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Garcia-Calvo E, García-García A, Rodríguez S, Martín R, García T. Unraveling the Properties of Phage Display Fab Libraries and Their Use in the Selection of Gliadin-Specific Probes by Applying High-Throughput Nanopore Sequencing. Viruses 2024; 16:686. [PMID: 38793567 PMCID: PMC11126117 DOI: 10.3390/v16050686] [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: 03/22/2024] [Revised: 04/19/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
Directed evolution is a pivotal strategy for new antibody discovery, which allowed the generation of high-affinity Fabs against gliadin from two antibody libraries in our previous studies. One of the libraries was exclusively derived from celiac patients' mRNA (immune library) while the other was obtained through a protein engineering approach (semi-immune library). Recent advances in high-throughput DNA sequencing techniques are revolutionizing research across genomics, epigenomics, and transcriptomics. In the present work, an Oxford Nanopore in-lab sequencing device was used to comprehensively characterize the composition of the constructed libraries, both at the beginning and throughout the phage-mediated selection processes against gliadin. A customized analysis pipeline was used to select high-quality reads, annotate chain distribution, perform sequence analysis, and conduct statistical comparisons between the different selection rounds. Some immunological attributes of the most representative phage variants after the selection process were also determined. Sequencing results revealed the successful transfer of the celiac immune response features to the immune library and the antibodies derived from it, suggesting the crucial role of these features in guiding the selection of high-affinity recombinant Fabs against gliadin. In summary, high-throughput DNA sequencing has improved our understanding of the selection processes aimed at generating molecular binders against gliadin.
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Affiliation(s)
| | - Aina García-García
- Department of Nutrition and Food Sciences, School of Veterinary Sciences, Universidad Complutense de Madrid, 28040 Madrid, Spain; (E.G.-C.); (S.R.); (R.M.); (T.G.)
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Kumar S, Bajpai P, Joyce C, Kabra SK, Lodha R, Burton DR, Briney B, Luthra K. B cell repertoire sequencing of HIV-1 pediatric elite-neutralizers identifies multiple broadly neutralizing antibody clonotypes. Front Immunol 2024; 15:1272493. [PMID: 38433846 PMCID: PMC10905035 DOI: 10.3389/fimmu.2024.1272493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 02/02/2024] [Indexed: 03/05/2024] Open
Abstract
Introduction A limited subset of HIV-1 infected adult individuals typically after at least 2-3 years of chronic infection, develop broadly neutralizing antibodies (bnAbs), suggesting that highly conserved neutralizing epitopes on the HIV-1 envelope glycoprotein are difficult for B cell receptors to effectively target, during natural infection. Recent studies have shown the evolution of bnAbs in HIV-1 infected infants. Methods We used bulk BCR sequencing (BCR-seq) to profile the B cell receptors from longitudinal samples (3 time points) collected from a rare pair of antiretroviralnaïve, HIV-1 infected pediatric monozygotic twins (AIIMS_329 and AIIMS_330) who displayed elite plasma neutralizing activity against HIV-1. Results BCR-seq of both twins revealed convergent antibody characteristics including V-gene use, CDRH3 lengths and somatic hypermutation (SHM). Further, antibody clonotypes with genetic features similar to highly potent bnAbs isolated from adults showed ongoing development in donor AIIMS_330 but not in AIIMS_329, corroborating our earlier findings based on plasma bnAbs responses. An increase in SHM was observed in sequences of the IgA isotype from AIIMS_330. Discussion This study suggests that children living with chronic HIV-1 can develop clonotypes of HIV-1 bnAbs against multiple envelope epitopes similar to those isolated from adults, highlighting that such B cells could be steered to elicit bnAbs responses through vaccines aimed to induce bnAbs against HIV-1 in a broad range of people including children.
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Affiliation(s)
- Sanjeev Kumar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, United States
- Center for Viral Systems Biology, The Scripps Research Institute, La Jolla, CA, United States
- International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States
| | - Prashant Bajpai
- International Centre for Genetic Engineering and Biotechnology (ICGEB)-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, India
| | - Collin Joyce
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, United States
- Center for Viral Systems Biology, The Scripps Research Institute, La Jolla, CA, United States
- International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States
| | - Sushil Kumar Kabra
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Rakesh Lodha
- Department of Pediatrics, All India Institute of Medical Sciences, New Delhi, India
| | - Dennis R. Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, United States
- Center for Viral Systems Biology, The Scripps Research Institute, La Jolla, CA, United States
- International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, United States
| | - Bryan Briney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA, United States
- Center for Viral Systems Biology, The Scripps Research Institute, La Jolla, CA, United States
- Multi-omics Vaccine Evaluation Consortium, The Scripps Research Institute, La Jolla, CA, United States
| | - Kalpana Luthra
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
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Miller WB, Baluška F, Reber AS. A revised central dogma for the 21st century:all biology is cognitive information processing. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023:S0079-6107(23)00057-3. [PMID: 37268025 DOI: 10.1016/j.pbiomolbio.2023.05.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/28/2023] [Accepted: 05/30/2023] [Indexed: 06/04/2023]
Abstract
Crick's Central Dogma has been a foundational aspect of 20th century biology, describing an implicit relationship governing the flow of information in biological systems in biomolecular terms. Accumulating scientific discoveries support the need for a revised Central Dogma to buttress evolutionary biology's still-fledgling migration from a Neodarwinian canon. A reformulated Central Dogma to meet contemporary biology is proposed: all biology is cognitive information processing. Central to this contention is the recognition that life is the self-referential state, instantiated within the cellular form. Self-referential cells act to sustain themselves and to do so, cells must be in consistent harmony with their environment. That consonance is achieved by the continuous assimilation of environmental cues and stresses as information to self-referential observers. All received cellular information must be analyzed to be deployed as cellular problem-solving to maintain homeorhetic equipoise. However, the effective implementation of information is definitively a function of orderly information management. Consequently, effective cellular problem-solving is information processing and management. The epicenter of that cellular information processing is its self-referential internal measurement. All further biological self-organization initiates from this obligate activity. As the internal measurement by cells of information is self-referential by definition, self-reference is biological self-organization, underpinning 21st century Cognition-Based Biology.
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Affiliation(s)
| | | | - Arthur S Reber
- Department of Psychology, University of British Columbia, Vancouver, BC, Canada.
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Deng X, Zhang M, Wang J, Zhou X, Xiao M. Characterization of clonal immunoglobulin heavy V-D-J gene rearrangements in Chinese patients with chronic lymphocytic leukemia: Clinical features and molecular profiles. Front Oncol 2023; 13:1120867. [PMID: 36874132 PMCID: PMC9978106 DOI: 10.3389/fonc.2023.1120867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 01/26/2023] [Indexed: 02/18/2023] Open
Abstract
Introduction Several prognostic factors of chronic lymphocytic leukemia (CLL) have been identified, such as cytogenetic aberrations and recurrent gene mutations. B-cell receptor (BCR) signaling plays an important role in the tumorigenesis of CLL, and its clinical significance in predicting prognosis is also under study. Methods Therefore, we assessed the already-known prognostic markers, immunoglobulin heavy chain (IGH) gene usage and the associations among these factors in 71 patients diagnosed with CLL in our center from October 2017 to March 2022. Sequencing of IGH gene rearrangements was performed using Sanger sequencing or IGH-based next-generation sequencing, and the results were further analyzed for distinct IGH/IGHD/IGHJ genes and the mutational status of the clonotypic IGHV (IGH variable) gene. Results In summary, by analyzing the distribution of potential prognostic factors in CLL patients, we displayed a landscape of molecular profiles, confirmed the predictive value of recurrent genetic mutations and chromosome aberrations, and found that IGHJ3 was associated with favorable markers (mutated IGHV, trisomy 12), while IGHJ6 tended to correlate with unfavorable factors (unmutated IGHV, del17p). Discussion These results provided an indication for IGH gene sequencing in predicting the prognosis of CLL.
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Affiliation(s)
- Xinyue Deng
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan, Hubei, China
| | - Meilan Zhang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan, Hubei, China
| | - Jiachen Wang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan, Hubei, China
| | - Xiaoxi Zhou
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan, Hubei, China
| | - Min Xiao
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Immunotherapy Research Center for Hematologic Diseases of Hubei Province, Wuhan, Hubei, China
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Kuraoka M, Curtis NC, Watanabe A, Tanno H, Shin S, Ye K, Macdonald E, Lavidor O, Kong S, Von Holle T, Windsor I, Ippolito GC, Georgiou G, Walter EB, Kelsoe G, Harrison SC, Moody MA, Bajic G, Lee J. Infant Antibody Repertoires during the First Two Years of Influenza Vaccination. mBio 2022; 13:e0254622. [PMID: 36314798 PMCID: PMC9765176 DOI: 10.1128/mbio.02546-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 09/19/2022] [Indexed: 01/11/2023] Open
Abstract
The first encounter with influenza virus biases later immune responses. This "immune imprinting," formerly from infection within a few years of birth, is in the United States now largely from immunization with a quadrivalent, split vaccine (IIV4 [quadrivalent inactivated influenza vaccine]). In a pilot study of IIV4 imprinting, we used single-cell cultures, next-generation sequencing, and plasma antibody proteomics to characterize the primary antibody responses to influenza in two infants during their first 2 years of seasonal influenza vaccination. One infant, who received only a single vaccination in year 1, contracted an influenza B virus (IBV) infection between the 2 years, allowing us to compare imprinting by infection and vaccination. That infant had a shift in hemagglutinin (HA)-reactive B cell specificity from largely influenza A virus (IAV) specific in year 1 to IBV specific in year 2, both before and after the year 2 vaccination. HA-reactive B cells from the other infant maintained a more evenly distributed specificity. In year 2, class-switched HA-specific B cell IGHV somatic hypermutation (SHM) levels reached the average levels seen in adults. The HA-reactive plasma antibody repertoires of both infants comprised a relatively small number of antibody clonotypes, with one or two very abundant clonotypes. Thus, after the year 2 boost, both infants had overall B cell profiles that resembled those of adult controls. IMPORTANCE Influenza virus is a moving target for the immune system. Variants emerge that escape protection from antibodies elicited by a previously circulating variant ("antigenic drift"). The immune system usually responds to a drifted influenza virus by mutating existing antibodies rather than by producing entirely new ones. Thus, immune memory of the earliest influenza virus exposure has a major influence on later responses to infection or vaccination ("immune imprinting"). In the many studies of influenza immunity in adult subjects, imprinting has been from an early infection, since only in the past 2 decades have infants received influenza immunizations. The work reported in this paper is a pilot study of imprinting by the flu vaccine in two infants, who received the vaccine before experiencing an influenza virus infection. The results suggest that a quadrivalent (four-subtype) vaccine may provide an immune imprint less dominated by one subtype than does a monovalent infection.
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Affiliation(s)
- Masayuki Kuraoka
- Department of Immunology, Duke University, Durham, North Carolina, USA
| | - Nicholas C. Curtis
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, USA
| | - Akiko Watanabe
- Department of Immunology, Duke University, Durham, North Carolina, USA
| | - Hidetaka Tanno
- Department of Chemical Engineering, University of Texas, Austin, Texas, USA
- Department of Molecular Biosciences, University of Texas, Austin, Texas, USA
- Department of Biomedical Engineering, University of Texas, Austin, Texas, USA
- Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas, USA
| | - Seungmin Shin
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, USA
| | - Kevin Ye
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, USA
| | - Elizabeth Macdonald
- Laboratory of Molecular Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Olivia Lavidor
- Laboratory of Molecular Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Susan Kong
- Laboratory of Molecular Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Tarra Von Holle
- Department of Pediatrics, Duke University, Durham, North Carolina, USA
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, USA
| | - Ian Windsor
- Laboratory of Molecular Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Gregory C. Ippolito
- Department of Molecular Biosciences, University of Texas, Austin, Texas, USA
- Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas, USA
| | - George Georgiou
- Department of Chemical Engineering, University of Texas, Austin, Texas, USA
- Department of Molecular Biosciences, University of Texas, Austin, Texas, USA
- Department of Biomedical Engineering, University of Texas, Austin, Texas, USA
- Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas, USA
| | - Emmanuel B. Walter
- Department of Pediatrics, Duke University, Durham, North Carolina, USA
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, USA
| | - Garnett Kelsoe
- Department of Immunology, Duke University, Durham, North Carolina, USA
- Department of Surgery, Duke University, Durham, North Carolina, USA
| | - Stephen C. Harrison
- Laboratory of Molecular Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - M. Anthony Moody
- Department of Immunology, Duke University, Durham, North Carolina, USA
- Department of Pediatrics, Duke University, Durham, North Carolina, USA
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, USA
| | - Goran Bajic
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jiwon Lee
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire, USA
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Landscapes and dynamic diversifications of B-cell receptor repertoires in COVID-19 patients. Hum Immunol 2021; 83:119-129. [PMID: 34785098 PMCID: PMC8566346 DOI: 10.1016/j.humimm.2021.10.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 10/29/2021] [Accepted: 10/29/2021] [Indexed: 01/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the pandemic of coronavirus disease 2019 (COVID-19). Great international efforts have been put into the development of prophylactic vaccines and neutralizing antibodies. However, the knowledge about the B cell immune response induced by the SARS-CoV-2 virus is still limited. Here, we report a comprehensive characterization of the dynamics of immunoglobin heavy chain (IGH) repertoire in COVID-19 patients. By using next-generation sequencing technology, we examined the temporal changes in the landscape of the patient's immunological status and found dramatic changes in the IGH within the patient's immune system after the onset of COVID-19 symptoms. Although different patients have distinct immune responses to SARS-CoV-2 infection, by employing clonotype overlap, lineage expansion, and clonotype network analyses, we observed a higher clonotype overlap and substantial lineage expansion of B cell clones 2-3 weeks after the onset of illness, which is of great importance to B-cell immune responses. Meanwhile, for preferences of V gene usage during SARS-CoV-2 infection, IGHV3-74 and IGHV4-34, and IGHV4-39 in COVID-19 patients were more abundant than those of healthy controls. Overall, we present an immunological resource for SARS-CoV-2 that could promote both therapeutic development as well as mechanistic research.
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Larson PA, Bartlett ML, Garcia K, Chitty J, Balkema-Buschmann A, Towner J, Kugelman J, Palacios G, Sanchez-Lockhart M. Genomic features of humoral immunity support tolerance model in Egyptian rousette bats. Cell Rep 2021; 35:109140. [PMID: 34010652 DOI: 10.1016/j.celrep.2021.109140] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 10/08/2020] [Accepted: 04/26/2021] [Indexed: 01/05/2023] Open
Abstract
Bats asymptomatically harbor many viruses that can cause severe human diseases. The Egyptian rousette bat (ERB) is the only known reservoir for Marburgviruses and Sosuga virus, making it an exceptional animal model to study antiviral mechanisms in an asymptomatic host. With this goal in mind, we constructed and annotated the immunoglobulin heavy chain locus, finding an expansion on immunoglobulin variable genes associated with protective human antibodies to different viruses. We also annotated two functional and distinct immunoglobulin epsilon genes and four distinctive functional immunoglobulin gamma genes. We described the Fc receptor repertoire in ERBs, including features that may affect activation potential, and discovered the lack of evolutionary conserved short pentraxins. These findings reinforce the hypothesis that a differential threshold of regulation and/or absence of key immune mediators may promote tolerance and decrease inflammation in ERBs.
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Affiliation(s)
- Peter A Larson
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - Maggie L Bartlett
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA; Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Karla Garcia
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA; Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Joseph Chitty
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | | | - Jonathan Towner
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Jeffrey Kugelman
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - Gustavo Palacios
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA.
| | - Mariano Sanchez-Lockhart
- Center for Genome Sciences, US Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA; Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA.
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Raybould MIJ, Rees AR, Deane CM. Current strategies for detecting functional convergence across B-cell receptor repertoires. MAbs 2021; 13:1996732. [PMID: 34781829 PMCID: PMC8604390 DOI: 10.1080/19420862.2021.1996732] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 10/10/2021] [Accepted: 10/12/2021] [Indexed: 12/11/2022] Open
Abstract
Convergence across B-cell receptor (BCR) and antibody repertoires has become instrumental in prioritizing candidates in recent rapid therapeutic antibody discovery campaigns. It has also increased our understanding of the immune system, providing evidence for the preferential selection of BCRs to particular (immunodominant) epitopes post vaccination/infection. These important implications for both drug discovery and immunology mean that it is essential to consider the optimal way to combine experimental and computational technology when probing BCR repertoires for convergence signatures. Here, we discuss the theoretical basis for observing BCR repertoire functional convergence and explore factors of study design that can impact functional signal. We also review the computational arsenal available to detect antibodies with similar functional properties, highlighting opportunities enabled by recent clustering algorithms that exploit structural similarities between BCRs. Finally, we suggest future areas of development that should increase the power of BCR repertoire functional clustering.
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Affiliation(s)
- Matthew I. J. Raybould
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, UK
| | | | - Charlotte M. Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, UK
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