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Lee H, Yoo DK, Han J, Kim KH, Noh J, Lee Y, Lee E, Kwon S, Chung J. Optimization of peripheral blood volume for in silico reconstitution of the human B cell receptor repertoire. FEBS Open Bio 2022; 12:1634-1643. [PMID: 35866358 PMCID: PMC9433817 DOI: 10.1002/2211-5463.13467] [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: 06/15/2022] [Revised: 07/08/2022] [Accepted: 07/20/2022] [Indexed: 11/30/2022] Open
Abstract
B cells recognize antigens via membrane‐expressed B‐cell receptors (BCR) and antibodies. Similar human BCR sequences are frequently found at a significantly higher frequency than that theoretically calculated. Patients infected with SARS‐CoV2 and HIV or with autoimmune diseases share very similar BCRs. Therefore, in silico reconstitution of BCR repertoires and identification of stereotypical BCR sequences related to human pathology have diagnostic potential. Furthermore, monitoring changes of clinically significant BCR sequences and isotype conversion has prognostic potential. For BCR repertoire analysis, peripheral blood (PB) is the most convenient source. However, the optimal human PB volume for in silico reconstitution of the BCR repertoire has not been studied in detail. Here, we sampled 5, 10, and 20 mL PB from the left arm and 40 mL PB from the right arm of two volunteers, reconstituted in silico PB BCR repertoires, and compared their composition. In both volunteers, PB sampling over 20 mL resulted in slight increases in functional unique sequences (FUSs) or almost no increase in repertoire diversity. All FUSs with a frequency above 0.08% or 0.03% in the 40 mL PB BCR repertoire were detected even in the 5 mL PB BCR repertoire from each volunteer. FUSs with a higher frequency were more likely to be found in BCR repertoires from reduced PB volume, and those coexisting in two repertoires showed a statistically significant correlation in frequency irrespective of sampled anatomical site. The correlation was more significant in higher‐frequency FUSs. These observations support the potential of BCR repertoire analysis for diagnosis.
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Affiliation(s)
- Hyunho Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Korea
| | - Duck Kyun Yoo
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, 03080, Korea.,Department of Biomedical Science, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - Jerome Han
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, 03080, Korea.,Department of Biomedical Science, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - Ki Hyun Kim
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, 03080, Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - Jinsung Noh
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Korea
| | - Yonghee Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Korea
| | - Eunjae Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, 03080, Korea.,Department of Biomedical Science, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - Sunghoon Kwon
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Korea.,Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, 08826, Korea.,BK21+ Creative Research Engineer Development for IT, Seoul National University, Seoul, 08826, Korea.,Bio-MAX Institute, Seoul National University, Seoul, 08826, Korea
| | - Junho Chung
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, 03080, Korea.,Department of Biomedical Science, Seoul National University College of Medicine, Seoul, 03080, Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, 03080, Korea
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Kim SI, Noh J, Kim S, Choi Y, Yoo DK, Lee Y, Lee H, Jung J, Kang CK, Song KH, Choe PG, Kim HB, Kim ES, Kim NJ, Seong MW, Park WB, Oh MD, Kwon S, Chung J. Stereotypic neutralizing V H antibodies against SARS-CoV-2 spike protein receptor binding domain in patients with COVID-19 and healthy individuals. Sci Transl Med 2021; 13:scitranslmed.abd6990. [PMID: 33397677 PMCID: PMC7875332 DOI: 10.1126/scitranslmed.abd6990] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/07/2020] [Accepted: 12/28/2020] [Indexed: 12/19/2022]
Abstract
Stereotypic antibodies (Abs) are produced in healthy individuals by preexisting naïve B cells that have not undergone somatic hypermutation or class switching. Kim et al. have identified stereotypic neutralizing Abs (nAbs) against SARS-CoV-2 spike protein receptor binding domain (RBD) in healthy individuals and patients with COVID-19. They detected RBD-specific stereotypic variable heavy chain (VH) Ab clonotypes composed of Ig heavy variable 3-53 (IGHV3-53) or IGHV3-66 and Ig heavy joining 6 (IGHJ6) genes in 13 of 17 patients with COVID-19. One stereotypic nAb could inhibit in vitro replication of a clinical isolate of SARS-CoV-2. These VH clonotypes were also found in 6 of 10 healthy individuals with no evidence of exposure to SARS-CoV-2, and together, these findings provide evidence of the presence of preexisting nAbs to SARS-CoV-2. Stereotypic antibody clonotypes exist in healthy individuals and may provide protective immunity against viral infections by neutralization. We observed that 13 of 17 patients with COVID-19 had stereotypic variable heavy chain (VH) antibody clonotypes directed against the receptor binding domain (RBD) of SARS-CoV-2 spike protein. These antibody clonotypes were composed of immunoglobulin heavy variable 3-53 (IGHV3-53) or IGHV3-66 and immunoglobulin heavy joining 6 (IGHJ6) genes. These clonotypes included IgM, IgG3, IgG1, IgA1, IgG2, and IgA2 subtypes and had minimal somatic mutations, which suggested swift class switching after SARS-CoV-2 infection. The different IGHV chains were paired with diverse light chains resulting in binding to the RBD of SARS-CoV-2 spike protein. Human antibodies specific for the RBD can neutralize SARS-CoV-2 by inhibiting entry into host cells. We observed that one of these stereotypic neutralizing antibodies could inhibit viral replication in vitro using a clinical isolate of SARS-CoV-2. We also found that these VH clonotypes existed in 6 of 10 healthy individuals, with IgM isotypes predominating. These findings suggest that stereotypic clonotypes can develop de novo from naïve B cells and not from memory B cells established from prior exposure to similar viruses. The expeditious and stereotypic expansion of these clonotypes may have occurred in patients infected with SARS-CoV-2 because they were already present.
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Affiliation(s)
- Sang Il Kim
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea.,Ischemic/Hypoxic Disease Institute, Seoul National University Medical Research Center, Seoul 03080, Republic of Korea
| | - Jinsung Noh
- Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Sujeong Kim
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea.,Department of Biomedical Science, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Younggeun Choi
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Duck Kyun Yoo
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea.,Ischemic/Hypoxic Disease Institute, Seoul National University Medical Research Center, Seoul 03080, Republic of Korea.,Department of Biomedical Science, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Yonghee Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyunho Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Jongtak Jung
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Chang Kyung Kang
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Kyoung-Ho Song
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Pyoeng Gyun Choe
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Hong Bin Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Eu Suk Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Nam-Joong Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Wan Beom Park
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Myoung-Don Oh
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Sunghoon Kwon
- Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, Republic of Korea. .,Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Republic of Korea.,BK21+ Creative Research Engineer Development for IT, Seoul National University, Seoul 08826, Republic of Korea.,Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Republic of Korea.,Institutes of Entrepreneurial BioConvergence, Seoul National University, Seoul 08826, Republic of Korea
| | - Junho Chung
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea. .,Department of Biomedical Science, Seoul National University College of Medicine, Seoul 03080, Republic of Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
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A High-Throughput Single-Clone Phage Fluorescence Microwell Immunoassay and Laser-Driven Clonal Retrieval System. Biomolecules 2020; 10:biom10040517. [PMID: 32235304 PMCID: PMC7226094 DOI: 10.3390/biom10040517] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 03/26/2020] [Indexed: 12/03/2022] Open
Abstract
Phage display is one of the most frequently used platform technologies utilized to screen and select therapeutic antibodies, and has contributed to the development of more than 10 therapeutic antibodies used in the clinic. Despite advantages like efficiency and low cost, it has intrinsic technical limitations, such as the asymmetrical amplification of the library after each round of biopanning, which is regarded as a reason for it yielding a very limited number of antigen binders. In this study, we developed a high-throughput single-clonal screening system comprised of fluorescence immunoassays and a laser-driven clonal DNA retrieval system using microchip technology. Using this system, from a single-chain variable fragment (scFv) library displayed on phages with a complexity of 5.21 × 105 harboring random mutations at five amino acid residues, more than 70,000 clones—corresponding to ~14% of the library complexity—were screened, resulting in 78 antigen-reactive scFv sequences with mutations restricted to the randomized residues. Our results demonstrate that this system can significantly reduce the number of biopanning rounds, or even eliminate the need for this process for libraries with lower complexity, providing an opportunity to obtain more diverse clones from the library.
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