Affiliation(s)
- Qilong Wang
- Center for Precision Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Huikun Zeng
- Center for Precision Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yan Zhu
- Center for Precision Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Minhui Wang
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yanfang Zhang
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xiujia Yang
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Haipei Tang
- Center for Precision Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Hongliang Li
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing, China
| | - Yuan Chen
- Center for Precision Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Cuiyu Ma
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Chunhong Lan
- Center for Precision Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Bin Liu
- School of Computer Science and Technology, Beijing Institute of Technology, Beijing, China
| | - Wei Yang
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- *Correspondence: Wei Yang, ; Xueqing Yu, ; Zhenhai Zhang, ;
| | - Xueqing Yu
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Division of Nephrology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- *Correspondence: Wei Yang, ; Xueqing Yu, ; Zhenhai Zhang, ;
| | - Zhenhai Zhang
- Center for Precision Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou, China
- *Correspondence: Wei Yang, ; Xueqing Yu, ; Zhenhai Zhang, ;
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13
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Long-term efficacy of nasal vaccination against enteric red mouth (ERM) disease and infectious hematopoietic necrosis (IHN) in juvenile rainbow trout (Oncorhynchus mykiss). Vaccine 2021; 40:229-238. [PMID: 34893343 DOI: 10.1016/j.vaccine.2021.11.077] [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: 07/11/2021] [Revised: 11/20/2021] [Accepted: 11/25/2021] [Indexed: 01/19/2023]
Abstract
Previous research demonstrated that bacterial and viral vaccines delivered via the nasal route in rainbow trout (Oncorhynchus mykiss) at 7 and 28 days post-vaccination are highly protective (>95% protection). Long-term protection following nasal vaccination in teleosts has not been evaluated. The goal of this study was to assess efficacy and immune responses at 6 months (mo) post-vaccination (mpv), and long-lasting immune responses at 12 mpv of two different vaccines: an inactivated enteric red mouth disease (ERM) Yersinia ruckeri bacterin and a live attenuated infectious hematopoietic necrosis virus (IHNV) vaccine. Juvenile rainbow trout were vaccinated for Y. ruckeri via intraperitoneal (I.P.) and intranasal (I.N.) routes, and for IHNV by intramuscular (I.M.) and I.N. routes, then challenged at 6 mpv. Immune responses were determined at 6 and 12 mpv. ERM vaccine I.P. delivery elicited significantly higher serum IgM-specific titers that remained elevated compared to mock-vaccinated fish at 6 mpv. By 12 mpv, antibody titers to Y. ruckeri were not significantly different across all treatments. Following Y. ruckeri challenge at 6 mpv, a significant difference in cumulative percent mortality (CPM) was found for I.P.-vaccinated fish but not I.N.-vaccinated fish. I.M. and I.N. vaccination with live attenuated IHNV did not result in significant specific serum IgM titers at 6 or 12 mpv. Yet, I.N.-vaccinated fish showed the lowest CPM 6 mpv indicating long-term protection that does not correlate with systemic IgM responses. Repertoire analyses confirmed unique expansions of VH-JH rearrangements in the spleen of rainbow trout 12 mpv that varied with the type of vaccine and route of vaccination. Combined, these data demonstrate that I.N. vaccination with a live attenuated viral vaccine confers long lasting protection, but I.N. ERM vaccination does not and booster before 6 mpv is recommended.
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14
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Horst A, Smakaj E, Natali EN, Tosoni D, Babrak LM, Meier P, Miho E. Machine Learning Detects Anti-DENV Signatures in Antibody Repertoire Sequences. Front Artif Intell 2021; 4:715462. [PMID: 34708197 PMCID: PMC8542978 DOI: 10.3389/frai.2021.715462] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/30/2021] [Indexed: 11/13/2022] Open
Abstract
Dengue infection is a global threat. As of today, there is no universal dengue fever treatment or vaccines unreservedly recommended by the World Health Organization. The investigation of the specific immune response to dengue virus would support antibody discovery as therapeutics for passive immunization and vaccine design. High-throughput sequencing enables the identification of the multitude of antibodies elicited in response to dengue infection at the sequence level. Artificial intelligence can mine the complex data generated and has the potential to uncover patterns in entire antibody repertoires and detect signatures distinctive of single virus-binding antibodies. However, these machine learning have not been harnessed to determine the immune response to dengue virus. In order to enable the application of machine learning, we have benchmarked existing methods for encoding biological and chemical knowledge as inputs and have investigated novel encoding techniques. We have applied different machine learning methods such as neural networks, random forests, and support vector machines and have investigated the parameter space to determine best performing algorithms for the detection and prediction of antibody patterns at the repertoire and antibody sequence levels in dengue-infected individuals. Our results show that immune response signatures to dengue are detectable both at the antibody repertoire and at the antibody sequence levels. By combining machine learning with phylogenies and network analysis, we generated novel sequences that present dengue-binding specific signatures. These results might aid further antibody discovery and support vaccine design.
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Affiliation(s)
- Alexander Horst
- School of Life Sciences, Institute of Medical Engineering and Medical Informatics, University of Applied Sciences and Arts Northwestern Switzerland FHNW, Muttenz, Switzerland
| | - Erand Smakaj
- School of Life Sciences, Institute of Medical Engineering and Medical Informatics, University of Applied Sciences and Arts Northwestern Switzerland FHNW, Muttenz, Switzerland
| | - Eriberto Noel Natali
- School of Life Sciences, Institute of Medical Engineering and Medical Informatics, University of Applied Sciences and Arts Northwestern Switzerland FHNW, Muttenz, Switzerland
| | - Deniz Tosoni
- School of Life Sciences, Institute of Medical Engineering and Medical Informatics, University of Applied Sciences and Arts Northwestern Switzerland FHNW, Muttenz, Switzerland
| | - Lmar Marie Babrak
- School of Life Sciences, Institute of Medical Engineering and Medical Informatics, University of Applied Sciences and Arts Northwestern Switzerland FHNW, Muttenz, Switzerland
| | - Patrick Meier
- School of Life Sciences, Institute of Medical Engineering and Medical Informatics, University of Applied Sciences and Arts Northwestern Switzerland FHNW, Muttenz, Switzerland
| | - Enkelejda Miho
- School of Life Sciences, Institute of Medical Engineering and Medical Informatics, University of Applied Sciences and Arts Northwestern Switzerland FHNW, Muttenz, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,aiNET GmbH, Basel, Switzerland
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15
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Ghraichy M, von Niederhäusern V, Kovaltsuk A, Galson JD, Deane CM, Trück J. Different B cell subpopulations show distinct patterns in their IgH repertoire metrics. eLife 2021; 10:73111. [PMID: 34661527 PMCID: PMC8560093 DOI: 10.7554/elife.73111] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/17/2021] [Indexed: 12/11/2022] Open
Abstract
Several human B cell subpopulations are recognised in the peripheral blood, which play distinct roles in the humoral immune response. These cells undergo developmental and maturational changes involving VDJ recombination, somatic hypermutation and class switch recombination, altogether shaping their immunoglobulin heavy chain (IgH) repertoire. Here, we sequenced the IgH repertoire of naïve, marginal zone, switched and plasma cells from 10 healthy adults along with matched unsorted and in silico separated CD19+ bulk B cells. Using advanced bioinformatic analysis and machine learning, we show that sorted B cell subpopulations are characterised by distinct repertoire characteristics on both the individual sequence and the repertoire level. Sorted subpopulations shared similar repertoire characteristics with their corresponding in silico separated subsets. Furthermore, certain IgH repertoire characteristics correlated with the position of the constant region on the IgH locus. Overall, this study provides unprecedented insight over mechanisms of B cell repertoire control in peripherally circulating B cell subpopulations.
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Affiliation(s)
- Marie Ghraichy
- Division of Immunology, University Children's Hospital and Children's Research Center, University of Zurich (UZH), Zurich, Switzerland
| | - Valentin von Niederhäusern
- Division of Immunology, University Children's Hospital and Children's Research Center, University of Zurich (UZH), Zurich, Switzerland
| | | | - Jacob D Galson
- Division of Immunology, University Children's Hospital and Children's Research Center, University of Zurich (UZH), Zurich, Switzerland.,Alchemab Therapeutics Ltd, London, United Kingdom
| | - Charlotte M Deane
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Johannes Trück
- Division of Immunology, University Children's Hospital and Children's Research Center, University of Zurich (UZH), Zurich, Switzerland
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16
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Progress and challenges in mass spectrometry-based analysis of antibody repertoires. Trends Biotechnol 2021; 40:463-481. [PMID: 34535228 DOI: 10.1016/j.tibtech.2021.08.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 12/22/2022]
Abstract
Humoral immunity is divided into the cellular B cell and protein-level antibody responses. High-throughput sequencing has advanced our understanding of both these fundamental aspects of B cell immunology as well as aspects pertaining to vaccine and therapeutics biotechnology. Although the protein-level serum and mucosal antibody repertoire make major contributions to humoral protection, the sequence composition and dynamics of antibody repertoires remain underexplored. This limits insight into important immunological and biotechnological parameters such as the number of antigen-specific antibodies, which are for example, relevant for pathogen neutralization, microbiota regulation, severity of autoimmunity, and therapeutic efficacy. High-resolution mass spectrometry (MS) has allowed initial insights into the antibody repertoire. We outline current challenges in MS-based sequence analysis of antibody repertoires and propose strategies for their resolution.
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17
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Van Tilbeurgh M, Lemdani K, Beignon AS, Chapon C, Tchitchek N, Cheraitia L, Marcos Lopez E, Pascal Q, Le Grand R, Maisonnasse P, Manet C. Predictive Markers of Immunogenicity and Efficacy for Human Vaccines. Vaccines (Basel) 2021; 9:579. [PMID: 34205932 PMCID: PMC8226531 DOI: 10.3390/vaccines9060579] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/22/2021] [Accepted: 05/24/2021] [Indexed: 02/07/2023] Open
Abstract
Vaccines represent one of the major advances of modern medicine. Despite the many successes of vaccination, continuous efforts to design new vaccines are needed to fight "old" pandemics, such as tuberculosis and malaria, as well as emerging pathogens, such as Zika virus and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Vaccination aims at reaching sterilizing immunity, however assessing vaccine efficacy is still challenging and underscores the need for a better understanding of immune protective responses. Identifying reliable predictive markers of immunogenicity can help to select and develop promising vaccine candidates during early preclinical studies and can lead to improved, personalized, vaccination strategies. A systems biology approach is increasingly being adopted to address these major challenges using multiple high-dimensional technologies combined with in silico models. Although the goal is to develop predictive models of vaccine efficacy in humans, applying this approach to animal models empowers basic and translational vaccine research. In this review, we provide an overview of vaccine immune signatures in preclinical models, as well as in target human populations. We also discuss high-throughput technologies used to probe vaccine-induced responses, along with data analysis and computational methodologies applied to the predictive modeling of vaccine efficacy.
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Affiliation(s)
- Matthieu Van Tilbeurgh
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
| | - Katia Lemdani
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
| | - Anne-Sophie Beignon
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
| | - Catherine Chapon
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
| | - Nicolas Tchitchek
- Unité de Recherche i3, Inserm UMR-S 959, Bâtiment CERVI, Hôpital de la Pitié-Salpêtrière, 75013 Paris, France;
| | - Lina Cheraitia
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
| | - Ernesto Marcos Lopez
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
| | - Quentin Pascal
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
| | - Roger Le Grand
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
| | - Pauline Maisonnasse
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
| | - Caroline Manet
- Immunology of Viral Infections and Autoimmune Diseases (IMVA), IDMIT Department, Institut de Biologie François-Jacob (IBJF), University Paris-Sud—INSERM U1184, CEA, 92265 Fontenay-Aux-Roses, France; (M.V.T.); (K.L.); (A.-S.B.); (C.C.); (L.C.); (E.M.L.); (Q.P.); (R.L.G.); (P.M.)
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18
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Marrero Diaz de Villegas R, Seki C, Mattion NM, König GA. Functional and in silico Characterization of Neutralizing Interactions Between Antibodies and the Foot-and-Mouth Disease Virus Immunodominant Antigenic Site. Front Vet Sci 2021; 8:554383. [PMID: 34026880 PMCID: PMC8137985 DOI: 10.3389/fvets.2021.554383] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 02/19/2021] [Indexed: 12/04/2022] Open
Abstract
Molecular knowledge of virus–antibody interactions is essential for the development of better vaccines and for a timely assessment of the spread and severity of epidemics. For foot-and-mouth disease virus (FMDV) research, in particular, computational methods for antigen–antibody (Ag–Ab) interaction, and cross-antigenicity characterization and prediction are critical to design engineered vaccines with robust, long-lasting, and wider response against different strains. We integrated existing structural modeling and prediction algorithms to study the surface properties of FMDV Ags and Abs and their interaction. First, we explored four modeling and two Ag–Ab docking methods and implemented a computational pipeline based on a reference Ag–Ab structure for FMDV of serotype C, to be used as a source protocol for the study of unknown interaction pairs of Ag–Ab. Next, we obtained the variable region sequence of two monoclonal IgM and IgG antibodies that recognize and neutralize antigenic site A (AgSA) epitopes from South America serotype A FMDV and developed two peptide ELISAs for their fine epitope mapping. Then, we applied the previous Ag–Ab molecular structure modeling and docking protocol further scored by functional peptide ELISA data. This work highlights a possible different behavior in the immune response of IgG and IgM Ab isotypes. The present method yielded reliable Ab models with differential paratopes and Ag interaction topologies in concordance with their isotype classes. Moreover, it demonstrates the applicability of computational prediction techniques to the interaction phenomena between the FMDV immunodominant AgSA and Abs, and points out their potential utility as a metric for virus-related, massive Ab repertoire analysis or as a starting point for recombinant vaccine design.
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Affiliation(s)
- Ruben Marrero Diaz de Villegas
- Instituto de Agrobiotecnología y Biología Molecular, Instituto Nacional de Tecnología Agropecuaria, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Buenos Aires, Argentina
| | - Cristina Seki
- Centro de Virología Animal, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Universidad Abierta Interamericana, Buenos Aires, Argentina
| | - Nora M Mattion
- Centro de Virología Animal, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Universidad Abierta Interamericana, Buenos Aires, Argentina
| | - Guido A König
- Instituto de Agrobiotecnología y Biología Molecular, Instituto Nacional de Tecnología Agropecuaria, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Buenos Aires, Argentina
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19
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Zhao M, Li X, Xie S, Gong M, Yan R, Zheng A, Xu Y, Wu H, Wang Z. The dynamics and association of B and T cell receptor repertoires upon antibody response to hepatitis B vaccination in healthy adults. Hum Vaccin Immunother 2021; 17:3203-3213. [PMID: 33861159 DOI: 10.1080/21645515.2021.1913028] [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] [Indexed: 12/13/2022] Open
Abstract
The Hepatitis B (HB) vaccine is efficacious in preventing hepatitis B virus infection. However, the association between antibody response to the HB vaccine and dynamic immune repertoire changes in different cell subsets remains unclear. Nine healthy participants were administered three doses of HB vaccine following the 0, 1, 6 month schedule. Peripheral CD4+ T, memory B (MB), naïve B (NB), and plasma cells (PCs) were sorted before vaccination and 7 days following each dose. The complementary determining region 3 of T-cell receptor β (TCRβ) chain and B-cell receptor (BCR) heavy chain (IgG, IgM, IgA) repertoires were analyzed by high-throughput sequencing. All nine participants elicited protective antibody titers to the vaccine at the end of immunization. Compared with the baseline, MB cells showed a significant increase in IgG usage and decreased IgM usage and repertoire diversity at the end of vaccination. TCRβ diversity changes were highly correlated with those of the BCR in MB cells in participants with a faster and robust antibody responses. The percentage of shared clonotypes between NB and MB cells, and MB cells and PCs were much higher than that between NB cells and PCs. The more clonotypes sharing the faster and stronger antibody responses were observed after HB vaccination. These results suggest the integral involvement of MB cells in vaccine immunization. Interaction between CD4+ T and MB cells and B cell differentiation may improve antibody response to HB vaccine.
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Affiliation(s)
- Miaoxian Zhao
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xueying Li
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Shi Xie
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Mingxing Gong
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Rong Yan
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Anqi Zheng
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ying Xu
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hongkai Wu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Zhanhui Wang
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
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20
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Richardson E, Galson JD, Kellam P, Kelly DF, Smith SE, Palser A, Watson S, Deane CM. A computational method for immune repertoire mining that identifies novel binders from different clonotypes, demonstrated by identifying anti-pertussis toxoid antibodies. MAbs 2021; 13:1869406. [PMID: 33427589 PMCID: PMC7808390 DOI: 10.1080/19420862.2020.1869406] [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] [Indexed: 12/19/2022] Open
Abstract
Due to their shared genetic history, antibodies from the same clonotype often bind to the same epitope. This knowledge is used in immune repertoire mining, where known binders are used to search bulk sequencing repertoires to identify new binders. However, current computational methods cannot identify epitope convergence between antibodies from different clonotypes, limiting the sequence diversity of antigen-specific antibodies that can be identified. We describe how the antibody binding site, the paratope, can be used to cluster antibodies with common antigen reactivity from different clonotypes. Our method, paratyping, uses the predicted paratope to identify these novel cross clonotype matches. We experimentally validated our predictions on a pertussis toxoid dataset. Our results show that even the simplest abstraction of the antibody binding site, using only the length of the loops involved and predicted binding residues, is sufficient to group antigen-specific antibodies and provide additional information to conventional clonotype analysis. Abbreviations: BCR: B-cell receptor; CDR: complementarity-determining region; PTx: pertussis toxoid
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Affiliation(s)
- Eve Richardson
- Department of Statistics, University of Oxford , Oxford, UK
| | - Jacob D Galson
- Alchemab Therapeutics Ltd , London, UK.,Division of Immunology, University Children's Hospital, University of Zurich, Zurich , Switzerland
| | - Paul Kellam
- Kymab Ltd , Cambridge, UK.,Department of Infectious Diseases, Faculty of Medicine, Imperial College London , London, UK
| | - Dominic F Kelly
- Department of Paediatrics, University of Oxford , Oxford, UK.,Oxford University Hospitals NHS Foundation Trust , Oxford, UK
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21
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The Importance of Prioritizing Pre and Posttransplant Immunizations in an Era of Vaccine Refusal and Epidemic Outbreaks. Transplantation 2020; 104:33-38. [PMID: 31876696 DOI: 10.1097/tp.0000000000002936] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Vaccine-preventable infections are occurring at epidemic rates both nationally and internationally. At the same time, rates of vaccine hesitancy and refusal are increasing across the country leading to decreased herd immunity. For immunosuppressed transplant recipients, this situation poses great risk. Currently, 1 in 6 pediatric solid organ transplant recipients is hospitalized with a vaccine-preventable infection in the first 5 years posttransplant. For many recipients, these infections result in significant morbidity, mortality, and increased hospitalization costs. Surprisingly, despite this risk many transplant recipients are not up-to-date on age appropriate immunizations at the time of transplant and thereafter. As a transplant community, we must prioritize immunizations in both pre and posttransplant care. Research is needed to understand how to monitor immune response to vaccines in immunosuppressed patients and when to optimally immunize patients posttransplant. Finally, recommendations about administration of live vaccines posttransplant may need to be reevaluated in the setting of measles outbreaks and decreased herd immunity.
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22
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Tu Z, Huang X, Fu J, Hu N, Zheng W, Li Y, Zhang Y. Landscape of variable domain of heavy-chain-only antibody repertoire from alpaca. Immunology 2020; 161:53-65. [PMID: 32506493 DOI: 10.1111/imm.13224] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 01/05/2023] Open
Abstract
Heavy-chain-only antibodies (HCAbs), which are devoid of light chains, have been found naturally occurring in various species including camelids and cartilaginous fish. Because of their high thermostability, refoldability and capacity for cell permeation, the variable regions of the heavy chain of HCAbs (VHHs) have been widely used in diagnosis, bio-imaging, food safety and therapeutics. Most immunogenetic and functional studies of HCAbs are based on case studies or a limited number of low-throughput sequencing data. A complete picture derived from more abundant high-throughput sequencing (HTS) data can help us gain deeper insights. We cloned and sequenced the full-length coding region of VHHs in Alpaca (Vicugna pacos) via HTS in this study. A new pipeline was developed to conduct an in-depth analysis of the HCAb repertoires. Various critical features, including the length distribution of complementarity-determining region 3 (CDR3), V(D)J usage, VJ pairing, germline-specific mutation rate and germline-specific scoring profiles (GSSPs), were systematically characterized. The quantitative data show that V(D)J usage and VHH recombination are highly biased. Interestingly, we found that the average CDR3 length of classical VHHs is longer than that of non-classical ones, whereas the mutation rates are similar in both kinds of VHHs. Finally, GSSPs were built to quantitatively describe and compare sequences that originate from each VJ pair. Overall, this study presents a comprehensive landscape of the HCAb repertoire, which can provide useful guidance for the modeling of somatic hypermutation and the design of novel functional VHHs or VHH repertoires via evolutionary profiles.
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Affiliation(s)
- Zhui Tu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA.,Jiangxi Province Key Laboratory of Modern Analytical Science, Nanchang University, Nanchang, China
| | - Xiaoqiang Huang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Jinheng Fu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China.,Jiangxi-OAI Joint Research Institution, Nanchang University, Nanchang, China
| | - Na Hu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China.,Jiangxi Province Key Laboratory of Modern Analytical Science, Nanchang University, Nanchang, China.,Maternal and Child Medical Research Institute, Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen, China
| | - Wei Zheng
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Yanping Li
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China.,Jiangxi Province Key Laboratory of Modern Analytical Science, Nanchang University, Nanchang, China.,Jiangxi-OAI Joint Research Institution, Nanchang University, Nanchang, China
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
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23
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Marks C, Deane CM. How repertoire data are changing antibody science. J Biol Chem 2020; 295:9823-9837. [PMID: 32409582 DOI: 10.1074/jbc.rev120.010181] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/28/2020] [Indexed: 12/13/2022] Open
Abstract
Antibodies are vital proteins of the immune system that recognize potentially harmful molecules and initiate their removal. Mammals can efficiently create vast numbers of antibodies with different sequences capable of binding to any antigen with high affinity and specificity. Because they can be developed to bind to many disease agents, antibodies can be used as therapeutics. In an organism, after antigen exposure, antibodies specific to that antigen are enriched through clonal selection, expansion, and somatic hypermutation. The antibodies present in an organism therefore report on its immune status, describe its innate ability to deal with harmful substances, and reveal how it has previously responded. Next-generation sequencing technologies are being increasingly used to query the antibody, or B-cell receptor (BCR), sequence repertoire, and the amount of BCR data in public repositories is growing. The Observed Antibody Space database, for example, currently contains over a billion sequences from 68 different studies. Repertoires are available that represent both the naive state (i.e. antigen-inexperienced) and that after immunization. This wealth of data has created opportunities to learn more about our immune system. In this review, we discuss the many ways in which BCR repertoire data have been or could be exploited. We highlight its utility for providing insights into how the naive immune repertoire is generated and how it responds to antigens. We also consider how structural information can be used to enhance these data and may lead to more accurate depictions of the sequence space and to applications in the discovery of new therapeutics.
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Affiliation(s)
- Claire Marks
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Charlotte M Deane
- Department of Statistics, University of Oxford, Oxford, United Kingdom
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24
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Fowler A, Galson JD, Trück J, Kelly DF, Lunter G. Inferring B cell specificity for vaccines using a Bayesian mixture model. BMC Genomics 2020; 21:176. [PMID: 32087698 PMCID: PMC7036227 DOI: 10.1186/s12864-020-6571-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 02/10/2020] [Indexed: 12/30/2022] Open
Abstract
Background Vaccines have greatly reduced the burden of infectious disease, ranking in their impact on global health second only after clean water. Most vaccines confer protection by the production of antibodies with binding affinity for the antigen, which is the main effector function of B cells. This results in short term changes in the B cell receptor (BCR) repertoire when an immune response is launched, and long term changes when immunity is conferred. Analysis of antibodies in serum is usually used to evaluate vaccine response, however this is limited and therefore the investigation of the BCR repertoire provides far more detail for the analysis of vaccine response. Results Here, we introduce a novel Bayesian model to describe the observed distribution of BCR sequences and the pattern of sharing across time and between individuals, with the goal to identify vaccine-specific BCRs. We use data from two studies to assess the model and estimate that we can identify vaccine-specific BCRs with 69% sensitivity. Conclusion Our results demonstrate that statistical modelling can capture patterns associated with vaccine response and identify vaccine specific B cells in a range of different data sets. Additionally, the B cells we identify as vaccine specific show greater levels of sequence similarity than expected, suggesting that there are additional signals of vaccine response, not currently considered, which could improve the identification of vaccine specific B cells.
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Affiliation(s)
- Anna Fowler
- Department of Biostatistics, University of Liverpool, Liverpool, UK.
| | - Jacob D Galson
- University Children's Hospital Zurich and the Children's Research Center, University of Zurich, Zurich, Switzerland
| | - Johannes Trück
- University Children's Hospital Zurich and the Children's Research Center, University of Zurich, Zurich, Switzerland
| | - Dominic F Kelly
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Center, Oxford, UK
| | - Gerton Lunter
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
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25
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Phad GE, Pushparaj P, Tran K, Dubrovskaya V, Àdori M, Martinez-Murillo P, Vázquez Bernat N, Singh S, Dionne G, O’Dell S, Bhullar K, Narang S, Sorini C, Villablanca EJ, Sundling C, Murrell B, Mascola JR, Shapiro L, Pancera M, Martin M, Corcoran M, Wyatt RT, Karlsson Hedestam GB. Extensive dissemination and intraclonal maturation of HIV Env vaccine-induced B cell responses. J Exp Med 2020; 217:e20191155. [PMID: 31704807 PMCID: PMC7041718 DOI: 10.1084/jem.20191155] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/12/2019] [Accepted: 10/03/2019] [Indexed: 12/22/2022] Open
Abstract
Well-ordered HIV-1 envelope glycoprotein (Env) trimers are prioritized for clinical evaluation, and there is a need for an improved understanding about how elicited B cell responses evolve following immunization. To accomplish this, we prime-boosted rhesus macaques with clade C NFL trimers and identified 180 unique Ab lineages from ∼1,000 single-sorted Env-specific memory B cells. We traced all lineages in high-throughput heavy chain (HC) repertoire (Rep-seq) data generated from multiple immune compartments and time points and expressed several as monoclonal Abs (mAbs). Our results revealed broad dissemination and high levels of somatic hypermutation (SHM) of most lineages, including tier 2 virus neutralizing lineages, following boosting. SHM was highest in the Ab complementarity determining regions (CDRs) but also surprisingly high in the framework regions (FRs), especially FR3. Our results demonstrate the capacity of the immune system to affinity-mature large numbers of Env-specific B cell lineages simultaneously, supporting the use of regimens consisting of repeated boosts to improve each Ab, even those belonging to less expanded lineages.
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Affiliation(s)
- Ganesh E. Phad
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Pradeepa Pushparaj
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Karen Tran
- International AIDS Vaccine Initiative, Neutralizing Antibody Center, Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA
| | - Viktoriya Dubrovskaya
- International AIDS Vaccine Initiative, Neutralizing Antibody Center, Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA
| | - Monika Àdori
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Paola Martinez-Murillo
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Néstor Vázquez Bernat
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Suruchi Singh
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Gilman Dionne
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY
| | - Sijy O’Dell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Komal Bhullar
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Sanjana Narang
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Chiara Sorini
- Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Eduardo J. Villablanca
- Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Christopher Sundling
- Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Benjamin Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Lawrence Shapiro
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY
| | - Marie Pancera
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Marcel Martin
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Richard T. Wyatt
- International AIDS Vaccine Initiative, Neutralizing Antibody Center, Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA
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26
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Lanzarotti E, Marcatili P, Nielsen M. T-Cell Receptor Cognate Target Prediction Based on Paired α and β Chain Sequence and Structural CDR Loop Similarities. Front Immunol 2019; 10:2080. [PMID: 31555288 PMCID: PMC6724566 DOI: 10.3389/fimmu.2019.02080] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 08/16/2019] [Indexed: 12/21/2022] Open
Abstract
T-cell receptors (TCR) mediate immune responses recognizing peptides in complex with major histocompatibility complexes (pMHC) displayed on the surface of cells. Resolving the challenge of predicting the cognate pMHC target of a TCR would benefit many applications in the field of immunology, including vaccine design/discovery and the development of immunotherapies. Here, we developed a model for prediction of TCR targets based on similarity to a database of TCRs with known targets. Benchmarking the model on a large set of TCRs with known target, we demonstrated how the predictive performance is increased (i) by focusing on CDRs rather than the full length TCR protein sequences, (ii) by incorporating information from paired α and β chains, and (iii) integrating information for all 6 CDR loops rather than just CDR3. Finally, we show how integration of the structure of CDR loops, as obtained through homology modeling, boosts the predictive power of the model, in particular in situations where no high-similarity TCRs are available for the query. These findings demonstrate that TCRs that bind to the same target also share, to a very high degree, sequence, and structural features. This observation has profound impact for future development of prediction models for TCR-pMHC interactions and for the use of such models for the rational design of T cell based therapies.
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Affiliation(s)
- Esteban Lanzarotti
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Paolo Marcatili
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Morten Nielsen
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina.,Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
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27
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Rettig TA, Nishiyama NC, Pecaut MJ, Chapes SK. Effects of skeletal unloading on the bone marrow antibody repertoire of tetanus toxoid and/or CpG treated C57BL/6J mice. LIFE SCIENCES IN SPACE RESEARCH 2019; 22:16-28. [PMID: 31421845 PMCID: PMC6703179 DOI: 10.1016/j.lssr.2019.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 06/04/2019] [Accepted: 06/13/2019] [Indexed: 06/10/2023]
Abstract
Spaceflight is known to impact the immune system in multiple ways. However, its effect on the antibody repertoire, especially in response to challenge, has not been well characterized. The development of the repertoire has multiple steps that could be affected by spaceflight, including V-(D-)J-gene segment rearrangement and the selection of complementarity determining regions (CDRs); specifically, CDR3, responsible for much of the diversity in the repertoire. We used skeletal unloading with the antiorthostatic suspension (AOS) model to simulate some of the physiological effects associated with spaceflight. Animals ± AOS were challenged with tetanus toxoid (TT) and/or CpG, an adjuvant. Two weeks after challenge, bone marrow was collected and sequenced using the Illumina MiSeq 2 × 300 platform. The resulting antibody repertoire was characterized, including V-, D- (heavy only), and J-gene segment usage, constant region usage, CDR3 length, and V(D)J combinations. We detected changes in gene-segment usage in response to AOS, TT, and CpG treatment in both the heavy and light chains. Additionally, changes were seen in the class-switched VH-gene repertoire. Alterations were also detected in V/J pairing for both the heavy and light chains, and changes in CDR3 length. We also detected lower levels of CDR3 AA overlap than detected in the splenic repertoire. These results demonstrate that AOS, TT, and CpG alter the bone marrow antibody repertoire however, it is still unclear from the data whether there is a loss of host antigen-specific responsiveness because of the change in gene use.
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Affiliation(s)
- Trisha A Rettig
- Division of Biology, Kansas State University, 1711 Claflin Rd, Manhattan, KS, USA; Department of Basic Sciences, Division of Biomedical Engineering Sciences, Loma Linda University, 11175 Campus St, Chan Shun Pavilion, Loma Linda, CA, USA
| | - Nina C Nishiyama
- Department of Basic Sciences, Division of Biomedical Engineering Sciences, Loma Linda University, 11175 Campus St, Chan Shun Pavilion, Loma Linda, CA, USA
| | - Michael J Pecaut
- Department of Basic Sciences, Division of Biomedical Engineering Sciences, Loma Linda University, 11175 Campus St, Chan Shun Pavilion, Loma Linda, CA, USA
| | - Stephen K Chapes
- Division of Biology, Kansas State University, 1711 Claflin Rd, Manhattan, KS, USA.
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28
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Ciabattini A, Olivieri R, Lazzeri E, Medaglini D. Role of the Microbiota in the Modulation of Vaccine Immune Responses. Front Microbiol 2019; 10:1305. [PMID: 31333592 PMCID: PMC6616116 DOI: 10.3389/fmicb.2019.01305] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 05/27/2019] [Indexed: 12/12/2022] Open
Abstract
The human immune system and the microbiota co-evolve, and their balanced relationship is based on crosstalk between the two systems through the course of life. This tight association and the overall composition and richness of the microbiota play an important role in the modulation of host immunity and may impact the immune response to vaccination. The availability of innovative technologies, such as next-generation sequencing (NGS) and correlated bioinformatics tools, allows a deeper investigation of the crosstalk between the microbiota and human immune responses. This review discusses the current knowledge on the influence of the microbiota on the immune response to vaccination and novel tools to deeply analyze the impact of the microbiome on vaccine responses.
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Affiliation(s)
- Annalisa Ciabattini
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Raffaela Olivieri
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Elisa Lazzeri
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Donata Medaglini
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, Siena, Italy
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29
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Profiling the TRB and IGH repertoire of patients with H5N6 Avian Influenza Virus Infection by high-throughput sequencing. Sci Rep 2019; 9:7429. [PMID: 31092835 PMCID: PMC6520366 DOI: 10.1038/s41598-019-43648-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 04/29/2019] [Indexed: 11/16/2022] Open
Abstract
Avian Influenza A (H5N6) Virus causes severe influenza disease in humans and is manifested by acute respiratory distress syndrome, multi-organ failure, and high mortality rates. T cells recognize antigens specifically through a membrane protein T cell receptor (TCR). To ward off a wide variety of pathogens, the human adaptive immune system harbors a vast array of TCRs, which are collectively referred to as the TCR repertoire. The B cell receptor (BCR) is involved in inducing the humoral immune response. The generation of a diverse T cell and B cell repertoire is essential for protection against infection. In this study, multiplex PCR based on genomic DNA amplicons and Illumina high-throughput sequencing (HTS) were applied to study the characteristics and polymorphisms of the TRB and IGH repertoire in the peripheral blood mononuclear cells (PBMCs) from two H5N6 AIV patients and six healthy donors (NC). The CDR3 average length in the AIV group was different from the NC group. The TRBV12-3, TRBV12-4, and TRBV15 gene segments and TRBV30/TRBJ1-2, TRBV12-3/TRBJ1-1 and IGHV3-11/IGHJ6 gene segment pairings also exhibited a higher usage in the PBMCs of AIV donors and may provide more information for generating more effective T/B cell targeted diagnosis/protection strategies.
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30
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Vázquez Bernat N, Corcoran M, Hardt U, Kaduk M, Phad GE, Martin M, Karlsson Hedestam GB. High-Quality Library Preparation for NGS-Based Immunoglobulin Germline Gene Inference and Repertoire Expression Analysis. Front Immunol 2019; 10:660. [PMID: 31024532 PMCID: PMC6459949 DOI: 10.3389/fimmu.2019.00660] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/11/2019] [Indexed: 12/13/2022] Open
Abstract
Next generation sequencing (NGS) of immunoglobulin (Ig) repertoires (Rep-seq) enables examination of the adaptive immune system at an unprecedented level. Applications include studies of expressed repertoires, gene usage, somatic hypermutation levels, Ig lineage tracing and identification of genetic variation within the Ig loci through inference methods. All these applications require starting libraries that allow the generation of sequence data with low error rate and optimal representation of the expressed repertoire. Here, we provide detailed protocols for the production of libraries suitable for human Ig germline gene inference and Ig repertoire studies. Various parameters used in the process were tested in order to demonstrate factors that are critical to obtain high quality libraries. We demonstrate an improved 5'RACE technique that reduces the length constraints of Illumina MiSeq based Rep-seq analysis but allows for the acquisition of sequences upstream of Ig V genes, useful for primer design. We then describe a 5' multiplex method for library preparation, which yields full length V(D)J sequences suitable for genotype identification and novel gene inference. We provide comprehensive sets of primers targeting IGHV, IGKV, and IGLV genes. Using the optimized protocol, we produced IgM, IgG, IgK, and IgL libraries and analyzed them using the germline inference tool IgDiscover to identify expressed germline V alleles. This process additionally uncovered three IGHV, one IGKV, and six IGLV novel alleles in a single individual, which are absent from the IMGT reference database, highlighting the need for further study of Ig genetic variation. The library generation protocols presented here enable a robust means of analyzing expressed Ig repertoires, identifying novel alleles and producing individualized germline gene databases from humans.
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Affiliation(s)
- Néstor Vázquez Bernat
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Uta Hardt
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Division of Rheumatology, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Mateusz Kaduk
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ganesh E. Phad
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Marcel Martin
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
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31
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Taylor SA, Malladi P, Pan X, Wechsler JB, Hulse KE, Perlman H, Whitington PF. Oligoclonal immunoglobulin repertoire in biliary remnants of biliary atresia. Sci Rep 2019; 9:4508. [PMID: 30872727 PMCID: PMC6418100 DOI: 10.1038/s41598-019-41148-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 03/01/2019] [Indexed: 12/13/2022] Open
Abstract
Biliary atresia (BA) is a neonatal cholestatic liver disease that is the leading cause of pediatric liver transplantation, however, the mechanism of disease remains unknown. There are two major forms of BA: isolated BA (iBA) comprises the majority of cases and is thought to result from an aberrant immune response to an environmental trigger, whereas syndromic BA (BASM) has associated malformations and is thought to arise from a congenital insult. To determine whether B cells in BA biliary remnants are antigen driven, we examined the immunoglobulin (Ig) repertoire of diseased tissue from each BA group. Deep sequencing of the Ig chain DNA was performed on iBA and BASM biliary remnants and lymph nodes obtained from the Childhood Liver Disease Research Network (ChiLDReN) repository. Statistical analysis of the Ig repertoire provided measures of Ig clonality and the Ig phenotype. Our data demonstrate that B cells infiltrate diseased iBA and BASM biliary remnant tissue. The Ig repertoires of iBA and BASM disease groups were oligoclonal supporting a role for an antigen-driven immune response in both sub-types. These findings shift the current understanding of BA and suggest a role for antigen stimulation in early iBA and BASM disease pathogenesis.
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Affiliation(s)
- Sarah A Taylor
- Department of Pediatrics, Ann and Robert H Lurie Children's Hospital of Chicago, Chicago, Illinois, United States. .,Stanley Manne Children's Research Institute, Chicago, Illinois, United States.
| | - Padmini Malladi
- Stanley Manne Children's Research Institute, Chicago, Illinois, United States
| | - Xiaomin Pan
- Stanley Manne Children's Research Institute, Chicago, Illinois, United States
| | - Joshua B Wechsler
- Department of Pediatrics, Ann and Robert H Lurie Children's Hospital of Chicago, Chicago, Illinois, United States
| | - Kathryn E Hulse
- Department of Medicine, Northwestern University, Chicago, Illinois, United States
| | - Harris Perlman
- Department of Medicine, Northwestern University, Chicago, Illinois, United States
| | - Peter F Whitington
- Department of Pediatrics, Ann and Robert H Lurie Children's Hospital of Chicago, Chicago, Illinois, United States.,Stanley Manne Children's Research Institute, Chicago, Illinois, United States
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32
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Lai L, Zhou X, Chen H, Luo Y, Sui W, Zhang J, Tang D, Yan Q, Dai Y. Composition and diversity analysis of the B-cell receptor immunoglobulin heavy chain complementarity-determining region 3 repertoire in patients with acute rejection after kidney transplantation using high-throughput sequencing. Exp Ther Med 2019; 17:2206-2220. [PMID: 30867706 PMCID: PMC6395953 DOI: 10.3892/etm.2019.7183] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 11/14/2018] [Indexed: 01/02/2023] Open
Abstract
The aim of the present study was to assess the genetic diversity of the B-cell receptor (BCR) in kidney transplant recipients with acute rejection. A total of three patients with acute rejection after kidney transplantation were examined by performing a composition and diversity analysis of the BCR immunoglobulin heavy chain (IGH) complementarity-determining region 3 (H-CDR3) repertoire. The peripheral blood mononuclear cells of patients were collected at 1 day prior to (Pre1), as well as 1 day (Post1) and 7 days (Post7) after the transplantation, and DNA was extracted. High-throughput sequencing technology was applied to determine the BCR repertoire. Raw sequences in FASTQ format were analyzed with the Basic Local Alignment Search Tool. The diversity of the BCR repertoire was assessed by calculating Shannon entropy, Simpson's diversity index, the Gini coefficient and highly expanded clone distributions. The diversity of the BCR repertoire at Pre1 was greater than that at Post1 or Post7. The diversity of the BCR repertoire was the lowest at Post1 and increased at Post7 but failed to reach the pre-transplantation levels. Patients exhibited the loss of seven IGH variable (IGHV)3 family genes, while five new genes were expressed at a low frequency. Furthermore, five IGHV-IGH joining (IGHJ) gene pairings, including IGHJ6-IGHV3-11, were detected in the patients. Up- and downregulated genes were assessed by calculating the expression frequencies of the IGH diversity and IGHV gene families at Post1 and Post7. The results of the H-CDR3 length distribution and H-CDR3 amino acid (AA) usage analyses indicated that in Case 1 and 2, the AA length was similar at mostly 14–18 AA, while that in Case 3 was relatively stable at 12–16 AA. In conclusion, the present results illustrate the diversity of H-CDR3 in patients with acute rejection after kidney transplantation may provide novel ideas, methods and means of monitoring and analyzing the immune status of patients under physiological and pathological conditions.
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Affiliation(s)
- Liusheng Lai
- Department of Nephrology, Guilin No. 924 Hospital, Guangxi Key Laboratory of Metabolic Disease Research, Guilin Key Laboratory of Kidney Disease Research, Guilin, Guangxi 541002, P.R. China
| | - Xianqing Zhou
- Department of Nephrology, Guilin No. 924 Hospital, Guangxi Key Laboratory of Metabolic Disease Research, Guilin Key Laboratory of Kidney Disease Research, Guilin, Guangxi 541002, P.R. China
| | - Huaizhou Chen
- Department of Nephrology, Guilin No. 924 Hospital, Guangxi Key Laboratory of Metabolic Disease Research, Guilin Key Laboratory of Kidney Disease Research, Guilin, Guangxi 541002, P.R. China
| | - Yadan Luo
- Department of Nephrology, Guilin No. 924 Hospital, Guangxi Key Laboratory of Metabolic Disease Research, Guilin Key Laboratory of Kidney Disease Research, Guilin, Guangxi 541002, P.R. China
| | - Weiguo Sui
- Department of Nephrology, Guilin No. 924 Hospital, Guangxi Key Laboratory of Metabolic Disease Research, Guilin Key Laboratory of Kidney Disease Research, Guilin, Guangxi 541002, P.R. China
| | - Jiaxing Zhang
- Department of Nephrology, Guilin No. 924 Hospital, Guangxi Key Laboratory of Metabolic Disease Research, Guilin Key Laboratory of Kidney Disease Research, Guilin, Guangxi 541002, P.R. China
| | - Donge Tang
- Clinical Medical Research Center of The Second Clinical Medical College, Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Qiang Yan
- Department of Nephrology, Guilin No. 924 Hospital, Guangxi Key Laboratory of Metabolic Disease Research, Guilin Key Laboratory of Kidney Disease Research, Guilin, Guangxi 541002, P.R. China
| | - Yong Dai
- Clinical Medical Research Center of The Second Clinical Medical College, Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
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33
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Wang L, Zhang W, Lin L, Li X, Saksena NK, Wu J, Wang S, Joyce JG, Zhang X, Yang H, Wang J, Wang IM, Liu X. A Comprehensive Analysis of the T and B Lymphocytes Repertoire Shaped by HIV Vaccines. Front Immunol 2018; 9:2194. [PMID: 30319643 PMCID: PMC6168627 DOI: 10.3389/fimmu.2018.02194] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 09/05/2018] [Indexed: 01/05/2023] Open
Abstract
The exploitation of various human immunodeficiency virus type-1 (HIV-1) vaccines has posed great challenges for the researchers in precisely evaluating the vaccine-induced immune responses, however, the understanding of vaccination response suffers from the lack of unbiased characterization of the immune landscape. The rapid development of high throughput sequencing (HTS) makes it possible to scrutinize the extremely complicated immunological responses during vaccination. In the current study, three vaccines, namely N36, N51, and 5-Helix based on the HIV-1 gp41 pre-hairpin fusion intermediate were applied in rhesus macaques. We assessed the longitudinal vaccine responses using HTS, which delineated the evolutionary features of both T cell and B cell receptor repertoires with extreme diversities. Upon vaccination, we unexpectedly found significant discrepancies in the landscapes of T-cell and B-cell repertoires, together with the detection of significant class switching and the lineage expansion of the B cell receptor or immunoglobulin heavy chain (IGH) repertoire. The vaccine-induced expansions of lineages were further evaluated for mutation rate, lineage abundance, and lineage size features in their IGH repertoires. Collectively, these findings conclude that the N51 vaccine displayed superior performance in inducing the class-switch of B cell isotypes and promoting mutations of IgM B cells. In addition, the systematic HTS analysis of the immune repertoires demonstrates its wide applicability in enhancing the understanding of immunologic changes during pathogen challenge, and will guide the development, evaluation, and exploitation of new generation of diagnostic markers, immunotherapies, and vaccine strategies.
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Affiliation(s)
- Longlong Wang
- BGI-Education Center, University of Chinese Academy of Sciences, Shenzhen, China
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Wei Zhang
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Liya Lin
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Xiao Li
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Nitin K. Saksena
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Jinghua Wu
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Shiyu Wang
- BGI-Education Center, University of Chinese Academy of Sciences, Shenzhen, China
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | | | - Xiuqing Zhang
- BGI-Education Center, University of Chinese Academy of Sciences, Shenzhen, China
- BGI-Shenzhen, Shenzhen, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China
- James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, China
- James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - I-Ming Wang
- Merck & Co., Inc., Kenilworth, NJ, United States
| | - Xiao Liu
- BGI-Shenzhen, Shenzhen, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
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34
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Kovaltsuk A, Leem J, Kelm S, Snowden J, Deane CM, Krawczyk K. Observed Antibody Space: A Resource for Data Mining Next-Generation Sequencing of Antibody Repertoires. THE JOURNAL OF IMMUNOLOGY 2018; 201:2502-2509. [PMID: 30217829 DOI: 10.4049/jimmunol.1800708] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 08/19/2018] [Indexed: 11/19/2022]
Abstract
Abs are immune system proteins that recognize noxious molecules for elimination. Their sequence diversity and binding versatility have made Abs the primary class of biopharmaceuticals. Recently, it has become possible to query their immense natural diversity using next-generation sequencing of Ig gene repertoires (Ig-seq). However, Ig-seq outputs are currently fragmented across repositories and tend to be presented as raw nucleotide reads, which means nontrivial effort is required to reuse the data for analysis. To address this issue, we have collected Ig-seq outputs from 55 studies, covering more than half a billion Ab sequences across diverse immune states, organisms (primarily human and mouse), and individuals. We have sorted, cleaned, annotated, translated, and numbered these sequences and make the data available via our Observed Antibody Space (OAS) resource at http://antibodymap.org The data within OAS will be regularly updated with newly released Ig-seq datasets. We believe OAS will facilitate data mining of immune repertoires for improved understanding of the immune system and development of better biotherapeutics.
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Affiliation(s)
- Aleksandr Kovaltsuk
- Department of Statistics, University of Oxford, Oxford OX1 3LB, United Kingdom; and
| | - Jinwoo Leem
- Department of Statistics, University of Oxford, Oxford OX1 3LB, United Kingdom; and
| | | | | | - Charlotte M Deane
- Department of Statistics, University of Oxford, Oxford OX1 3LB, United Kingdom; and
| | - Konrad Krawczyk
- Department of Statistics, University of Oxford, Oxford OX1 3LB, United Kingdom; and
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35
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Abstract
For high-throughput sequencing and quantification of immunoglobulin repertoires, most methodologies use RNA. However, output varies enormously between recombined genes due to different promoter strengths and differential activation of lymphocyte subsets, precluding quantitation of recombinants on a per-cell basis. To date, DNA-based approaches have used V gene primer cocktails, with substantial inherent biases. Here, we describe VDJ sequencing (VDJ-seq), which accurately quantitates immunoglobulin diversity at the DNA level in an unbiased manner. This is accomplished with a single primer-extension step using biotinylated J gene primers. By addition of unique molecular identifiers (UMIs) before primer extension, we reliably remove duplicate sequences and correct for sequencing and PCR errors. Furthermore, VDJ-seq captures productive and nonproductive VDJ and DJ recombination events on a per-cell basis. Library preparation takes 3 d, with 2 d of sequencing and 1 d of data processing and analysis.
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36
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Devulapally PR, Bürger J, Mielke T, Konthur Z, Lehrach H, Yaspo ML, Glökler J, Warnatz HJ. Simple paired heavy- and light-chain antibody repertoire sequencing using endoplasmic reticulum microsomes. Genome Med 2018; 10:34. [PMID: 29703216 PMCID: PMC5921987 DOI: 10.1186/s13073-018-0542-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 04/12/2018] [Indexed: 12/21/2022] Open
Abstract
Existing methods for paired antibody heavy- and light-chain repertoire sequencing rely on specialized equipment and are limited by their commercial availability and high costs. Here, we report a novel simple and cost-effective emulsion-based single-cell paired antibody repertoire sequencing method that employs only basic laboratory equipment. We performed a proof-of-concept using mixed mouse hybridoma cells and we also showed that our method can be used for discovery of novel antigen-specific monoclonal antibodies by sequencing human CD19+ B cell IgM and IgG repertoires isolated from peripheral whole blood before and seven days after Td (Tetanus toxoid/Diphtheria toxoid) booster immunization. We anticipate broad applicability of our method for providing insights into adaptive immune responses associated with various diseases, vaccinations, and cancer immunotherapies.
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Affiliation(s)
- Praneeth Reddy Devulapally
- Otto Warburg Laboratory Gene Regulation and Systems Biology of Cancer, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Jörg Bürger
- Microscopy and Cryo-Electron Microscopy Service Group, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin, Berlin, Germany
| | - Thorsten Mielke
- Microscopy and Cryo-Electron Microscopy Service Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Zoltán Konthur
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | - Hans Lehrach
- Alacris Theranostics GmbH, Berlin, Germany.,Dahlem Centre for Genome Research and Medical Systems Biology, Berlin, Germany
| | - Marie-Laure Yaspo
- Otto Warburg Laboratory Gene Regulation and Systems Biology of Cancer, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Alacris Theranostics GmbH, Berlin, Germany
| | - Jörn Glökler
- Department of Molecular Biotechnology and Functional Genomics, Institute of Applied Biosciences, Technical University of Applied Sciences Wildau, Wildau, Brandenburg, Germany
| | - Hans-Jörg Warnatz
- Otto Warburg Laboratory Gene Regulation and Systems Biology of Cancer, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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37
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Characterization of the naive murine antibody repertoire using unamplified high-throughput sequencing. PLoS One 2018; 13:e0190982. [PMID: 29320559 PMCID: PMC5761896 DOI: 10.1371/journal.pone.0190982] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 12/22/2017] [Indexed: 12/22/2022] Open
Abstract
Antibody specificity and diversity are generated through the enzymatic splicing of genomic gene segments within each B cell. Antibodies are heterodimers of heavy- and light-chains encoded on separate loci. We studied the antibody repertoire from pooled, splenic tissue of unimmunized, adult female C57BL/6J mice, using high-throughput sequencing (HTS) without amplification of antibody transcripts. We recovered over 90,000 heavy-chain and over 135,000 light-chain immunoglobulin sequences. Individual V-, D-, and J-gene segment usage was uniform among the three mouse pools, particularly in highly abundant gene segments, with low frequency V-gene segments not being detected in all pools. Despite the similar usage of individual gene segments, the repertoire of individual B-cell CDR3 amino acid sequences in each mouse pool was highly varied, affirming the combinatorial diversity in the B-cell pool that has been previously demonstrated. There also was some skewing in the V-gene segments that were detected depending on chromosomal location. This study presents a unique, non-primer biased glimpse of the conventionally housed, unimmunized antibody repertoire of the C57BL6/J mouse.
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38
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Ghraichy M, Galson JD, Kelly DF, Trück J. B-cell receptor repertoire sequencing in patients with primary immunodeficiency: a review. Immunology 2017; 153:145-160. [PMID: 29140551 DOI: 10.1111/imm.12865] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 10/25/2017] [Accepted: 11/07/2017] [Indexed: 12/17/2022] Open
Abstract
The advent of next-generation sequencing (NGS) now allows a detailed assessment of the adaptive immune system in health and disease. In particular, high-throughput B-cell receptor (BCR) repertoire sequencing provides detailed information about the functionality and abnormalities of the B-cell system. However, it is mostly unknown how the BCR repertoire is altered in the context of primary immunodeficiencies (PID) and whether findings are consistent throughout phenotypes and genotypes. We have performed an extensive literature search of the published work on BCR repertoire sequencing in PID patients, including several forms of predominantly antibody disorders and combined immunodeficiencies. It is somewhat surprising that BCR repertoires, even from severe clinical phenotypes, often show only mild abnormalities and that diversity or immunoglobulin gene segment usage is generally preserved to some extent. Despite the great variety of wet laboratory and analytical methods that were used in the different studies, several findings are common to most investigated PIDs, such as the increased usage of gene segments that are associated with self-reactivity. These findings suggest that BCR repertoire characteristics may be used to assess the functionality of the B-cell compartment irrespective of the underlying defect. With the use of NGS approaches, there is now the opportunity to apply BCR repertoire sequencing to multiple patients and explore the PID BCR repertoire in more detail. Ultimately, using BCR repertoire sequencing in translational research could aid the management of PID patients by improving diagnosis, estimating functionality of the immune system and improving assessment of prognosis.
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Affiliation(s)
- Marie Ghraichy
- Division of Immunology, University Children's Hospital Zurich, Zurich, Switzerland.,Children's Research Center, University Children's Hospital, University of Zurich, Zurich, Switzerland
| | - Jacob D Galson
- Children's Research Center, University Children's Hospital, University of Zurich, Zurich, Switzerland.,University of Zurich, Zurich, Switzerland
| | - Dominic F Kelly
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK
| | - Johannes Trück
- Division of Immunology, University Children's Hospital Zurich, Zurich, Switzerland.,Children's Research Center, University Children's Hospital, University of Zurich, Zurich, Switzerland.,University of Zurich, Zurich, Switzerland
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39
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Lushova AA, Biazrova MG, Prilipov AG, Sadykova GK, Kopylov TA, Filatov AV. Next-Generation Techniques for Discovering Human Monoclonal Antibodies. Mol Biol 2017; 51:782-787. [PMID: 32214477 PMCID: PMC7088925 DOI: 10.1134/s0026893317060103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Accepted: 05/12/2017] [Indexed: 01/09/2023]
Abstract
Monoclonal antibodies have found wide applications in the treatment of cancer, as well as of autoimmune, infectious, and other diseases. Several dozen new antibodies are currently undergoing different stages of clinical trials, and some of them will soon be added to the list of immunotherapeutic drugs. Most of these antibodies have been generated using hybridoma technology or a phage display. In recent years, new methods of obtaining human monoclonal antibodies have been actively developing. These methods rely on sequencing immunoglobulin genes from B lymphocytes, as well as on the creation of antibody-secreting stable B-cell lines. The term next-generation antibody-discovery platforms has already been established in the literature to refer to these approaches. Our review focuses on describing the results obtained by these methods.
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Affiliation(s)
- A A Lushova
- 1Institute of Immunology, Federal Medical-Biological Agency of Russia, Moscow, 115478 Russia
| | - M G Biazrova
- 1Institute of Immunology, Federal Medical-Biological Agency of Russia, Moscow, 115478 Russia
| | - A G Prilipov
- 2Ivanovsky Institute of Virology, Gamaleya Scientific Research Institute of Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, 123098 Russia
| | - G K Sadykova
- 2Ivanovsky Institute of Virology, Gamaleya Scientific Research Institute of Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, 123098 Russia
| | - T A Kopylov
- 3Orekhovich Institute of Biomedical Chemistry, Moscow, 119121 Russia
| | - A V Filatov
- 1Institute of Immunology, Federal Medical-Biological Agency of Russia, Moscow, 115478 Russia
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40
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Kovaltsuk A, Krawczyk K, Galson JD, Kelly DF, Deane CM, Trück J. How B-Cell Receptor Repertoire Sequencing Can Be Enriched with Structural Antibody Data. Front Immunol 2017; 8:1753. [PMID: 29276518 PMCID: PMC5727015 DOI: 10.3389/fimmu.2017.01753] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 11/27/2017] [Indexed: 12/24/2022] Open
Abstract
Next-generation sequencing of immunoglobulin gene repertoires (Ig-seq) allows the investigation of large-scale antibody dynamics at a sequence level. However, structural information, a crucial descriptor of antibody binding capability, is not collected in Ig-seq protocols. Developing systematic relationships between the antibody sequence information gathered from Ig-seq and low-throughput techniques such as X-ray crystallography could radically improve our understanding of antibodies. The mapping of Ig-seq datasets to known antibody structures can indicate structurally, and perhaps functionally, uncharted areas. Furthermore, contrasting naïve and antigenically challenged datasets using structural antibody descriptors should provide insights into antibody maturation. As the number of antibody structures steadily increases and more and more Ig-seq datasets become available, the opportunities that arise from combining the two types of information increase as well. Here, we review how these data types enrich one another and show potential for advancing our knowledge of the immune system and improving antibody engineering.
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Affiliation(s)
| | - Konrad Krawczyk
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Jacob D Galson
- Division of Immunology and the Children's Research Center, University Children's Hospital, University of Zürich, Zürich, Switzerland
| | - Dominic F Kelly
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Center, Oxford, United Kingdom
| | - Charlotte M Deane
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Johannes Trück
- Division of Immunology and the Children's Research Center, University Children's Hospital, University of Zürich, Zürich, Switzerland
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41
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VanDuijn MM, Dekker LJ, van IJcken WFJ, Sillevis Smitt PAE, Luider TM. Immune Repertoire after Immunization As Seen by Next-Generation Sequencing and Proteomics. Front Immunol 2017; 8:1286. [PMID: 29085363 PMCID: PMC5650670 DOI: 10.3389/fimmu.2017.01286] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 09/25/2017] [Indexed: 01/24/2023] Open
Abstract
The immune system produces a diverse repertoire of immunoglobulins in response to foreign antigens. During B-cell development, VDJ recombination and somatic mutations generate diversity, whereas selection processes remove it. Using both proteomic and NGS approaches, we characterized the immune repertoires in groups of rats after immunization with purified antigens. Proteomics and NGS data on the repertoire are in qualitative agreement, but did show quantitative differences that may relate to differences between the biological niches that were sampled for these approaches. Both methods contributed complementary information in the characterization of the immune repertoire. It was found that the immune repertoires resulting from each antigen had many similarities that allowed samples to cluster together, and that mutated immunoglobulin peptides were shared among animals with a response to the same antigen significantly more than for different antigens. However, the number of shared sequences decreased in a log-linear fashion relative to the number of animals that share them, which may affect future applications. A phylogenetic analysis on the NGS reads showed that reads from different individuals immunized with the same antigen populated distinct branches of the phylogram, an indication that the repertoire had converged. Also, similar mutation patterns were found in branches of the phylogenetic tree that were associated with antigen-specific immunoglobulins through proteomics data. Thus, data from different analysis methods and different experimental platforms show that the immunoglobulin repertoires of immunized animals have overlapping and converging features. With additional research, this may enable interesting applications in biotechnology and clinical diagnostics.
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Affiliation(s)
| | | | | | | | - Theo M Luider
- Department of Neurology, Erasmus MC, Rotterdam, Netherlands
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42
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Castro R, Navelsaker S, Krasnov A, Du Pasquier L, Boudinot P. Describing the diversity of Ag specific receptors in vertebrates: Contribution of repertoire deep sequencing. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 75:28-37. [PMID: 28259700 DOI: 10.1016/j.dci.2017.02.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 02/16/2017] [Accepted: 02/22/2017] [Indexed: 06/06/2023]
Abstract
During the last decades, gene and cDNA cloning identified TCR and Ig genes across vertebrates; genome sequencing of TCR and Ig loci in many species revealed the different organizations selected during evolution under the pressure of generating diverse repertoires of Ag receptors. By detecting clonotypes over a wide range of frequency, deep sequencing of Ig and TCR transcripts provides a new way to compare the structure of expressed repertoires in species of various sizes, at different stages of development, with different physiologies, and displaying multiple adaptations to the environment. In this review, we provide a short overview of the technologies currently used to produce global description of immune repertoires, describe how they have already been used in comparative immunology, and we discuss the future potential of such approaches. The development of these methodologies in new species holds promise for new discoveries concerning particular adaptations. As an example, understanding the development of adaptive immunity across metamorphosis in frogs has been made possible by such approaches. Repertoire sequencing is now widely used, not only in basic research but also in the context of immunotherapy and vaccination. Analysis of fish responses to pathogens and vaccines has already benefited from these methods. Finally, we also discuss potential advances based on repertoire sequencing of multigene families of immune sensors and effectors in invertebrates.
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Affiliation(s)
- Rosario Castro
- Department of Animal Health, Faculty of Veterinary Sciences, Complutense University, Madrid, Spain
| | - Sofie Navelsaker
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine, Department of Basic Sciences and Aquatic Medicine, Adamstuen Campus, Oslo 0454, Norway; Virologie et Immunologie Moléculaires, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | | | | | - Pierre Boudinot
- Virologie et Immunologie Moléculaires, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
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43
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Khavrutskii IV, Chaudhury S, Stronsky SM, Lee DW, Benko JG, Wallqvist A, Bavari S, Cooper CL. Quantitative Analysis of Repertoire-Scale Immunoglobulin Properties in Vaccine-Induced B-Cell Responses. Front Immunol 2017; 8:910. [PMID: 28855898 PMCID: PMC5557726 DOI: 10.3389/fimmu.2017.00910] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 07/17/2017] [Indexed: 12/15/2022] Open
Abstract
Recent advances in the next-generation sequencing of B-cell receptors (BCRs) enable the characterization of humoral responses at a repertoire-wide scale and provide the capability for identifying unique features of immune repertoires in response to disease, vaccination, or infection. Immunosequencing now readily generates 103–105 sequences per sample; however, statistical analysis of these repertoires is challenging because of the high genetic diversity of BCRs and the elaborate clonal relationships among them. To date, most immunosequencing analyses have focused on reporting qualitative trends in immunoglobulin (Ig) properties, such as usage or somatic hypermutation (SHM) percentage of the Ig heavy chain variable (IGHV) gene segment family, and on reducing complex Ig property distributions to simple summary statistics. However, because Ig properties are typically not normally distributed, any approach that fails to assess the distribution as a whole may be inadequate in (1) properly assessing the statistical significance of repertoire differences, (2) identifying how two repertoires differ, and (3) determining appropriate confidence intervals for assessing the size of the differences and their potential biological relevance. To address these issues, we have developed a technique that uses Wilcox’ robust statistics toolbox to identify statistically significant vaccine-specific differences between Ig repertoire properties. The advantage of this technique is that it can determine not only whether but also where the distributions differ, even when the Ig repertoire properties are non-normally distributed. We used this technique to characterize murine germinal center (GC) B-cell repertoires in response to a complex Ebola virus-like particle (eVLP) vaccine candidate with known protective efficacy. The eVLP-mediated GC B-cell responses were highly diverse, consisting of thousands of clonotypes. Despite this staggering diversity, we identified statistically significant differences between non-immunized, vaccine only, and vaccine-plus-adjuvant groups in terms of Ig properties, including IGHV-family usage, SHM percentage, and characteristics of the BCR complementarity-determining region. Most notably, our analyses identified a robust eVLP-specific feature—enhanced IGHV8-family usage in B-cell repertoires. These findings demonstrate the utility of our technique in identifying statistically significant BCR repertoire differences following vaccination. More generally, our approach is potentially applicable to a wide range of studies in infection, vaccination, auto-immunity, and cancer.
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Affiliation(s)
- Ilja V Khavrutskii
- Department of Defense Biotechnology High Performance Computing Software Applications Institute (BHSAI), Telemedicine and Advanced Technology Research Center, United States Army Medical Research and Materiel Command, Fort Detrick, MD, United States
| | - Sidhartha Chaudhury
- Department of Defense Biotechnology High Performance Computing Software Applications Institute (BHSAI), Telemedicine and Advanced Technology Research Center, United States Army Medical Research and Materiel Command, Fort Detrick, MD, United States
| | - Sabrina M Stronsky
- Molecular and Translational Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, MD, United States
| | - Donald W Lee
- Department of Defense Biotechnology High Performance Computing Software Applications Institute (BHSAI), Telemedicine and Advanced Technology Research Center, United States Army Medical Research and Materiel Command, Fort Detrick, MD, United States
| | - Jacqueline G Benko
- Molecular and Translational Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, MD, United States
| | - Anders Wallqvist
- Department of Defense Biotechnology High Performance Computing Software Applications Institute (BHSAI), Telemedicine and Advanced Technology Research Center, United States Army Medical Research and Materiel Command, Fort Detrick, MD, United States
| | - Sina Bavari
- Molecular and Translational Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, MD, United States
| | - Christopher L Cooper
- Molecular and Translational Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, MD, United States
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44
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Novel Approaches to Analyze Immunoglobulin Repertoires. Trends Immunol 2017; 38:471-482. [PMID: 28566130 DOI: 10.1016/j.it.2017.05.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 04/25/2017] [Accepted: 05/04/2017] [Indexed: 11/21/2022]
Abstract
Analysis of immunoglobulin (Ig) repertoires aims to comprehend Ig diversity with the goal of predicting humoral immune responses in the context of infection, vaccination, autoimmunity, and malignancies. The first next-generation sequencing (NGS) analyses of bulk B cell populations dramatically advanced sampling depth over previous low-throughput single-cell-based protocols, albeit at the expense of accuracy and loss of chain-pairing information. In recent years the field has substantially differentiated, with bulk analyses becoming more accurate while single-cell approaches have gained in throughput. Additionally, new platforms striving to combine high throughput and chain pairing have been developed as well as various computational tools for analysis. Here we review the developments of the past 4-5 years and discuss the open challenges.
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45
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Callan CG, Mora T, Walczak AM. Repertoire sequencing and the statistical ensemble approach to adaptive immunity. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.coisb.2016.12.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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46
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Characteristics Peripheral Blood IgG and IgM Heavy Chain Complementarity Determining Region 3 Repertoire before and after Immunization with Recombinant HBV Vaccine. PLoS One 2017; 12:e0170479. [PMID: 28114326 PMCID: PMC5256919 DOI: 10.1371/journal.pone.0170479] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 01/05/2017] [Indexed: 02/05/2023] Open
Abstract
Immunization with recombinant HBV vaccine induces specific immune responses in human causing B lymphocytes to produce protective HBsAb, and to form memory B lymphocytes, thereby facilitating HBV immunity in the body. However, B lymphocytes heterogeneity and characteristics are not fully elucidated. In this study, we conducted high-throughput sequencing of BCR heavy chain CDR3 repertoires in 3 healthy volunteers before and after the third immunization with recombinant HBV vaccine. We used Roche 454 Genome Sequencer FLX system to perform a comparative analysis of IgM and IgG H chain CDR3 repertoires. First, we found that the diversity of IgG H chain CDR3 repertoires was 1/6 of IgM on average. Moreover, after the third immunization with HBV vaccine, the diversity of IgG H chain CDR3 repertoires was 1/26 of IgM on average. Second, we detected relatively high levels of HBsAbs in all the healthy volunteers after immunization with HBV vaccine. The volunteers shared a small number of CDR3 sequences before and after immunization, and among each other. However, we did not find completely identical BCR H chain CDR3 amino acid sequences in these volunteers. Lastly, after immunization with recombinant HBV vaccine, the volunteers showed high frequency of IgG H chain CDR3 amino acid sequences mostly resulting from rearrangements of IGHV, IGHD and IGHJ, suggesting that the mechanism of high frequency CDR3 generation might be associated with the maturation of IgG affinity (somatic hypermutation) during the recombinant HBV vaccine-induced B lymphocyte responses. This study identified the characteristics and changes of BCR CDR3 repertoires before and after immunization with HBV vaccine, and evaluated the performance of the sequencing technology for this application. Our findings provide a basis for further research in B lymphocyte generated HBsAb heterogeneity and monitoring the maintenance of memory B lymphocytes.
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Chan SK, Rahumatullah A, Lai JY, Lim TS. Naïve Human Antibody Libraries for Infectious Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1053:35-59. [PMID: 29549634 PMCID: PMC7120739 DOI: 10.1007/978-3-319-72077-7_3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Many countries are facing an uphill battle in combating the spread of infectious diseases. The constant evolution of microorganisms magnifies the problem as it facilitates the re-emergence of old infectious diseases as well as promote the introduction of new and more deadly variants. Evidently, infectious diseases have contributed to an alarming rate of mortality worldwide making it a growing concern. Historically, antibodies have been used successfully to prevent and treat infectious diseases since the nineteenth century using antisera collected from immunized animals. The inherent ability of antibodies to trigger effector mechanisms aids the immune system to fight off pathogens that invades the host. Immune libraries have always been an important source of antibodies for infectious diseases due to the skewed repertoire generated post infection. Even so, the role and ability of naïve antibody libraries should not be underestimated. The naïve repertoire has its own unique advantages in generating antibodies against target antigens. This chapter will highlight the concept, advantages and application of human naïve libraries as a source to isolate antibodies against infectious disease target antigens.
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Affiliation(s)
- Soo Khim Chan
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Anizah Rahumatullah
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Jing Yi Lai
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden, Penang, Malaysia.
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Minden, 11800, Penang, Malaysia.
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Adams RM, Mora T, Walczak AM, Kinney JB. Measuring the sequence-affinity landscape of antibodies with massively parallel titration curves. eLife 2016; 5. [PMID: 28035901 PMCID: PMC5268739 DOI: 10.7554/elife.23156] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 12/27/2016] [Indexed: 11/30/2022] Open
Abstract
Despite the central role that antibodies play in the adaptive immune system and in biotechnology, much remains unknown about the quantitative relationship between an antibody’s amino acid sequence and its antigen binding affinity. Here we describe a new experimental approach, called Tite-Seq, that is capable of measuring binding titration curves and corresponding affinities for thousands of variant antibodies in parallel. The measurement of titration curves eliminates the confounding effects of antibody expression and stability that arise in standard deep mutational scanning assays. We demonstrate Tite-Seq on the CDR1H and CDR3H regions of a well-studied scFv antibody. Our data shed light on the structural basis for antigen binding affinity and suggests a role for secondary CDR loops in establishing antibody stability. Tite-Seq fills a large gap in the ability to measure critical aspects of the adaptive immune system, and can be readily used for studying sequence-affinity landscapes in other protein systems. DOI:http://dx.doi.org/10.7554/eLife.23156.001 Antibodies are proteins produced by cells of the immune system to tag or neutralize potential threats to the body, such as foreign substances and disease-causing microbes. Antibodies do this by binding to target molecules called antigens. An antibody’s ability to bind to an antigen depends on the sequence of amino acids – the building blocks of proteins – that make up the antibody. Through a process that randomizes this sequence of amino acids, the immune system generates a vast pool of antibodies that are able to target almost any foreign antigen that exists in nature. Currently, little is understood about how the sequence of amino acids in an antibody determines how strongly that antibody binds to its antigen target – a property referred to as the antibody’s binding affinity. Answering this fundamental question requires techniques that can measure the affinities of many different antibodies at the same time. However, previous high-throughput methods have been unable to provide quantitative measurements of binding affinities. These kinds of measurements are difficult because an antibody’s amino acid sequence governs more than just binding affinity: it also affects how easy it is to produce that antibody, and what fraction of antibody molecules work properly. Adams et al. now describe a new method, named “Tite-Seq”, that overcomes these issues. First, thousands of different antibodies are displayed on the surface of yeast cells, with each cell carrying a single kind of antibody. These cells are then incubated with fluorescently labeled antigen at a wide range of different concentrations. Next, the yeast cells are sorted based on how brightly they glow; brighter cells have more antigen bound to them, and so it is possible to calculate how much of the antigen is bound to each kind of antibody at each concentration. Plotting these data provides a “binding curve” for each antibody, which is then used to read off the antibody’s binding affinity in a way that is not affected by the factors that have plagued other high-throughput methods. Tite-Seq is thus able to measure the binding affinities for thousands of different antibodies at the same time. This will potentially allow researchers to address many fundamental and yet unanswered questions about how the immune system works. Tite-Seq can also be used to measure how amino acid sequence affects the binding affinity of proteins other than antibodies. DOI:http://dx.doi.org/10.7554/eLife.23156.002
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Affiliation(s)
- Rhys M Adams
- Laboratoire de Physique Théorique, UMR8549, CNRS, École Normale Supérieure, Paris, France.,Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
| | - Thierry Mora
- Laboratoire de Physique Statistique, UMR8550, CNRS, École Normale Supérieure, Paris, France
| | - Aleksandra M Walczak
- Laboratoire de Physique Théorique, UMR8549, CNRS, École Normale Supérieure, Paris, France
| | - Justin B Kinney
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, United States
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49
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Galson JD, Trück J, Kelly DF, van der Most R. Investigating the effect of AS03 adjuvant on the plasma cell repertoire following pH1N1 influenza vaccination. Sci Rep 2016; 6:37229. [PMID: 27849037 PMCID: PMC5110968 DOI: 10.1038/srep37229] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 10/26/2016] [Indexed: 12/24/2022] Open
Abstract
Influenza pandemics require rapid deployment of effective vaccines for control. Adjuvants such as AS03 improve vaccine immunogenicity, but this mechanism is poorly understood. We used high-throughput B cell receptor sequencing of plasma cells produced following AS03-adjuvanted and non-adjuvanted 2009 pandemic H1N1 vaccination, as well as pre-pandemic seasonal influenza vaccination to elucidate the effect of the adjuvant on the humoral immune response. By analyzing mutation levels, it was possible to distinguish sequences from cells that were recently activated from naïve B cells from those that were activated by memory recall. We show that the adjuvant functions through two mechanisms. First, the adjuvant stimulates increased activation of naïve B cells, thus reducing immune interference with previous vaccine responses. Second, the adjuvant is able to increase the adaptability of the recalled cells to give improved specificity to the new vaccine antigen. We thus show how AS03 enhances pH1N1 immune responses, and reduces immune interference.
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Affiliation(s)
- J. D. Galson
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Center, Oxford, United Kingdom
| | - J. Trück
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Center, Oxford, United Kingdom
- Paediatric Immunology, University Children’s Hospital Zürich, Switzerland
| | - D. F. Kelly
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Center, Oxford, United Kingdom
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50
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Hou D, Ying T, Wang L, Chen C, Lu S, Wang Q, Seeley E, Xu J, Xi X, Li T, Liu J, Tang X, Zhang Z, Zhou J, Bai C, Wang C, Byrne-Steele M, Qu J, Han J, Song Y. Immune Repertoire Diversity Correlated with Mortality in Avian Influenza A (H7N9) Virus Infected Patients. Sci Rep 2016; 6:33843. [PMID: 27669665 PMCID: PMC5037391 DOI: 10.1038/srep33843] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 09/02/2016] [Indexed: 01/09/2023] Open
Abstract
Specific changes in immune repertoires at genetic level responding to the lethal H7N9 virus are still poorly understood. We performed deep sequencing on the T and B cells from patients recently infected with H7N9 to explore the correlation between clinical outcomes and immune repertoire alterations. T and B cell repertoires display highly dynamic yet distinct clonotype alterations. During infection, T cell beta chain repertoire continues to contract while the diversity of immunoglobulin heavy chain repertoire recovers. Patient recovery is correlated to the diversity of T cell and B cell repertoires in different ways – higher B cell diversity and lower T cell diversity are found in survivors. The sequences clonally related to known antibodies with binding affinity to H7 hemagglutinin could be identified from survivors. These findings suggest that utilizing deep sequencing may improve prognostication during influenza infection and could help in development of antibody discovery methodologies for the treatment of virus infection.
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Affiliation(s)
- Dongni Hou
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Tianlei Ying
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Lili Wang
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Cuicui Chen
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Shuihua Lu
- Department of Respiratory Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Qin Wang
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Eric Seeley
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of California, San Francisco, CA 94143, USA
| | - Jianqing Xu
- Department of Respiratory Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Xiuhong Xi
- Department of Respiratory Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Tao Li
- Department of Respiratory Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Jie Liu
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Xinjun Tang
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Zhiyong Zhang
- Department of Respiratory Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Jian Zhou
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Chunxue Bai
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Chunlin Wang
- HudsonAlpha Institute for Biotechnology, Alabama, AL35806, USA
| | | | - Jieming Qu
- Department of Pulmonary Medicine, Ruijin Hospital, Shanghai Jiaotong University, Shanghai, 200025, China
| | - Jian Han
- HudsonAlpha Institute for Biotechnology, Alabama, AL35806, USA
| | - Yuanlin Song
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.,Department of Respiratory Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China.,Department of Pulmonary Medicine, Zhongshan Hospital, Qingpu Branch, Shanghai, 200032, China
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