1
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Yan Q, Zhang Y, Hou R, Pan W, Liang H, Gao X, Deng W, Huang X, Qu L, Tang C, He P, Liu B, Wang Q, Zhao X, Lin Z, Chen Z, Li P, Han J, Xiong X, Zhao J, Li S, Niu X, Chen L. Deep immunoglobulin repertoire sequencing depicts a comprehensive atlas of spike-specific antibody lineages shared among COVID-19 convalescents. Emerg Microbes Infect 2024; 13:2290841. [PMID: 38044868 PMCID: PMC10810631 DOI: 10.1080/22221751.2023.2290841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/29/2023] [Indexed: 12/05/2023]
Abstract
Neutralizing antibodies are a key component in protective humoral immunity against SARS-CoV-2. Currently, available technologies cannot track epitope-specific antibodies in global antibody repertoires. Thus, the comprehensive repertoire of spike-specific neutralizing antibodies elicited by SARS-CoV-2 infection is not fully understood. We therefore combined high-throughput immunoglobulin heavy chain (IgH) repertoire sequencing, and structural and bioinformatics analysis to establish an antibodyomics pipeline, which enables tracking spike-specific antibody lineages that target certain neutralizing epitopes. We mapped the neutralizing epitopes on the spike and determined the epitope-preferential antibody lineages. This analysis also revealed numerous overlaps between immunodominant neutralizing antibody-binding sites and mutation hotspots on spikes as observed so far in SARS-CoV-2 variants. By clustering 2677 spike-specific antibodies with 360 million IgH sequences that we sequenced, a total of 329 shared spike-specific antibody clonotypes were identified from 33 COVID-19 convalescents and 24 SARS-CoV-2-naïve individuals. Epitope mapping showed that the shared antibody responses target not only neutralizing epitopes on RBD and NTD but also non-neutralizing epitopes on S2. The immunodominance of neutralizing antibody response is determined by the occurrence of specific precursors in human naïve B-cell repertoires. We identified that only 28 out of the 329 shared spike-specific antibody clonotypes persisted for at least 12 months. Among them, long-lived IGHV3-53 antibodies are likely to evolve cross-reactivity to Omicron variants through accumulating somatic hypermutations. Altogether, we created a comprehensive atlas of spike-targeting antibody lineages in COVID-19 convalescents and antibody precursors in human naïve B cell repertoires, providing a valuable reference for future vaccine design and evaluation.
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Affiliation(s)
- Qihong Yan
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Yudi Zhang
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- University of Chinese Academy of Science, Beijing, People’s Republic of China
| | - Ruitian Hou
- Guangzhou Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Wenjing Pan
- Hengyang Medical School, University of South China, Hengyang, People’s Republic of China
- Nanjing ARP Biotechnology Co., Ltd, Nanjing, People’s Republic of China
| | - Huan Liang
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Xijie Gao
- Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Weiqi Deng
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- University of Chinese Academy of Science, Beijing, People’s Republic of China
| | - Xiaohan Huang
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Linbing Qu
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Congli Tang
- Nanjing ARP Biotechnology Co., Ltd, Nanjing, People’s Republic of China
| | - Ping He
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- Guangzhou National Laboratory, Guangzhou, People’s Republic of China
| | - Banghui Liu
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Qian Wang
- Guangzhou National Laboratory, Guangzhou, People’s Republic of China
| | - Xinwei Zhao
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- Guangzhou National Laboratory, Guangzhou, People’s Republic of China
| | - Zihan Lin
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- University of Chinese Academy of Science, Beijing, People’s Republic of China
| | - Zhaoming Chen
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Pingchao Li
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Jian Han
- iRepertoire Inc., Huntsville, AL, USA
| | - Xiaoli Xiong
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
- Guangzhou National Laboratory, Guangzhou, People’s Republic of China
| | - Song Li
- Hengyang Medical School, University of South China, Hengyang, People’s Republic of China
| | - Xuefeng Niu
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Ling Chen
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, People’s Republic of China
- Guangzhou Institute of Infectious Disease, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, People’s Republic of China
- Guangzhou National Laboratory, Guangzhou, People’s Republic of China
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2
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Zhu X, Ma E, Ning K, Feng X, Quan W, Wang F, Zhu C, Ma Y, Dong Y, Jiang Q. A comparative analysis of TCR immune repertoire in COVID-19 patients. Hum Immunol 2024; 85:110795. [PMID: 38582657 DOI: 10.1016/j.humimm.2024.110795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/08/2024]
Abstract
The coronavirus disease 2019 (COVID-19) has merged as a global health threat since its outbreak in December 2019. Despite widespread recognition, there has been a paucity of studies focusing on the T cell receptor (TCR) bias in adaptive immunity induced by SARS-CoV-2. This research conducted a comparative analysis of the TCR immune repertoire to identify notable αβ TCR bias sequences associated with the SARS-CoV-2 virus antigen. The present study encompassed 73 symptomatic COVID-19 patients, categorized as moderate/mild or severe/critical, along with 9 healthy controls. Our findings revealed specific TCR chains prominently utilized by moderate and severe patients, identified as TRAV30-J34-TRBV3-1-J2-7 and TRAV12-3-J6-TRBV28-J1-1, respectively. Additionally, our research explored critical TCR preferences in the bronchoalveolar lavage fluid (BALF) of COVID-19 patients at various disease stages. Indeed, monitoring the dynamics of immune repertoire changes in COVID-19 patients could serve as a crucial biomarker for predicting disease progression and recovery. Furthermore, the study explored TCR bias in both peripheral blood mononuclear cells (PBMCs) and BALF. The most common αβ VJ pair observed in BALF was TRAV12-3-J18-TRBV7-6-J2-7. In addition, a comparative analysis with the VDJdb database indicated that the HLA-A*02:01 allele exhibited the widest distribution and highest frequency in COVID-19 patients across different periods. This comprehensive examination provided a global characterization of the TCR immune repertoire in COVID-19 patients, contributing significantly to our understanding of TCR bias induced by SARS-CoV-2.
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MESH Headings
- Humans
- COVID-19/immunology
- SARS-CoV-2/immunology
- Male
- Female
- Middle Aged
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- Adult
- Bronchoalveolar Lavage Fluid/immunology
- Aged
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- Adaptive Immunity/immunology
- Severity of Illness Index
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Affiliation(s)
- Xiao Zhu
- School of Computer and Control Engineering, Yantai University, Yantai, Shandong, China; Lead Contact.
| | - Enze Ma
- School of Computer Science and Information Engineering, Harbin Normal University, Harbin, Heilongjiang, China
| | - Ke Ning
- School of Computer Science and Information Engineering, Harbin Normal University, Harbin, Heilongjiang, China
| | - Xiangyan Feng
- Department of Hematology, Yantai Yuhuangding Hospital Affiliated to Qingdao University, Yantai, Shandong, China.
| | - Wei Quan
- School of Computer and Control Engineering, Yantai University, Yantai, Shandong, China
| | - Fei Wang
- School of Computer and Control Engineering, Yantai University, Yantai, Shandong, China
| | - Chaoqun Zhu
- School of Computer and Control Engineering, Yantai University, Yantai, Shandong, China
| | - Yuanjun Ma
- School of Computer and Control Engineering, Yantai University, Yantai, Shandong, China
| | - Yucui Dong
- Department of Immunology, Binzhou Medical University, Yantai, Shandong, China
| | - Qinghua Jiang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China.
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3
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Xiao J, Luo Y, Li Y, Yao X. The characteristics of BCR-CDR3 repertoire in COVID-19 patients and SARS-CoV-2 vaccinated volunteers. J Med Virol 2024; 96:e29488. [PMID: 38415507 DOI: 10.1002/jmv.29488] [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: 11/04/2023] [Revised: 02/02/2024] [Accepted: 02/13/2024] [Indexed: 02/29/2024]
Abstract
The global COVID-19 pandemic has caused more than 1 billion infections, and numerous SARS-CoV-2 vaccines developed rapidly have been administered over 10 billion doses. The world is continuously concerned about the cytokine storms induced by the interaction between SARS-CoV-2 and host, long COVID, breakthrough infections postvaccination, and the impact of SARS-CoV-2 variants. BCR-CDR3 repertoire serves as a molecular target for monitoring the antiviral response "trace" of B cells, evaluating the effects, mechanisms, and memory abilities of individual responses to B cells, and has been successfully applied in analyzing the infection mechanisms, vaccine improvement, and neutralizing antibodies preparation of influenza virus, HIV, MERS, and Ebola virus. Based on research on BCR-CDR3 repertoire of COVID-19 patients and volunteers who received different SARS-CoV-2 vaccines in multiple laboratories worldwide, we focus on analyzing the characteristics and changes of BCR-CDR3 repertoire, such as diversity, clonality, V&J genes usage and pairing, SHM, CSR, shared CDR3 clones, as well as the summary on BCR sequences targeting virus-specific epitopes in the preparation and application research of SARS-CoV-2 potential therapeutic monoclonal antibodies. This review provides comparative data and new research schemes for studying the possible mechanisms of differences in B cell response between SARS-CoV-2 infection or vaccination, and supplies a foundation for improving vaccines after SARS-CoV-2 mutations and potential antibody therapy for infected individuals.
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Affiliation(s)
- Jiaping Xiao
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, Guizhou, China
- Fushun People's Hospital, Zigong, Sichuan, China
| | - Yan Luo
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, Guizhou, China
| | - Yangyang Li
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, Guizhou, China
| | - Xinsheng Yao
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, Guizhou, China
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4
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Feng B, Zheng D, Yang L, Su Z, Tang L, Zhu Y, Xu X, Wang Q, Lin Q, Hu J, Lin M, Huang L, Zhou X, Liu H, Li S, Pan W, Shi R, Lu Y, Wu B, Ding B, Wang Z, Guo J, Zhang Z, Zheng G, Liu Y. Post-hospitalization rehabilitation alleviates long-term immune repertoire alteration in COVID-19 convalescent patients. Cell Prolif 2023; 56:e13450. [PMID: 36938980 PMCID: PMC10542649 DOI: 10.1111/cpr.13450] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/27/2023] [Accepted: 03/02/2023] [Indexed: 03/21/2023] Open
Abstract
The global pandemic of Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an once-in-a-lifetime public health crisis. Among hundreds of millions of people who have contracted with or are being infected with COVID-19, the question of whether COVID-19 infection may cause long-term health concern, even being completely recovered from the disease clinically, especially immune system damage, needs to be addressed. Here, we performed seven-chain adaptome immune repertoire analyses on convalescent COVID-19 patients who have been discharged from hospitals for at least 6 months. Surprisingly, we discovered lymphopenia, reduced number of unique CDR3s, and reduced diversity of the TCR/BCR immune repertoire in convalescent COVID-19 patients. In addition, the BCR repertoire appears to be activated, which is consistent with the protective antibody titres, but serological experiments reveal significantly lower IL-4 and IL-7 levels in convalescent patients compared to those in healthy controls. Finally, in comparison with convalescent patients who did not receive post-hospitalization rehabilitation, the convalescent patients who received post-hospitalization rehabilitation had attenuated immune repertoire abnormality, almost back to the level of healthy control, despite no detectable clinic demographic difference. Overall, we report the potential long-term immunological impairment for COVID-19 infection, and correction of this impairment via post-hospitalization rehabilitation may offer a new prospect for COVID-19 recovery strategy.
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5
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Xing Y, Li Y, Feng L, Huo R, Ma X, Dong Y, Liu D, Niu Y, Tian X, Chen E. Predictors of COVID-19 Severity in Elderly Patients Infected by Omicron in China, 18 December 2022-5 February 2023. Infect Drug Resist 2023; 16:4505-4518. [PMID: 37457796 PMCID: PMC10349581 DOI: 10.2147/idr.s418622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 07/06/2023] [Indexed: 07/18/2023] Open
Abstract
Purpose To analyze the clinical characteristics and prognosis of patients hospitalized with non-severe, severe pneumonia and death in Omicron COVID-19. Patients and Methods We collected clinical data from 118 patients with COVID-19 in China from 18 December, 2022 and 5 February, 2023. According to the outcome, the patients were divided into non-severe group, severe group and death group. Subsequently, we statistically analyzed the general condition, clinical manifestations, laboratory parameters, NLR, MLR, PLR and HALP of these groups. We also retrospectively analyzed the possible factors affecting the prognostic regression of patients with COVID-19. Results A total of 118 COVID-19 patients were enrolled in this study, including 64 non-severe patients, 38 severe patients and 16 death patients. Compared with the non-severe group, T lymphocytes, B lymphocytes, Th1, Th2, Th17, Treg cells, IgA, IgG, IgM in the severe and death groups decreased more significantly (P<0.05). The levels of myocardial markers, ALT, AST, BUN, Cr, D-dimer, fibrinogen, NLR, MLR and PLR in the severe and death groups were significantly higher than those in the non-severe group (P<0.05). The level of HALP was significantly lower than that of non-severe group (P<0.05). MLR is not only an independent risk factor for the transition from non-severe to severe disease, but also an independent risk factor for predicting the possibility of death in COVID-19 patients. Conclusion The analysis of COVID-19 patients in China showed that severe patients were older, more likely to have related complications, lower lymphocyte count, liver and kidney function disorder, glucose and lipid metabolism disorders, myocardial injury, and abnormal coagulation function, suggesting the need for early anticoagulant therapy. In addition, NLR, MLR, PLR and HALP can be used as biomarkers to evaluate the severity and prognosis of COVID-19 patients.
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Affiliation(s)
- Yanqing Xing
- The Second Hospital of Shanxi Medical University, Taiyuan, People’s Republic of China
| | - Yupeng Li
- The Second Hospital of Shanxi Medical University, Taiyuan, People’s Republic of China
| | - Liting Feng
- The Second Hospital of Shanxi Medical University, Taiyuan, People’s Republic of China
| | - Rujie Huo
- The Second Hospital of Shanxi Medical University, Taiyuan, People’s Republic of China
| | - Xinkai Ma
- The Second Hospital of Shanxi Medical University, Taiyuan, People’s Republic of China
| | - Yanting Dong
- The Second Hospital of Shanxi Medical University, Taiyuan, People’s Republic of China
| | - Dai Liu
- The Second Hospital of Shanxi Medical University, Taiyuan, People’s Republic of China
| | - Yuheng Niu
- The First Hospital of Shanxi Medical University, Taiyuan, People’s Republic of China
| | - Xinrui Tian
- The Second Hospital of Shanxi Medical University, Taiyuan, People’s Republic of China
| | - Erjing Chen
- The Second Hospital of Shanxi Medical University, Taiyuan, People’s Republic of China
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6
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Bao X, Zhong Y, Yang C, Chen Y, Han Y, Lin X, Huang C, Wang K, Liu Z, Li C. T-Cell Repertoire Analysis in the Conjunctiva of Murine Dry Eye Model. Invest Ophthalmol Vis Sci 2023; 64:14. [PMID: 36877515 PMCID: PMC10007900 DOI: 10.1167/iovs.64.3.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023] Open
Abstract
Purpose Dry eye is closely related to the activation and proliferation of immune cells, especially T cells. However, the determination of the preferential T-cell clonotypes is technically challenging. This study aimed to investigate the characterization of T-cell receptor (TCR) repertoire in the conjunctiva during dry eye. Methods A desiccating stress animal model was established using C57/BL6 mice (8-10 weeks, female). After 7 days of stress stimulation, the slit-lamp image and Oregon-green-dextran staining were used to evaluate the ocular surface injury. Periodic acid-Schiff staining was used to measure the number of goblet cells. Flow cytometry was used to detect the activation and proliferation of T cells in the conjunctiva and cervical lymph nodes. Next-generation sequencing was used to detect the αβ TCR repertoire of the conjunctiva. Results The αβ TCR diversity increased significantly in the dry eye group, including the higher CDR3 amino acid length, marked gene usage on TCR V and J gene segments, extensive V(D)J recombination, and distinct CDR3 aa motifs. More important, several T-cell clonotypes were uniquely identified in dry eye. Furthermore, these perturbed rearrangements were reversed after glucocorticoid administration. Conclusions A comprehensive analysis of the αβ TCR repertoire in the conjunctiva of the dry eye mouse model was performed. Data in this study contributed significantly to the research on dry eye pathogenesis by demonstrating the TCR gene distribution and disease-specific TCR signatures. This study further provided some potential predictive T-cell biomarkers for future studies.
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Affiliation(s)
- Xiaorui Bao
- Fujian Provincial Key Laboratory of Ophthalmology and Visual Science, Eye Institute & Affiliated Xiamen Eye Center, School of Medicine, Xiamen University, Xiamen, Fujian, China.,Department of Ophthalmology, Xiang'an Hospital of Xiamen University, Xiamen, Fujian, China
| | - Yanlin Zhong
- Fujian Provincial Key Laboratory of Ophthalmology and Visual Science, Eye Institute & Affiliated Xiamen Eye Center, School of Medicine, Xiamen University, Xiamen, Fujian, China.,Department of Ophthalmology, Xiang'an Hospital of Xiamen University, Xiamen, Fujian, China
| | - Chunyan Yang
- School of Life Science, Xiamen University, Xiamen, Fujian, China
| | - Yujie Chen
- Fujian Provincial Key Laboratory of Ophthalmology and Visual Science, Eye Institute & Affiliated Xiamen Eye Center, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Yi Han
- Fujian Provincial Key Laboratory of Ophthalmology and Visual Science, Eye Institute & Affiliated Xiamen Eye Center, School of Medicine, Xiamen University, Xiamen, Fujian, China.,Department of Ophthalmology, Xiang'an Hospital of Xiamen University, Xiamen, Fujian, China
| | - Xiang Lin
- Department of Ophthalmology, Xiang'an Hospital of Xiamen University, Xiamen, Fujian, China
| | - Caihong Huang
- Fujian Provincial Key Laboratory of Ophthalmology and Visual Science, Eye Institute & Affiliated Xiamen Eye Center, School of Medicine, Xiamen University, Xiamen, Fujian, China.,Department of Ophthalmology, Xiang'an Hospital of Xiamen University, Xiamen, Fujian, China
| | - Kejia Wang
- Fujian Provincial Key Laboratory of Ophthalmology and Visual Science, Eye Institute & Affiliated Xiamen Eye Center, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Zuguo Liu
- Fujian Provincial Key Laboratory of Ophthalmology and Visual Science, Eye Institute & Affiliated Xiamen Eye Center, School of Medicine, Xiamen University, Xiamen, Fujian, China.,Department of Ophthalmology, Xiang'an Hospital of Xiamen University, Xiamen, Fujian, China.,The First Affiliated Hospital of University of South China, Hengyang, Hunan, China
| | - Cheng Li
- Fujian Provincial Key Laboratory of Ophthalmology and Visual Science, Eye Institute & Affiliated Xiamen Eye Center, School of Medicine, Xiamen University, Xiamen, Fujian, China.,Department of Ophthalmology, Xiang'an Hospital of Xiamen University, Xiamen, Fujian, China
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7
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Vakhitova M, Myshkin M, Staroverov D, Shagina I, Izraelson M, Tverdova N, Britanova O, Merzlyak E. A Rapid Method for Detection of Antigen-Specific B Cells. Cells 2023; 12:cells12050774. [PMID: 36899909 PMCID: PMC10000731 DOI: 10.3390/cells12050774] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/17/2023] [Accepted: 02/24/2023] [Indexed: 03/05/2023] Open
Abstract
The global SARS-CoV-2 pandemic has united the efforts of many scientists all over the world to develop wet-lab techniques and computational approaches aimed at the identification of antigen-specific T and B cells. The latter provide specific humoral immunity that is essential for the survival of COVID-19 patients, and vaccine development has essentially been based on these cells. Here, we implemented an approach that integrates the sorting of antigen-specific B cells and B-cell receptor mRNA sequencing (BCR-seq), followed by computational analysis. This rapid and cost-efficient method allowed us to identify antigen-specific B cells in the peripheral blood of patients with severe COVID-19 disease. Subsequently, specific BCRs were extracted, cloned, and produced as full antibodies. We confirmed their reactivity toward the spike RBD domain. Such an approach can be effective for the monitoring and identification of B cells participating in an individual immune response.
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Affiliation(s)
- Mariia Vakhitova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Mikhail Myshkin
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Dmitriy Staroverov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Institute of Translation Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Irina Shagina
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Institute of Translation Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Mark Izraelson
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Nadezhda Tverdova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Olga Britanova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Institute of Translation Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
- Correspondence: (O.B.); (E.M.)
| | - Ekaterina Merzlyak
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Institute of Translation Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
- Correspondence: (O.B.); (E.M.)
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8
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Shin J, Ham B, Seo JH, Lee SB, Park IA, Gong G, Kim SB, Lee HJ. Immune repertoire and responses to neoadjuvant TCHP therapy in HER2-positive breast cancer. Ther Adv Med Oncol 2023; 15:17588359231157654. [PMID: 36865681 PMCID: PMC9972050 DOI: 10.1177/17588359231157654] [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: 08/17/2022] [Accepted: 01/30/2023] [Indexed: 03/02/2023] Open
Abstract
Background Despite the introduction of trastuzumab, pathologic complete response (pCR) is not attained in approximately 30-40% of Human epithelial growth factor receptor-2-positive breast cancer. Tumor-infiltrating lymphocytes (TIL) have been suggested as a predictive marker of treatment response, albeit not always effective. We investigated the relationship between trastuzumab, docetaxel, carboplatin, and pertuzumab (TCHP) treatment and immune repertoire as a treatment response predictor. Design In all, 35 cases were divided into two experimental groups: 10 and 25 cases in the preliminary and main experiments, respectively. In the preliminary experiment, the biopsy tissues before TCHP treatment and the surgical tissues after TCHP treatment were compared. In the main experiment, the biopsy tissues before TCHP treatment were compared according to the TCHP treatment response. Methods The T-cell repertoire for TRA, TRB, TRG, and TRD, and B-cell repertoire for immunoglobulin heavy, immunoglobulin kappa, and immunoglobulin lambda were evaluated. Whole transcriptome sequencing was also performed. Results In the preliminary experiment, the density and richness of the T-cell receptor (TCR) and B-cell receptor (BCR) repertoires decreased after treatment, regardless of TCHP response. In the main experiment, the Shannon's entropy index, density, and length of CDR3 of the TCR and BCR repertoires did not differ significantly in patients who did and did not achieve pCR. The pCR and non-pCR subgroups according to the level of TILs revealed that the non-pCR/lowTIL group had a higher proportion of low-frequency clones than the pCR/lowTIL group in TRA (non-pCR/lowTIL versus pCR/lowTIL, 0.01-0.1%, 63% versus 45.3%; <0.01%, 32.9% versus 51.8%, p < 0.001) and TRB (non-pCR/lowTIL versus pCR/lowTIL, 0.01-0.1%, 26.5% versus 14.7%; <0.01%, 72.0% versus 84.1%, p < 0.001). Conclusions The role of the diversity, richness, and density of the TCR and BCR repertoires as predictive markers for TCHP response was not identified. Compositions of low-frequency clones could be candidates for predictive factors of TCHP response; however, validation studies and further research are necessary.
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Affiliation(s)
- Junyoung Shin
- Department of Pathology, Asan Medical Center,
University of Ulsan College of Medicine, Seoul, Korea
| | | | | | - Sae Byul Lee
- Department of Breast Surgery, Asan Medical
Center, University of Ulsan College of Medicine, Seoul, Korea
| | - In Ah Park
- Department of Pathology, Kangbuk Samsung
Hospital, Seoul, Republic of Korea
| | - Gyungyub Gong
- Department of Pathology, Asan Medical Center,
University of Ulsan College of Medicine, Seoul, Korea
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9
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Jia C, Zhou Z, Pan W, Zhang P, Yang M, Zhao M, Li B, Liu P, Zhang Q, Kong X, Li K, Yue T, Cai T, Wang Z, De Clercq E, Li S, Li G, Liu J, Wu H, Lu Q. Immune repertoire sequencing reveals an abnormal adaptive immune system in COVID-19 survivors. J Med Virol 2023; 95:e28340. [PMID: 36420584 PMCID: PMC10107439 DOI: 10.1002/jmv.28340] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/20/2022] [Accepted: 11/18/2022] [Indexed: 11/25/2022]
Abstract
Accumulating evidence suggests that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) impairs the adaptive immune system during acute infection. Still, it remains largely unclear whether the frequency and functions of T and B cells return to normal after the recovery of Coronavirus Disease 2019 (COVID-19). Here, we analyzed immune repertoires and SARS-CoV-2-specific neutralization antibodies in a prospective cohort of 40 COVID-19 survivors with a 6-month follow-up after hospital discharge. Immune repertoire sequencing revealed abnormal T- and B-cell expression and function with large T cell receptor/B cell receptor clones, decreased diversity, abnormal class-switch recombination, and somatic hypermutation. A decreased number of B cells but an increased proportion of CD19+ CD138+ B cells were found in COVID-19 survivors. The proportion of CD4+ T cells, especially circulating follicular helper T (cTfh) cells, was increased, whereas the frequency of CD3+ CD4- T cells was decreased. SARS-CoV-2-specific neutralization IgG and IgM antibodies were identified in all survivors, especially those recorded with severe COVID-19 who showed a higher inhibition rate of neutralization antibodies. All severe cases complained of more than one COVID-19 sequelae after 6 months of recovery. Overall, our findings indicate that SARS-CoV-2-specific antibodies remain detectable even after 6 months of recovery. Because of their abnormal adaptive immune system with a low number of CD3+ CD4- T cells and high susceptibility to infections, COVID-19 patients might need more time and medical care to fully recover from immune abnormalities and tissue damage.
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Affiliation(s)
- Chen Jia
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhiguo Zhou
- The First Hospital of Changsha, Changsha, Hunan Province, China
| | - Wenjing Pan
- Nanjing ARP Biotechnology Co., Ltd., Nanjing, Jiangsu, China
| | - Pan Zhang
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
| | - Ming Yang
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Mingming Zhao
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Bo Li
- The First Hospital of Changsha, Changsha, Hunan Province, China
| | - Ping Liu
- The First Hospital of Changsha, Changsha, Hunan Province, China
| | - Qianqian Zhang
- The First Hospital of Changsha, Changsha, Hunan Province, China
| | - Xianglong Kong
- The First Hospital of Changsha, Changsha, Hunan Province, China
| | - Keyu Li
- The First Hospital of Changsha, Changsha, Hunan Province, China
| | - Tingting Yue
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
| | - Ting Cai
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
| | - Zijun Wang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing, China.,Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - Erik De Clercq
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, Hunan, China
| | - Guangdi Li
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
| | - Jiyang Liu
- The First Hospital of Changsha, Changsha, Hunan Province, China
| | - Haijing Wu
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qianjin Lu
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.,Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing, China.,Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
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10
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Qi H, Xue JB, Lai DY, Li A, Tao SC. Current advances in antibody-based serum biomarker studies: From protein microarray to phage display. Proteomics Clin Appl 2022; 16:e2100098. [PMID: 36071670 DOI: 10.1002/prca.202100098] [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] [Received: 01/26/2022] [Revised: 08/16/2022] [Accepted: 09/05/2022] [Indexed: 12/30/2022]
Abstract
PURPOSE This review aims to summarize the technological advances in the field of antibody-based biomarker studies by proteome microarray and phage display. In addition, the possible development directions of this field are also discussed. EXPERIMENTAL DESIGN We have focused on the antibody profiling by proteome microarray and phage display, including the technological advances, the tools/resources constructed, and the characteristics of both platforms. RESULTS With the help of tools/resources and technological advances in proteome microarray and phage display, the efficiency of profiling antibody-based biomarkers in serum samples has been greatly improved. CONCLUSIONS In the past few years, proteome microarray and phage display, especially the latter one, have already demonstrated their capacity and efficiency for biomarker identification. In the near future, we believe that more antibody-based biomarkers could be identified, and some of them could eventually be developed into real clinical applications.
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Affiliation(s)
- Huan Qi
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Jun-Biao Xue
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Dan-Yun Lai
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Ang Li
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Sheng-Ce Tao
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
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11
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Yan Q, Hou R, Huang X, Zhang Y, He P, Zhang Y, Liu B, Wang Q, Rao H, Chen X, Zhao X, Niu X, Zhao J, Xiong X, Chen L. Shared IGHV1-69-encoded neutralizing antibodies contribute to the emergence of L452R substitution in SARS-CoV-2 variants. Emerg Microbes Infect 2022; 11:2749-2761. [PMID: 36288106 PMCID: PMC9662066 DOI: 10.1080/22221751.2022.2140611] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
SARS-CoV-2 variants continue to emerge facing established herd immunity. L452R, previously featured in the Delta variant, quickly emerged in Omicron subvariants, including BA.4/BA.5, implying a continued selection pressure on this residue. The underlying links between spike mutations and their selective pressures remain incompletely understood. Here, by analyzing 221 structurally characterized antibodies, we found that IGHV1-69-encoded antibodies preferentially contact L452 using germline-encoded hydrophobic residues at the tip of HCDR2 loop. Whereas somatic hypermutations or VDJ rearrangements are required to acquire L452-contacting hydrophobic residues for non-IGHV1-69 encoded antibodies. Antibody repertoire analysis revealed that IGHV1-69 L452-contacting antibody lineages are commonly induced among COVID-19 convalescents but non-IGHV1-69 encoded antibodies exhibit limited prevalence. In addition, we experimentally demonstrated that L452R renders most published IGHV1-69 antibodies ineffective. Furthermore, we found that IGHV1-69 L452-contacting antibodies are enriched in convalescents experienced Omicron BA.1 (without L452R) breakthrough infections but rarely found in Delta (with L452R) breakthrough infections. Taken together, these findings support that IGHV1-69 population antibodies contribute to selection pressure for L452 substitution. This study thus provides a better understanding of SARS-CoV-2 variant genesis and immune evasion.
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Affiliation(s)
- Qihong Yan
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ruitian Hou
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Science, Beijing, China
| | - Xiaohan Huang
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Science, Beijing, China
| | - Yanjun Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Ping He
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Science, Beijing, China
| | - Yudi Zhang
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Science, Beijing, China
| | - Banghui Liu
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Qian Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Haiyue Rao
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xianying Chen
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xinwei Zhao
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xuefeng Niu
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiaoli Xiong
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Ling Chen
- State Key Laboratory of Respiratory Disease, Guangdong Laboratory of Computational Biomedicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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12
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Discriminating cross-reactivity in polyclonal IgG1 responses against SARS-CoV-2 variants of concern. Nat Commun 2022; 13:6103. [PMID: 36243713 PMCID: PMC9568977 DOI: 10.1038/s41467-022-33899-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 10/07/2022] [Indexed: 12/24/2022] Open
Abstract
Existing assays to measure antibody cross-reactivity against different SARS-CoV-2 spike (S) protein variants lack the discriminatory power to provide insights at the level of individual clones. Using a mass spectrometry-based approach we are able to monitor individual donors' IgG1 clonal responses following a SARS-CoV-2 infection. We monitor the plasma clonal IgG1 profiles of 8 donors who had experienced an infection by either the wild type Wuhan Hu-1 virus or one of 3 VOCs (Alpha, Beta and Gamma). In these donors we chart the full plasma IgG1 repertoires as well as the IgG1 repertoires targeting the SARS-CoV-2 spike protein trimer VOC antigens. The plasma of each donor contains numerous anti-spike IgG1 antibodies, accounting for <0.1% up to almost 10% of all IgG1s. Some of these antibodies are VOC-specific whereas others do recognize multiple or even all VOCs. We show that in these polyclonal responses, each clone exhibits a distinct cross-reactivity and also distinct virus neutralization capacity. These observations support the need for a more personalized look at the antibody clonal responses to infectious diseases.
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13
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He P, Liu B, Gao X, Yan Q, Pei R, Sun J, Chen Q, Hou R, Li Z, Zhang Y, Zhao J, Sun H, Feng B, Wang Q, Yi H, Hu P, Li P, Zhang Y, Chen Z, Niu X, Zhong X, Jin L, Liu X, Qu K, Ciazynska KA, Carter AP, Briggs JAG, Chen J, Liu J, Chen X, He J, Chen L, Xiong X. SARS-CoV-2 Delta and Omicron variants evade population antibody response by mutations in a single spike epitope. Nat Microbiol 2022; 7:1635-1649. [PMID: 36151403 PMCID: PMC9519457 DOI: 10.1038/s41564-022-01235-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 08/12/2022] [Indexed: 12/18/2022]
Abstract
Population antibody response is thought to be important in selection of virus variants. We report that SARS-CoV-2 infection elicits a population immune response that is mediated by a lineage of VH1-69 germline antibodies. A representative antibody R1-32 from this lineage was isolated. By cryo-EM, we show that it targets a semi-cryptic epitope in the spike receptor-binding domain. Binding to this non-ACE2 competing epitope results in spike destruction, thereby inhibiting virus entry. On the basis of epitope location, neutralization mechanism and analysis of antibody binding to spike variants, we propose that recurrent substitutions at 452 and 490 are associated with immune evasion of the identified population antibody response. These substitutions, including L452R (present in the Delta variant), disrupt interactions mediated by the VH1-69-specific hydrophobic HCDR2 to impair antibody-antigen association, enabling variants to escape. The first Omicron variants were sensitive to antibody R1-32 but subvariants that harbour L452R quickly emerged and spread. Our results provide insights into how SARS-CoV-2 variants emerge and evade host immune responses.
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Affiliation(s)
- Ping He
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Science, Beijing, China
| | - Banghui Liu
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xijie Gao
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health - Guangdong Laboratory), Guangzhou, China
| | - Qihong Yan
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Rongjuan Pei
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Jing Sun
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qiuluan Chen
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health - Guangdong Laboratory), Guangzhou, China
| | - Ruitian Hou
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Science, Beijing, China
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Zimu Li
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yanjun Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Hao Sun
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
| | - Bo Feng
- School of Biomedical Sciences, Huaqiao University, Quanzhou, China
| | - Qian Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Haisu Yi
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Peiyu Hu
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Pingchao Li
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yudi Zhang
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Science, Beijing, China
| | - Zhilong Chen
- School of Biomedical Sciences, Huaqiao University, Quanzhou, China
- Xiamen United Institute of Respiratory Health, Xiamen, China
| | - Xuefeng Niu
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiaolin Zhong
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health - Guangdong Laboratory), Guangzhou, China
| | - Liang Jin
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health - Guangdong Laboratory), Guangzhou, China
| | | | - Kun Qu
- Infectious Diseases Translational Research Programme, Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Katarzyna A Ciazynska
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Andrew P Carter
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - John A G Briggs
- Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jizheng Chen
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, Guangdong Province, China
| | - Jinsong Liu
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xinwen Chen
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, Guangdong Province, China.
| | - Jun He
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health - Guangdong Laboratory), Guangzhou, China.
| | - Ling Chen
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health - Guangdong Laboratory), Guangzhou, China.
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China.
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, Guangdong Province, China.
| | - Xiaoli Xiong
- State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health - Guangdong Laboratory), Guangzhou, China.
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14
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Pogorelyy MV, Rosati E, Minervina AA, Mettelman RC, Scheffold A, Franke A, Bacher P, Thomas PG. Resolving SARS-CoV-2 CD4 + T cell specificity via reverse epitope discovery. Cell Rep Med 2022; 3:100697. [PMID: 35841887 PMCID: PMC9247234 DOI: 10.1016/j.xcrm.2022.100697] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 05/08/2022] [Accepted: 06/24/2022] [Indexed: 11/24/2022]
Abstract
The current strategy to detect immunodominant T cell responses focuses on the antigen, employing large peptide pools to screen for functional cell activation. However, these approaches are labor and sample intensive and scale poorly with increasing size of the pathogen peptidome. T cell receptors (TCRs) recognizing the same epitope frequently have highly similar sequences, and thus, the presence of large sequence similarity clusters in the TCR repertoire likely identify the most public and immunodominant responses. Here, we perform a meta-analysis of large, publicly available single-cell and bulk TCR datasets from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected individuals to identify public CD4+ responses. We report more than 1,200 αβTCRs forming six prominent similarity clusters and validate histocompatibility leukocyte antigen (HLA) restriction and epitope specificity predictions for five clusters using transgenic T cell lines. Collectively, these data provide information on immunodominant CD4+ T cell responses to SARS-CoV-2 and demonstrate the utility of the reverse epitope discovery approach.
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Affiliation(s)
- Mikhail V Pogorelyy
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38103, USA
| | - Elisa Rosati
- Institute of Clinical Molecular Biology, Christian-Albrecht University of Kiel, Kiel, Germany; Institute of Immunology, Christian-Albrecht University of Kiel, Kiel, Germany
| | - Anastasia A Minervina
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38103, USA
| | - Robert C Mettelman
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38103, USA
| | - Alexander Scheffold
- Institute of Immunology, Christian-Albrecht University of Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrecht University of Kiel, Kiel, Germany
| | - Petra Bacher
- Institute of Clinical Molecular Biology, Christian-Albrecht University of Kiel, Kiel, Germany; Institute of Immunology, Christian-Albrecht University of Kiel, Kiel, Germany.
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38103, USA.
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15
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Song C, Pan W, Brown B, Tang C, Huang Y, Chen H, Peng N, Wang Z, Weber D, Byrne-Steele M, Wu H, Liu H, Deng Y, He N, Li S. Immune repertoire analysis of normal Chinese donors at different ages. Cell Prolif 2022; 55:e13311. [PMID: 35929064 DOI: 10.1111/cpr.13311] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/21/2022] [Accepted: 06/24/2022] [Indexed: 11/28/2022] Open
Abstract
OBJECTIVES This study investigated the characteristics of the immune repertoire in normal Chinese individuals of different ages. MATERIALS AND METHODS In this study, all seven receptor chains from both B and T cells in peripheral blood of 16 normal Chinese individuals from two age groups were analyzed using high-throughput sequencing and dimer-avoided multiplex PCR amplification. Normal in this study is defined as no chronic, infectious or autoimmune disease within 6 months prior to blood draw. RESULTS We found that compared with the younger group, the clonal expression of T-cell receptor repertoire increased in the older group, while diversity decreased. In addition, we found that the T-cell receptor repertoire was more significantly affected by age than the B-cell receptor repertoire, including significant differences in the use of the unique TCR-alpha and TCR-beta V-J gene combinations, in the two groups of normal participants. We further analyzed the degree of complementarity determining region 3 sequence sharing between the two groups, and found shared TCR-alpha, TCR-gamma, immunoglobulin-kappa and immunoglobulin-lambda chain complementarity determining region 3 sequences in all subjects. CONCLUSION Taken together, our study gives us a better understanding of the immune repertoire of different normal Chinese people, and these results can be applied to the treatment of age-related diseases. Immune repertoire analysis also allows us to observe participant's wellness, aiding in early-stage diagnosis.
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Affiliation(s)
- Cailing Song
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
| | - Wenjing Pan
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China.,Nanjing ARP Biotechnology Co., Ltd., Nanjing, China
| | | | - Congli Tang
- Nanjing ARP Biotechnology Co., Ltd., Nanjing, China
| | - Yunqi Huang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
| | - Houao Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
| | - Nan Peng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
| | - Zhe Wang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China.,Guangdong Provincial Hospital of Chinese Medicine & Guangdong Provincial Academy of Chinese Medical Sciences, Guangzhou, China
| | | | | | - Haijing Wu
- Department of Dermatology, Second Xiangya Hospital, Hunan Key Laboratory of Medical Epigenomics, Central South University, Changsha, China
| | - Hongna Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China.,Nanjing ARP Biotechnology Co., Ltd., Nanjing, China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
| | - Nongyue He
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, China
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16
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T-Cell Receptor Repertoire Sequencing and Its Applications: Focus on Infectious Diseases and Cancer. Int J Mol Sci 2022; 23:ijms23158590. [PMID: 35955721 PMCID: PMC9369427 DOI: 10.3390/ijms23158590] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 11/17/2022] Open
Abstract
The immune system is a dynamic feature of each individual and a footprint of our unique internal and external exposures. Indeed, the type and level of exposure to physical and biological agents shape the development and behavior of this complex and diffuse system. Many pathological conditions depend on how our immune system responds or does not respond to a pathogen or a disease or on how the regulation of immunity is altered by the disease itself. T-cells are important players in adaptive immunity and, together with B-cells, define specificity and monitor the internal and external signals that our organism perceives through its specific receptors, TCRs and BCRs, respectively. Today, high-throughput sequencing (HTS) applied to the TCR repertoire has opened a window of opportunity to disclose T-cell repertoire development and behavior down to the clonal level. Although TCR repertoire sequencing is easily accessible today, it is important to deeply understand the available technologies for choosing the best fit for the specific experimental needs and questions. Here, we provide an updated overview of TCR repertoire sequencing strategies, providers and applications to infectious diseases and cancer to guide researchers’ choice through the multitude of available options. The possibility of extending the TCR repertoire to HLA characterization will be of pivotal importance in the near future to understand how specific HLA genes shape T-cell responses in different pathological contexts and will add a level of comprehension that was unthinkable just a few years ago.
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17
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Zheng B, Yang Y, Chen L, Wu M, Zhou S. B-Cell Receptor Repertoire Sequencing: Deeper Digging into the Mechanisms and Clinical Aspects of Immune-mediated Diseases. iScience 2022; 25:105002. [PMID: 36157582 PMCID: PMC9494237 DOI: 10.1016/j.isci.2022.105002] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
B cells play an essential role in adaptive immunity and are intimately correlated with pleiotropic immune-mediated diseases. Each B cell occupies a unique B cell receptor (BCR), and all BCRs throughout our body form “BCR repertoire.” With the development of sequencing technology and coupled bioinformatics, accumulating evidence indicates that BCR repertoire largely varies under physiological and pathological conditions. Therefore, comprehensive grasp of BCR repertoire will provide new insights into the pathogenesis of immune-mediated diseases and help exploit efficient diagnostic and treatment strategies. In this review, we start with an overview of BCR repertoire and related sequencing technologies and summarize their current applications in immune-mediated diseases. We also underscore the challenges of this emerging field and propose promising future directions in advancing BCR repertoire exploration.
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Affiliation(s)
- Bohao Zheng
- Wuxi School of Medicine, Jiangnan University, Wuxi, P. R. China
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, P. R. China
| | - Yuqing Yang
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, P. R. China
| | - Lin Chen
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, P. R. China
| | - Mengrui Wu
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, P. R. China
| | - Shengtao Zhou
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE and State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, P. R. China
- Corresponding author
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18
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Differential chromatin accessibility in peripheral blood mononuclear cells underlies COVID-19 disease severity prior to seroconversion. Sci Rep 2022; 12:11714. [PMID: 35810186 PMCID: PMC9271053 DOI: 10.1038/s41598-022-15668-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/28/2022] [Indexed: 01/25/2023] Open
Abstract
SARS-CoV-2 infection triggers profound and variable immune responses in human hosts. Chromatin remodeling has been observed in individuals severely ill or convalescing with COVID-19, but chromatin remodeling early in disease prior to anti-spike protein IgG seroconversion has not been defined. We performed the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) and RNA-seq on peripheral blood mononuclear cells (PBMCs) from outpatients with mild or moderate symptom severity at different stages of clinical illness. Early in the disease course prior to IgG seroconversion, modifications in chromatin accessibility associated with mild or moderate symptoms were already robust and included severity-associated changes in accessibility of genes in interleukin signaling, regulation of cell differentiation and cell morphology. Furthermore, single-cell analyses revealed evolution of the chromatin accessibility landscape and transcription factor motif accessibility for individual PBMC cell types over time. The most extensive remodeling occurred in CD14+ monocytes, where sub-populations with distinct chromatin accessibility profiles were observed prior to seroconversion. Mild symptom severity was marked by upregulation of classical antiviral pathways, including those regulating IRF1 and IRF7, whereas in moderate disease, these classical antiviral signals diminished, suggesting dysregulated and less effective responses. Together, these observations offer novel insight into the epigenome of early mild SARS-CoV-2 infection and suggest that detection of chromatin remodeling in early disease may offer promise for a new class of diagnostic tools for COVID-19.
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19
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Richard D, Phillip S, Hosseinali A, Gracie DZ, Hai L, January W, Holtgrewe M, Charlotte T, Melina M, Xiaomin W, Zehra K, Jacopo S, Jan-Moritz D, Ralf-Harto H, Bernd H, Anja B, Sandra S, Dilduz T, Norbert S, Martin W, Stefan H, Carsten S, Wolfgang P, Leif E S, Dieter B, Florian K, Toumy G, Ulf L, Jan B, Khai L, Rubelt F, Bettina H. Highly multiplexed immune repertoire sequencing links multiple lymphocyte classes with severity of response to COVID-19. EClinicalMedicine 2022; 48:101438. [PMID: 35600330 PMCID: PMC9106482 DOI: 10.1016/j.eclinm.2022.101438] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 04/15/2022] [Accepted: 04/19/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Disease progression of subjects with coronavirus disease 2019 (COVID-19) varies dramatically. Understanding the various types of immune response to SARS-CoV-2 is critical for better clinical management of coronavirus outbreaks and to potentially improve future therapies. Disease dynamics can be characterized by deciphering the adaptive immune response. METHODS In this cross-sectional study we analyzed 117 peripheral blood immune repertoires from healthy controls and subjects with mild to severe COVID-19 disease to elucidate the interplay between B and T cells. We used an immune repertoire Primer Extension Target Enrichment method (immunoPETE) to sequence simultaneously human leukocyte antigen (HLA) restricted T cell receptor beta chain (TRB) and unrestricted T cell receptor delta chain (TRD) and immunoglobulin heavy chain (IgH) immune receptor repertoires. The distribution was analyzed of TRB, TRD and IgH clones between healthy and COVID-19 infected subjects. Using McFadden's Adjusted R2 variables were examined for a predictive model. The aim of this study is to analyze the influence of the adaptive immune repertoire on the severity of the disease (value on the World Health Organization Clinical Progression Scale) in COVID-19. FINDINGS Combining clinical metadata with clonotypes of three immune receptor heavy chains (TRB, TRD, and IgH), we found significant associations between COVID-19 disease severity groups and immune receptor sequences of B and T cell compartments. Logistic regression showed an increase in shared IgH clonal types and decrease of TRD in subjects with severe COVID-19. The probability of finding shared clones of TRD clonal types was highest in healthy subjects (controls). Some specific TRB clones seems to be present in severe COVID-19 (Figure S7b). The most informative models (McFadden´s Adjusted R2=0.141) linked disease severity with immune repertoire measures across all three cell types, as well as receptor-specific cell counts, highlighting the importance of multiple lymphocyte classes in disease progression. INTERPRETATION Adaptive immune receptor peripheral blood repertoire measures are associated with COVID-19 disease severity. FUNDING The study was funded with grants from the Berlin Institute of Health (BIH).
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Affiliation(s)
| | - Suwalski Phillip
- Department of Cardiology, Charité Universitätsmedizin Berlin, Berlin, DE 10117, Germany
| | | | | | - Lin Hai
- Roche Sequencing Solutions Pleasanton, CA 94588, United States
| | - Weiner January
- Core Unit Bioinformatics Berlin, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, DE 10178, Germany
| | - Manuel Holtgrewe
- Core Unit Bioinformatics Berlin, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, DE 10178, Germany
| | - Thibeault Charlotte
- Department of Infectious Diseases and Respiratory Medicine, Charité Universitätsmedizin Berlin, DE 12203, Germany
| | - Müller Melina
- Department of Cardiology, Charité Universitätsmedizin Berlin, Berlin, DE 10117, Germany
| | - Wang Xiaomin
- Department of Cardiology, Charité Universitätsmedizin Berlin, Berlin, DE 10117, Germany
| | - Karadeniz Zehra
- Department of Cardiology, Charité Universitätsmedizin Berlin, Berlin, DE 10117, Germany
| | - Saccomanno Jacopo
- Department of Infectious Diseases and Respiratory Medicine, Charité Universitätsmedizin Berlin, DE 12203, Germany
| | - Doehn Jan-Moritz
- Department of Infectious Diseases and Respiratory Medicine, Charité Universitätsmedizin Berlin, DE 12203, Germany
| | - Hübner Ralf-Harto
- Department of Infectious Diseases and Respiratory Medicine, Charité Universitätsmedizin Berlin, DE 12203, Germany
| | | | - Blüher Anja
- Signature Diagnostics GmbH, DE 14473, Germany
| | | | - Telman Dilduz
- Roche Sequencing Solutions Pleasanton, CA 94588, United States
| | - Suttorp Norbert
- Department of Infectious Diseases and Respiratory Medicine, Charité Universitätsmedizin Berlin, DE 12203, Germany
| | - Witzenrath Martin
- Department of Infectious Diseases and Respiratory Medicine, Charité Universitätsmedizin Berlin, DE 12203, Germany
| | - Hippenstiel Stefan
- Department of Infectious Diseases and Respiratory Medicine, Charité Universitätsmedizin Berlin, DE 12203, Germany
| | - Skurk Carsten
- Department of Cardiology, Charité Universitätsmedizin Berlin, Berlin, DE 10117, Germany
| | - Poller Wolfgang
- Department of Cardiology, Charité Universitätsmedizin Berlin, Berlin, DE 10117, Germany
| | - Sander Leif E
- Department of Infectious Diseases and Respiratory Medicine, Charité Universitätsmedizin Berlin, DE 12203, Germany
| | - Beule Dieter
- Core Unit Bioinformatics Berlin, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, DE 10178, Germany
| | - Kurth Florian
- Department of Infectious Diseases and Respiratory Medicine, Charité Universitätsmedizin Berlin, DE 12203, Germany
| | | | - Landmesser Ulf
- Department of Cardiology, Charité Universitätsmedizin Berlin, Berlin, DE 10117, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Germany
| | - Berka Jan
- Roche Sequencing Solutions Pleasanton, CA 94588, United States
| | - Luong Khai
- Roche Sequencing Solutions Pleasanton, CA 94588, United States
| | | | - Florian Rubelt
- Roche Sequencing Solutions Pleasanton, CA 94588, United States
| | - Heidecker Bettina
- Department of Cardiology, Charité Universitätsmedizin Berlin, Berlin, DE 10117, Germany
- Corresponding authors.
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20
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Kockelbergh H, Evans S, Deng T, Clyne E, Kyriakidou A, Economou A, Luu Hoang KN, Woodmansey S, Foers A, Fowler A, Soilleux EJ. Utility of Bulk T-Cell Receptor Repertoire Sequencing Analysis in Understanding Immune Responses to COVID-19. Diagnostics (Basel) 2022; 12:diagnostics12051222. [PMID: 35626377 PMCID: PMC9140453 DOI: 10.3390/diagnostics12051222] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 01/27/2023] Open
Abstract
Measuring immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 19 (COVID-19), can rely on antibodies, reactive T cells and other factors, with T-cell-mediated responses appearing to have greater sensitivity and longevity. Because each T cell carries an essentially unique nucleic acid sequence for its T-cell receptor (TCR), we can interrogate sequence data derived from DNA or RNA to assess aspects of the immune response. This review deals with the utility of bulk, rather than single-cell, sequencing of TCR repertoires, considering the importance of study design, in terms of cohort selection, laboratory methods and analysis. The advances in understanding SARS-CoV-2 immunity that have resulted from bulk TCR repertoire sequencing are also be discussed. The complexity of sequencing data obtained by bulk repertoire sequencing makes analysis challenging, but simple descriptive analyses, clonal analysis, searches for specific sequences associated with immune responses to SARS-CoV-2, motif-based analyses, and machine learning approaches have all been applied. TCR repertoire sequencing has demonstrated early expansion followed by contraction of SARS-CoV-2-specific clonotypes, during active infection. Maintenance of TCR repertoire diversity, including the maintenance of diversity of anti-SARS-CoV-2 response, predicts a favourable outcome. TCR repertoire narrowing in severe COVID-19 is most likely a consequence of COVID-19-associated lymphopenia. It has been possible to follow clonotypic sequences longitudinally, which has been particularly valuable for clonotypes known to be associated with SARS-CoV-2 peptide/MHC tetramer binding or with SARS-CoV-2 peptide-induced cytokine responses. Closely related clonotypes to these previously identified sequences have been shown to respond with similar kinetics during infection. A possible superantigen-like effect of the SARS-CoV-2 spike protein has been identified, by means of observing V-segment skewing in patients with severe COVID-19, together with structural modelling. Such a superantigen-like activity, which is apparently absent from other coronaviruses, may be the basis of multisystem inflammatory syndrome and cytokine storms in COVID-19. Bulk TCR repertoire sequencing has proven to be a useful and cost-effective approach to understanding interactions between SARS-CoV-2 and the human host, with the potential to inform the design of therapeutics and vaccines, as well as to provide invaluable pathogenetic and epidemiological insights.
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Affiliation(s)
- Hannah Kockelbergh
- Department of Health Data Science, Institute of Population Health, University of Liverpool, Liverpool L69 3GF, UK;
| | - Shelley Evans
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; (S.E.); (T.D.); (E.C.); (K.N.L.H.); (S.W.)
| | - Tong Deng
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; (S.E.); (T.D.); (E.C.); (K.N.L.H.); (S.W.)
| | - Ella Clyne
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; (S.E.); (T.D.); (E.C.); (K.N.L.H.); (S.W.)
| | - Anna Kyriakidou
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 1QP, UK; (A.K.); (A.E.)
| | - Andreas Economou
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 1QP, UK; (A.K.); (A.E.)
| | - Kim Ngan Luu Hoang
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; (S.E.); (T.D.); (E.C.); (K.N.L.H.); (S.W.)
| | - Stephen Woodmansey
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; (S.E.); (T.D.); (E.C.); (K.N.L.H.); (S.W.)
- Department of Respiratory Medicine, University Hospitals of Morecambe Bay, Kendal LA9 7RG, UK
| | - Andrew Foers
- Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7YF, UK;
| | - Anna Fowler
- Department of Health Data Science, Institute of Population Health, University of Liverpool, Liverpool L69 3GF, UK;
- Correspondence: (A.F.); (E.J.S.)
| | - Elizabeth J. Soilleux
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK; (S.E.); (T.D.); (E.C.); (K.N.L.H.); (S.W.)
- Correspondence: (A.F.); (E.J.S.)
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21
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Giroux NS, Ding S, McClain MT, Burke TW, Petzold E, Chung HA, Rivera GO, Wang E, Xi R, Bose S, Rotstein T, Nicholson BP, Chen T, Henao R, Sempowski GD, Denny TN, De Ussel MI, Satterwhite LL, Ko ER, Ginsburg GS, Kraft BD, Tsalik EL, Shen X, Woods C. Differential chromatin accessibility in peripheral blood mononuclear cells underlies COVID-19 disease severity prior to seroconversion. RESEARCH SQUARE 2022:rs.3.rs-1479864. [PMID: 35411343 PMCID: PMC8996625 DOI: 10.21203/rs.3.rs-1479864/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
SARS-CoV-2 infection triggers profound and variable immune responses in human hosts. Chromatin remodeling has been observed in individuals severely ill or convalescing with COVID-19, but chromatin remodeling early in disease prior to anti-spike protein IgG seroconversion has not been defined. We performed the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) and RNA-seq on peripheral blood mononuclear cells (PBMCs) from outpatients with mild or moderate symptom severity at different stages of clinical illness. Early in the disease course prior to IgG seroconversion, modifications in chromatin accessibility associate with mild or moderate symptoms are already robust and include severity-associated changes in accessibility of genes in interleukin signaling, regulation of cell differentiation and cell morphology. Furthermore, single-cell analyses revealed evolution of the chromatin accessibility landscape and transcription factor motif accessibility for individual PBMC cell types over time. The most extensive remodeling occurred in CD14+ monocytes, where sub-populations with distinct chromatin accessibility profiles were observed prior to seroconversion. Mild symptom severity is marked by upregulation classical antiviral pathways including those regulating IRF1 and IRF7, whereas in moderate disease these classical antiviral signals diminish suggesting dysregulated and less effective responses. Together, these observations offer novel insight into the epigenome of early mild SARS-CoV-2 infection and suggest that detection of chromatin remodeling in early disease may offer promise for a new class of diagnostic tools for COVID-19.
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22
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Qiao L, Cui X, Jia L, Gao Y, Wang W, Wei F, Zhang Z, Chen D, Ma Y, Zhang Y. Peripheral immune phenotypes and T cell receptor repertoire in pneumocystis pneumonia in HIV-1 infected patients. Clin Immunol 2022; 237:108985. [DOI: 10.1016/j.clim.2022.108985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 03/16/2022] [Accepted: 03/22/2022] [Indexed: 11/24/2022]
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23
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Chen L, Pang P, Qi H, Yan K, Ren Y, Ma M, Cao R, Li H, Hu C, Li Y, Xia J, Lai D, Dong Y, Jiang H, Zhang H, Shan H, Tao S, Liu S. Evaluation of Spike Protein Epitopes by Assessing the Dynamics of Humoral Immune Responses in Moderate COVID-19. Front Immunol 2022; 13:770982. [PMID: 35371042 PMCID: PMC8971992 DOI: 10.3389/fimmu.2022.770982] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 02/15/2022] [Indexed: 12/11/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is caused by a novel coronavirus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The spike protein (S) of SARS-CoV-2 is a major target for diagnosis and vaccine development because of its essential role in viral infection and host immunity. Currently, time-dependent responses of humoral immune system against various S protein epitopes are poorly understood. In this study, enzyme-linked immunosorbent assay (ELISA), peptide microarray, and antibody binding epitope mapping (AbMap) techniques were used to systematically analyze the dynamic changes of humoral immune responses against the S protein in a small cohort of moderate COVID-19 patients who were hospitalized for approximately two months after symptom onset. Recombinant truncated S proteins, target S peptides, and random peptides were used as antigens in the analyses. The assays demonstrated the dynamic IgM- and IgG recognition and reactivity against various S protein epitopes with patient-dependent patterns. Comprehensive analysis of epitope distribution along the spike gene sequence and spatial structure of the homotrimer S protein demonstrated that most IgM- and IgG-reactive peptides were clustered into similar genomic regions and were located at accessible domains. Seven S peptides were generally recognized by IgG antibodies derived from serum samples of all COVID-19 patients. The dynamic immune recognition signals from these seven S peptides were comparable to those of the entire S protein or truncated S1 protein. This suggested that the humoral immune system recognized few conserved S protein epitopes in most COVID-19 patients during the entire duration of humoral immune response after symptom onset. Furthermore, in this cohort, individual patients demonstrated stable immune recognition to certain S protein epitopes throughout their hospitalization period. Therefore, the dynamic characteristics of humoral immune responses to S protein have provided valuable information for accurate diagnosis and immunotherapy of COVID-19 patients.
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Affiliation(s)
- Lingyun Chen
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
- Department of Proteomics, Beijing Genomics Institution, Shenzhen, China
| | - Pengfei Pang
- Center for Interventional Medicine, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Huan Qi
- Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, China
| | - Keqiang Yan
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
- Department of Proteomics, Beijing Genomics Institution, Shenzhen, China
| | - Yan Ren
- Department of Proteomics, Beijing Genomics Institution, Shenzhen, China
| | - Mingliang Ma
- Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, China
| | - Ruyin Cao
- Department of Proteomics, Beijing Genomics Institution, Shenzhen, China
| | - Hua Li
- State Key laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Chuansheng Hu
- State Key laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Yang Li
- Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, China
| | - Jun Xia
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
- Department of Proteomics, Beijing Genomics Institution, Shenzhen, China
| | - Danyun Lai
- Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, China
| | - Yuliang Dong
- Department of Proteomics, Beijing Genomics Institution, Shenzhen, China
| | - Hewei Jiang
- Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, China
| | - Hainan Zhang
- Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, China
| | - Hong Shan
- Center for Interventional Medicine, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
- *Correspondence: Siqi Liu, ; Shengce Tao, ; Hong Shan,
| | - Shengce Tao
- Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, China
- *Correspondence: Siqi Liu, ; Shengce Tao, ; Hong Shan,
| | - Siqi Liu
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
- Department of Proteomics, Beijing Genomics Institution, Shenzhen, China
- *Correspondence: Siqi Liu, ; Shengce Tao, ; Hong Shan,
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24
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Ercanoglu MS, Gieselmann L, Dähling S, Poopalasingam N, Detmer S, Koch M, Korenkov M, Halwe S, Klüver M, Di Cristanziano V, Janicki H, Schlotz M, Worczinski J, Gathof B, Gruell H, Zehner M, Becker S, Vanshylla K, Kreer C, Klein F. No substantial preexisting B cell immunity against SARS-CoV-2 in healthy adults. iScience 2022; 25:103951. [PMID: 35224466 PMCID: PMC8857777 DOI: 10.1016/j.isci.2022.103951] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/22/2021] [Accepted: 02/16/2022] [Indexed: 11/29/2022] Open
Abstract
Preexisting immunity against SARS-CoV-2 may have critical implications for our understanding of COVID-19 susceptibility and severity. The presence and clinical relevance of a preexisting B cell immunity remain to be fully elucidated. Here, we provide a detailed analysis of the B cell immunity to SARS-CoV-2 in unexposed individuals. To this end, we extensively investigated SARS-CoV-2 humoral immunity in 150 adults sampled pre-pandemically. Comprehensive screening of donor plasma and purified IgG samples for binding and neutralization in various functional assays revealed no substantial activity against SARS-CoV-2 but broad reactivity to endemic betacoronaviruses. Moreover, we analyzed antibody sequences of 8,174 putatively SARS-CoV-2-reactive B cells at a single cell level and generated and tested 158 monoclonal antibodies. None of these antibodies displayed relevant binding or neutralizing activity against SARS-CoV-2. Taken together, our results show no evidence of competent preexisting antibody and B cell immunity against SARS-CoV-2 in unexposed adults. Comprehensive analysis of the B cell response to SARS-CoV-2 in pre-pandemic samples No substantial plasma and IgG reactivity against SARS-CoV-2 MAbs isolated from pre-pandemic samples showed no SARS-CoV-2 neutralizing activity No indication of competent preexisting B cell immunity against SARS-CoV-2
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Affiliation(s)
- Meryem Seda Ercanoglu
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Lutz Gieselmann
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany.,German Center for Infection Research, Partner Site Bonn-Cologne, 50931 Cologne, Germany
| | - Sabrina Dähling
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Nareshkumar Poopalasingam
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Susanne Detmer
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Manuel Koch
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany.,Institute for Dental Research and Oral Musculoskeletal Biology and Center for Biochemistry, University of Cologne, 50931 Cologne, Germany
| | - Michael Korenkov
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Sandro Halwe
- Institute of Virology, Philipps University Marburg, Hans-Meerwein-Straße 2, 35042 Marburg, Germany.,German Center for Infection Research, Partner Site Giessen-Marburg-Langen, 35043 Marburg, Germany
| | - Michael Klüver
- Institute of Virology, Philipps University Marburg, Hans-Meerwein-Straße 2, 35042 Marburg, Germany.,German Center for Infection Research, Partner Site Giessen-Marburg-Langen, 35043 Marburg, Germany
| | - Veronica Di Cristanziano
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Hanna Janicki
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Maike Schlotz
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Johanna Worczinski
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Birgit Gathof
- Institute of Transfusion Medicine, Faculty of Medicine and University Hospital Cologne, 50937 Cologne, Germany
| | - Henning Gruell
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany.,German Center for Infection Research, Partner Site Bonn-Cologne, 50931 Cologne, Germany
| | - Matthias Zehner
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany.,German Center for Infection Research, Partner Site Bonn-Cologne, 50931 Cologne, Germany
| | - Stephan Becker
- Institute of Virology, Philipps University Marburg, Hans-Meerwein-Straße 2, 35042 Marburg, Germany.,German Center for Infection Research, Partner Site Giessen-Marburg-Langen, 35043 Marburg, Germany
| | - Kanika Vanshylla
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Christoph Kreer
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany.,German Center for Infection Research, Partner Site Bonn-Cologne, 50931 Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
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25
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Wu M, Pan W, Jia C, He Z, Zhao M, Tang C, Chang C, Li S, Wu H, Lu Q. Systemic lupus erythematosus patients contain B cell receptor repertoires sensitive to immunosuppressive drugs. Eur J Immunol 2022; 52:669-680. [PMID: 35092307 DOI: 10.1002/eji.202149596] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 11/30/2021] [Accepted: 01/03/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Meiyu Wu
- Hunan Key Laboratory of Medical Epigenomics Department of Dermatology Second Xiangya Hospital Central South University Changsha China
| | - Wenjing Pan
- Nanjing ARP Biotechnology Co., Ltd Nanjing China
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices Hunan University of Technology Zhuzhou China
| | - Chen Jia
- Hunan Key Laboratory of Medical Epigenomics Department of Dermatology Second Xiangya Hospital Central South University Changsha China
| | - Zhenghao He
- Hunan Key Laboratory of Medical Epigenomics Department of Dermatology Second Xiangya Hospital Central South University Changsha China
| | - Ming Zhao
- Hunan Key Laboratory of Medical Epigenomics Department of Dermatology Second Xiangya Hospital Central South University Changsha China
| | - Congli Tang
- Nanjing ARP Biotechnology Co., Ltd Nanjing China
| | - Christopher Chang
- Christopher Chang Division of Rheumatology Allergy and Clinical Immunology University of California at Davis School of Medicine Davis California USA
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices Hunan University of Technology Zhuzhou China
| | - Haijing Wu
- Hunan Key Laboratory of Medical Epigenomics Department of Dermatology Second Xiangya Hospital Central South University Changsha China
| | - Qianjin Lu
- Hunan Key Laboratory of Medical Epigenomics Department of Dermatology Second Xiangya Hospital Central South University Changsha China
- Institute of Dermatology Chinese Academy of Medical Sciences and Peking Union Medical College Nanjing China
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26
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Li Y, Hu J, Wang Y, Liu D, Shi Y, Zhang J, Liu Y, Lin D, Lin J, Hu W, He H, Wang W, Fan W, Li L, Wang D, Wang K, Xu J. T-Cell Repertoire Characteristics of Asymptomatic and Re-Detectable Positive COVID-19 Patients. Front Immunol 2022; 12:769442. [PMID: 35154070 PMCID: PMC8828559 DOI: 10.3389/fimmu.2021.769442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/24/2021] [Indexed: 01/01/2023] Open
Abstract
The prevention of the COVID-19 pandemic is highly complicated by the prevalence of asymptomatic and recurrent infection. Many previous immunological studies have focused on symptomatic and convalescent patients, while the immune responses in asymptomatic patients and re-detectable positive cases remain unclear. Here we comprehensively analyzed the peripheral T-cell receptor (TCR) repertoire of 54 COVID-19 patients in different courses, including asymptomatic, symptomatic, convalescent, and re-detectable positive cases. We identified a set of V-J gene combinations characterizing the upward immune responses through asymptomatic and symptomatic courses. Furthermore, some of these V-J combinations could be awakened in the re-detectable positive cases, which may help predict the risk of recurrent infection. Therefore, TCR repertoire examination has the potential to strengthen the clinical surveillance and the immunotherapy development for COVID-19.
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Affiliation(s)
- Yizhe Li
- Department of Laboratory Medicine, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
| | - Jian Hu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yongsi Wang
- Department of Translational Medicine Research Institute, Guangzhou Huayin Medical Laboratory Center Ltd., Guangzhou, China
| | - Dongdong Liu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yaling Shi
- Department of Laboratory Medicine, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Jiaqi Zhang
- Department of Laboratory Medicine, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yuntao Liu
- Emergency Department, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Dongzi Lin
- Department of Laboratory Medicine, The Fourth People’s Hospital of Foshan, Foshan, China
| | - Jing Lin
- Department of Clinical Laboratory, The First People’s Hospital of Foshan, Foshan, China
| | - Wei Hu
- Department of Laboratory Medicine, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
| | - Haolan He
- Department of Infectious Diseases, Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Wei Wang
- Department of Laboratory Medicine, The Fourth People’s Hospital of Foshan, Foshan, China
| | - Wentao Fan
- Department of Translational Medicine Research Institute, Guangzhou Huayin Medical Laboratory Center Ltd., Guangzhou, China
| | - Linlin Li
- Department of Translational Medicine Research Institute, Guangzhou Huayin Medical Laboratory Center Ltd., Guangzhou, China
| | - Dawei Wang
- Department of Pulmonary and Critical Care Medicine, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
| | - Kejian Wang
- The Third Affiliated Hospital of Shandong First Medical University (Affiliated Hospital of Shandong Academy of Medical Sciences), Jinan, China
- Innovative Institute of Chinese Medicine and Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jianhua Xu
- Department of Laboratory Medicine, Shunde Hospital of Guangzhou University of Chinese Medicine, Foshan, China
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27
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Gededzha MP, Mampeule N, Gandini A, Mayne ES. SARS-CoV-2 Host Immunogenetic Biomarkers. Methods Mol Biol 2022; 2511:133-147. [PMID: 35838957 DOI: 10.1007/978-1-0716-2395-4_10] [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] [Indexed: 06/15/2023]
Abstract
SARS-CoV-2 causes generally mild symptoms, with approximately 10-20% of cases progressing to severe disease. The pathophysiologic mechanisms by which SARS-CoV-2 causes severe disease are largely unknown. Data have indicated the involvement of different immunogenetic markers such as HLA, T, and B cells, to be associated with disease outcome. This has led to interest in these genes as potential biomarkers of SARS-CoV-2 susceptibility and for predicting prognosis and response to vaccines and other therapeutic strategies. In this chapter, we discussed outline protocols for characterizing these potential biomarkers and methods for identifying SARS-CoV-2 biomarkers using the Luminex® 100/200 technology and next-generation sequencing.
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Affiliation(s)
- Maemu P Gededzha
- Department of Immunology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- National Health Laboratory Services, Johannesburg, South Africa.
| | - Nakampe Mampeule
- Department of Immunology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Health Laboratory Services, Johannesburg, South Africa
| | - Anastasia Gandini
- Department of Immunology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Health Laboratory Services, Johannesburg, South Africa
| | - Elizabeth S Mayne
- Department of Immunology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Health Laboratory Services, Johannesburg, South Africa
- Division of Immunology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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28
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Nitahara Y, Nakagama Y, Kaku N, Candray K, Michimuko Y, Tshibangu-Kabamba E, Kaneko A, Yamamoto H, Mizobata Y, Kakeya H, Yasugi M, Kido Y. High-Resolution Linear Epitope Mapping of the Receptor Binding Domain of SARS-CoV-2 Spike Protein in COVID-19 mRNA Vaccine Recipients. Microbiol Spectr 2021; 9:e0096521. [PMID: 34756082 PMCID: PMC8579840 DOI: 10.1128/spectrum.00965-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/21/2021] [Indexed: 12/14/2022] Open
Abstract
The prompt rollout of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mRNA vaccine is facilitating population immunity, which is becoming more dominant than natural infection-mediated immunity. In the midst of coronavirus disease 2019 (COVID-19) vaccine deployment, understanding the epitope profiles of vaccine-elicited antibodies will be the first step in assessing the functionality of vaccine-induced immunity. In this study, the high-resolution linear epitope profiles of Pfizer-BioNTech COVID-19 mRNA vaccine recipients and COVID-19 patients were delineated by using microarrays mapped with overlapping peptides of the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. The vaccine-induced antibodies targeting the RBD had a broader distribution across the RBD than that induced by the natural infection. Half-maximal neutralization titers were measured in vitro by live virus neutralization assays. As a result, relatively lower neutralizability was observed in vaccine recipient sera, when normalized to a total anti-RBD IgG titer. However, mutation panel assays targeting the SARS-CoV-2 variants of concern have shown that the vaccine-induced epitope variety, rich in breadth, may grant resistance against future viral evolutionary escapes, serving as an advantage of vaccine-induced immunity. IMPORTANCE Establishing vaccine-based population immunity has been the key factor in attaining herd protection. Thanks to expedited worldwide research efforts, the potency of mRNA vaccines against the coronavirus disease 2019 (COVID-19) is now incontestable. The next debate is regarding the coverage of SARS-CoV-2 variants. In the midst of vaccine deployment, it is of importance to describe the similarities and differences between the immune responses of COVID-19 vaccine recipients and naturally infected individuals. In this study, we demonstrated that the antibody profiles of vaccine recipients are richer in variety, targeting a key protein of the invading virus, than those of naturally infected individuals. Vaccine-elicited antibodies included more nonneutralizing antibodies than infection-elicited antibodies, and their breadth in antibody variations suggested possible resilience against future SARS-CoV-2 variants. The antibody profile achieved by vaccinations in naive individuals provides important insight into the first step toward vaccine-based population immunity.
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Affiliation(s)
- Yuko Nitahara
- Department of Parasitology & Research Center for Infectious Disease Sciences, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Yu Nakagama
- Department of Parasitology & Research Center for Infectious Disease Sciences, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Natsuko Kaku
- Department of Parasitology & Research Center for Infectious Disease Sciences, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Katherine Candray
- Department of Parasitology & Research Center for Infectious Disease Sciences, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Yu Michimuko
- Department of Parasitology & Research Center for Infectious Disease Sciences, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Evariste Tshibangu-Kabamba
- Department of Parasitology & Research Center for Infectious Disease Sciences, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Akira Kaneko
- Department of Parasitology & Research Center for Infectious Disease Sciences, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Hiromasa Yamamoto
- Department of Traumatology and Critical Care Medicine, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Yasumitsu Mizobata
- Department of Traumatology and Critical Care Medicine, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Hiroshi Kakeya
- Department of Infection Control Science, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Mayo Yasugi
- Department of Veterinary Science, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
- Osaka International Research Center for Infectious Diseases, Osaka Prefecture University, Izumisano, Osaka, Japan
- Asian Health Science Research Institute, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - Yasutoshi Kido
- Department of Parasitology & Research Center for Infectious Disease Sciences, Graduate School of Medicine, Osaka City University, Osaka, Japan
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29
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Atanackovic D, Avila SV, Lutfi F, de Miguel-Perez D, Fan X, Sanchez-Petitto G, Vander Mause E, Siglin J, Baddley J, Mannuel HD, Alkhaldi H, Hankey KG, Lapidus R, Kleinberg M, Rabin J, Shanholtz C, Rolfo C, Rapoport AP, Dahiya S, Luetkens T. Deep dissection of the antiviral immune profile of patients with COVID-19. Commun Biol 2021; 4:1389. [PMID: 34916602 PMCID: PMC8677724 DOI: 10.1038/s42003-021-02852-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 11/02/2021] [Indexed: 12/23/2022] Open
Abstract
In light of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants potentially undermining humoral immunity, it is important to understand the fine specificity of the antiviral antibodies. We screened 20 COVID-19 patients for antibodies against 9 different SARS-CoV-2 proteins observing responses against the spike (S) proteins, the receptor-binding domain (RBD), and the nucleocapsid (N) protein which were of the IgG1 and IgG3 subtypes. Importantly, mutations which typically occur in the B.1.351 "South African" variant, significantly reduced the binding of anti-RBD antibodies. Nine of 20 patients were critically ill and were considered high-risk (HR). These patients showed significantly higher levels of transforming growth factor beta (TGF-β) and myeloid-derived suppressor cells (MDSC), and lower levels of CD4+ T cells expressing LAG-3 compared to standard-risk (SR) patients. HR patients evidenced significantly higher anti-S1/RBD IgG antibody levels and an increased neutralizing activity. Importantly, a large proportion of S protein-specific antibodies were glycosylation-dependent and we identified a number of immunodominant linear epitopes within the S1 and N proteins. Findings derived from this study will not only help us to identify the most relevant component of the anti-SARS-CoV-2 humoral immune response but will also enable us to design more meaningful immunomonitoring methods for anti-COVID-19 vaccines.
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Affiliation(s)
- Djordje Atanackovic
- Transplant and Cellular Therapy Program, Department of Medicine, University of Maryland School of Medicine and Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA.
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD, USA.
| | - Stephanie V Avila
- Transplant and Cellular Therapy Program, Department of Medicine, University of Maryland School of Medicine and Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA
| | - Forat Lutfi
- University of Maryland School of Medicine and Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA
| | - Diego de Miguel-Perez
- University of Maryland School of Medicine and Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA
| | - Xiaoxuan Fan
- University of Maryland School of Medicine and Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA
| | - Gabriela Sanchez-Petitto
- University of Maryland School of Medicine and Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA
| | - Erica Vander Mause
- Transplant and Cellular Therapy Program, Department of Medicine, University of Maryland School of Medicine and Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA
| | - Jonathan Siglin
- University of Maryland School of Medicine and Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA
| | - John Baddley
- Division of Infectious Diseases, University of Maryland School of Medicine and Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA
| | - Heather D Mannuel
- Hematology/Oncology, University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA
- Baltimore Veterans Affairs Medical Center, Baltimore, MD, USA
| | - Hanan Alkhaldi
- University of Maryland School of Medicine and Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA
| | - Kim G Hankey
- Transplant and Cellular Therapy Program, Department of Medicine, University of Maryland School of Medicine and Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA
| | - Rena Lapidus
- University of Maryland School of Medicine and Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA
| | - Michael Kleinberg
- Division of Infectious Diseases, University of Maryland School of Medicine and Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA
| | - Joseph Rabin
- R. Adams Cowley Shock Trauma Center, Department of Surgery, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Carl Shanholtz
- Division of Pulmonary and Critical Care Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Christian Rolfo
- University of Maryland School of Medicine and Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA
| | - Aaron P Rapoport
- Transplant and Cellular Therapy Program, Department of Medicine, University of Maryland School of Medicine and Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA
| | - Saurabh Dahiya
- Transplant and Cellular Therapy Program, Department of Medicine, University of Maryland School of Medicine and Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA
| | - Tim Luetkens
- Transplant and Cellular Therapy Program, Department of Medicine, University of Maryland School of Medicine and Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland, Baltimore, MD, USA
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30
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Analysis of B cell receptor repertoires reveals key signatures of systemic B cell response after SARS-CoV-2 infection. J Virol 2021; 96:e0160021. [PMID: 34878902 PMCID: PMC8865482 DOI: 10.1128/jvi.01600-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
A comprehensive study of the B cell response against SARS-CoV-2 could be significant for understanding the immune response and developing therapeutical antibodies and vaccines. To define the dynamics and characteristics of the antibody repertoire following SARS-CoV-2 infection, we analyzed the mRNA transcripts of immunoglobulin heavy chain (IgH) repertoires of 24 peripheral blood samples collected between 3 and 111 days after symptom onset from 10 COVID-19 patients. Massive clonal expansion of naive B cells with limited somatic hypermutation (SHM) was observed in the second week after symptom onset. The proportion of low-SHM IgG clones strongly correlated with spike-specific IgG antibody titers, highlighting the significant activation of naive B cells in response to a novel virus infection. The antibody isotype switching landscape showed a transient IgA surge in the first week after symptom onset, followed by a sustained IgG elevation that lasted for at least 3 months. SARS-CoV-2 infection elicited poly-germ line reactive antibody responses. Interestingly, 17 different IGHV germ line genes recombined with IGHJ6 showed significant clonal expansion. By comparing the IgH repertoires that we sequenced with the 774 reported SARS-CoV-2–reactive monoclonal antibodies (MAbs), 13 shared spike-specific IgH clusters were found. These shared spike-specific IgH clusters are derived from the same lineage of several recently published neutralizing MAbs, including CC12.1, CC12.3, C102, REGN10977, and 4A8. Furthermore, identical spike-specific IgH sequences were found in different COVID-19 patients, suggesting a highly convergent antibody response to SARS-CoV-2. Our analysis based on sequencing antibody repertoires from different individuals revealed key signatures of the systemic B cell response induced by SARS-CoV-2 infection. IMPORTANCE Although the canonical delineation of serum antibody responses following SARS-CoV-2 infection has been well established, the dynamics of antibody repertoire at the mRNA transcriptional level has not been well understood, especially the correlation between serum antibody titers and the antibody mRNA transcripts. In this study, we analyzed the IgH transcripts and characterized the B cell clonal expansion and differentiation, isotype switching, and somatic hypermutation in COVID-19 patients. This study provided insights at the repertoire level for the B cell response after SARS-CoV-2 infection.
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31
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Rosati E, Pogorelyy MV, Minervina AA, Scheffold A, Franke A, Bacher P, Thomas PG. Characterization of SARS-CoV-2 public CD4+ αβ T cell clonotypes through reverse epitope discovery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.11.19.469229. [PMID: 34845450 PMCID: PMC8629193 DOI: 10.1101/2021.11.19.469229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
UNLABELLED The amount of scientific data and level of public sharing produced as a consequence of the COVID-19 pandemic, as well as the speed at which these data were produced, far exceeds any previous effort against a specific disease condition. This unprecedented situation allows for development and application of new research approaches. One of the major technical hurdles in immunology is the characterization of HLA-antigen-T cell receptor (TCR) specificities. Most approaches aim to identify reactive T cells starting from known antigens using functional assays. However, the need for a reverse approach identifying the antigen specificity of orphan TCRs is increasing. Utilizing large public single-cell gene expression and TCR datasets, we identified highly public CD4 + T cell responses to SARS-CoV-2, covering >75% of the analysed population. We performed an integrative meta-analysis to deeply characterize these clonotypes by TCR sequence, gene expression, HLA-restriction, and antigen-specificity, identifying strong and public CD4 + immunodominant responses with confirmed specificity. CD4 + COVID-enriched clonotypes show T follicular helper functional features, while clonotypes depleted in SARS-CoV-2 individuals preferentially had a central memory phenotype. In total we identify more than 1200 highly public CD4+ T cell clonotypes reactive to SARS-CoV-2. TCR similarity analysis showed six prominent TCR clusters, for which we predicted both HLA-restriction and cognate SARS-CoV-2 immunodominant epitopes. To validate our predictions we used an independent cohort of TCR repertoires before and after vaccination with ChAdOx1 , a replication-deficient simian adenovirus-vectored vaccine, encoding the SARS-CoV-2 spike protein. We find statistically significant enrichment of the predicted spike-reactive TCRs after vaccination with ChAdOx1 , while the frequency of TCRs specific to other SARS-CoV-2 proteins remains stable. Thus, the CD4-associated TCR repertoire differentiates vaccination from natural infection. In conclusion, our study presents a novel reverse epitope discovery approach that can be used to infer HLA- and antigen-specificity of orphan TCRs in any context, such as viral infections, antitumor immune responses, or autoimmune disease. HIGHLIGHTS Identification of highly public CD4+ T cell responses to SARS-CoV-2Systematic prediction of exact immunogenic HLA class II epitopes for CD4+ T cell responseMethodological framework for reverse epitope discovery, which can be applied to other disease contexts and may provide essential insights for future studies and clinical applications.
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32
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Mazzoni A, Salvati L, Maggi L, Annunziato F, Cosmi L. Hallmarks of immune response in COVID-19: Exploring dysregulation and exhaustion. Semin Immunol 2021; 55:101508. [PMID: 34728121 PMCID: PMC8547971 DOI: 10.1016/j.smim.2021.101508] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/11/2021] [Accepted: 10/15/2021] [Indexed: 01/08/2023]
Abstract
One and half year following the occurrence of COVID-19 pandemic, significant efforts from laboratories all over the world generated a huge amount of data describing the prototypical features of immunity in the course of SARS-CoV-2 infection. In this Review, we rationalize and organize the main observations, trying to define a “core” signature of immunity in COVID-19. We identified six hallmarks describing the main alterations occurring in the early infection phase and in the course of the disease, which predispose to severe illness. The six hallmarks are dysregulated type I IFN activity, hyperinflammation, lymphopenia, lymphocyte impairment, dysregulated myeloid response, and heterogeneous adaptive immunity to SARS-CoV-2. Dysregulation and exhaustion came out as the trait d’union, connecting abnormalities affecting both innate and adaptive immunity, humoral and cellular responses.
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Affiliation(s)
- Alessio Mazzoni
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Lorenzo Salvati
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Laura Maggi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Francesco Annunziato
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.
| | - Lorenzo Cosmi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
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33
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Single-cell immune profiling reveals distinct immune response in asymptomatic COVID-19 patients. Signal Transduct Target Ther 2021; 6:342. [PMID: 34531370 PMCID: PMC8443960 DOI: 10.1038/s41392-021-00753-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 08/26/2021] [Accepted: 08/26/2021] [Indexed: 12/13/2022] Open
Abstract
While some individuals infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) present mild-to-severe disease, many SARS-CoV-2-infected individuals are asymptomatic. We sought to identify the distinction of immune response between asymptomatic and moderate patients. We performed single-cell transcriptome and T-cell/B-cell receptor (TCR/BCR) sequencing in 37 longitudinal collected peripheral blood mononuclear cell samples from asymptomatic, moderate, and severe patients with healthy controls. Asymptomatic patients displayed increased CD56briCD16− natural killer (NK) cells and upregulation of interferon-gamma in effector CD4+ and CD8+ T cells and NK cells. They showed more robust TCR clonal expansion, especially in effector CD4+ T cells, but lack strong BCR clonal expansion compared to moderate patients. Moreover, asymptomatic patients have lower interferon-stimulated genes (ISGs) expression in general but large interpatient variability, whereas moderate patients showed various magnitude and temporal dynamics of the ISGs expression across multiple cell populations but lower than a patient with severe disease. Our data provide evidence of different immune signatures to SARS-CoV-2 in asymptomatic infections.
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34
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Liu H, Pan W, Tang C, Tang Y, Wu H, Yoshimura A, Deng Y, He N, Li S. The methods and advances of adaptive immune receptors repertoire sequencing. Theranostics 2021; 11:8945-8963. [PMID: 34522220 PMCID: PMC8419057 DOI: 10.7150/thno.61390] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/09/2021] [Indexed: 12/13/2022] Open
Abstract
The adaptive immune response is a powerful tool, capable of recognizing, binding to, and neutralizing a vast number of internal and external threats via T or B lymphatic receptors with widespread sets of antigen specificities. The emergence of high-throughput sequencing technology and bioinformatics provides opportunities for research in the fields of life sciences and medicine. The analysis and annotation for immune repertoire data can reveal biologically meaningful information, including immune prediction, target antigens, and effective evaluation. Continuous improvements of the immunological repertoire sequencing methods and analysis tools will help to minimize the experimental and calculation errors and realize the immunological information to meet the clinical requirements. That said, the clinical application of adaptive immune repertoire sequencing requires appropriate experimental methods and standard analytical tools. At the population cell level, we can acquire the overview of cell groups, but the information about a single cell is not obtained accurately. The information that is ignored may be crucial for understanding the heterogeneity of each cell, gene expression and drug response. The combination of high-throughput sequencing and single-cell technology allows us to obtain single-cell information with low-cost and high-throughput. In this review, we summarized the current methods and progress in this area.
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Affiliation(s)
- Hongmei Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Wenjing Pan
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Congli Tang
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Yujie Tang
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Haijing Wu
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hu-nan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China
| | - Akihiko Yoshimura
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Nongyue He
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
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35
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Massive surge of mRNA expression of clonal B-cell receptor in patients with COVID-19. Heliyon 2021; 7:e07748. [PMID: 34395931 PMCID: PMC8352648 DOI: 10.1016/j.heliyon.2021.e07748] [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: 04/02/2021] [Revised: 07/19/2021] [Accepted: 08/06/2021] [Indexed: 12/03/2022] Open
Abstract
Background Antibody production is one of the primary mechanisms for recovery from coronavirus disease 2019 (COVID-19). It is speculated that massive clonal expansion of B cells, which can produce clinically meaningful neutralizing antibodies, occurs in patients who recover on the timing of acquiring adaptive immunity. Methods To evaluate fluctuations in clonal B cells and the size of the clones, we chronologically assessed the B-cell receptor (BCR) repertoire in three patients with COVID-19 who recovered around 10 days after symptom onset. Results We focused on the three dominant clonotypes (top 3) in each individual. The percentage frequencies of the top 3 clonotypes increased rapidly and accounted for 27.8 % on day 9 in patient 1, 10.4 % on day 12 in patient 2, and 10.8 % on day 11 in patient 3, respectively. The frequencies of these top 3 clonotypes rapidly decreased as the patients’ clinical symptoms improved. Furthermore, BCR network analysis revealed that accumulation of clusters composed of similar complementarity-determining region 3 (CDR3) sequences were rapidly formed, grew, and reached their maximum size around 10 days after symptom onset. Conclusions BCR repertoire analysis revealed that a massive surge of some unique BCRs occurs during the acquisition of adaptive immunity and recovery. The peaks were more prominent than expected. These results provide insight into the important role of BCRs in the recovery from COVID-19 and raise the possibility of developing neutralizing antibodies as COVID-19 immunotherapy.
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36
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Kaidashev I, Shlykova O, Izmailova O, Torubara O, Yushchenko Y, Tyshkovska T, Kyslyi V, Belyaeva A, Maryniak D. Host gene variability and SARS-CoV-2 infection: A review article. Heliyon 2021; 7:e07863. [PMID: 34458641 PMCID: PMC8382593 DOI: 10.1016/j.heliyon.2021.e07863] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/15/2021] [Accepted: 08/19/2021] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2 is a global threat that influenced healthcare systems around the world. This virus caused an infection in humans with different clinical signs and syndromes, severity, and mortality. The key components of the COVID-19 molecular pathogenesis are coronavirus entry and replication, antigen presentation, humoral and cellular immunity, cytokine storm, coronavirus immune evasion. The analysis of recent literature displayed possible molecular targets in the key components of the COVID-19 pathogenesis. Some of these targets might have gene polymorphisms that influenced the COVID-19 course. Unfortunately, several findings are still putative or extrapolated from SARS and MERS experimental investigations or clinical trials. We systematised original data about gene polymorphisms of possible molecular targets and associations with the COVID-19 course. Most data were obtained for angiotensin-converting enzymes 1 and 2, TMPRSS2 gene polymorphisms. Only a few results were found for gene polymorphisms of adhesion molecules, interferon system components, cytokines, and transcriptional factors, oxidative stress and metabolic molecules, as well as haemocoagulation. Understanding the host gene variability and its associations with COVID-19 can provide insights into the disease pathogenesis, individual susceptibility to SARS-CoV-2 infection, severity, complications, and mortality prognosis for the disease. Besides, these data might help in the identification of appropriate targets for intervention.
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Affiliation(s)
- I. Kaidashev
- Poltava State Medical University, Poltava, Ukraine
| | - O. Shlykova
- Poltava State Medical University, Poltava, Ukraine
| | - O. Izmailova
- Poltava State Medical University, Poltava, Ukraine
| | - O. Torubara
- Poltava State Medical University, Poltava, Ukraine
| | | | | | - V. Kyslyi
- Poltava State Medical University, Poltava, Ukraine
| | - A. Belyaeva
- Poltava State Medical University, Poltava, Ukraine
| | - D. Maryniak
- Poltava State Medical University, Poltava, Ukraine
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37
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Prokop JW, Hartog NL, Chesla D, Faber W, Love CP, Karam R, Abualkheir N, Feldmann B, Teng L, McBride T, Leimanis ML, English BK, Holsworth A, Frisch A, Bauss J, Kalpage N, Derbedrossian A, Pinti RM, Hale N, Mills J, Eby A, VanSickle EA, Pageau SC, Shankar R, Chen B, Carcillo JA, Sanfilippo D, Olivero R, Bupp CP, Rajasekaran S. High-Density Blood Transcriptomics Reveals Precision Immune Signatures of SARS-CoV-2 Infection in Hospitalized Individuals. Front Immunol 2021; 12:694243. [PMID: 34335605 PMCID: PMC8322982 DOI: 10.3389/fimmu.2021.694243] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/30/2021] [Indexed: 12/27/2022] Open
Abstract
The immune response to COVID-19 infection is variable. How COVID-19 influences clinical outcomes in hospitalized patients needs to be understood through readily obtainable biological materials, such as blood. We hypothesized that a high-density analysis of host (and pathogen) blood RNA in hospitalized patients with SARS-CoV-2 would provide mechanistic insights into the heterogeneity of response amongst COVID-19 patients when combined with advanced multidimensional bioinformatics for RNA. We enrolled 36 hospitalized COVID-19 patients (11 died) and 15 controls, collecting 74 blood PAXgene RNA tubes at multiple timepoints, one early and in 23 patients after treatment with various therapies. Total RNAseq was performed at high-density, with >160 million paired-end, 150 base pair reads per sample, representing the most sequenced bases per sample for any publicly deposited blood PAXgene tube study. There are 770 genes significantly altered in the blood of COVID-19 patients associated with antiviral defense, mitotic cell cycle, type I interferon signaling, and severe viral infections. Immune genes activated include those associated with neutrophil mechanisms, secretory granules, and neutrophil extracellular traps (NETs), along with decreased gene expression in lymphocytes and clonal expansion of the acquired immune response. Therapies such as convalescent serum and dexamethasone reduced many of the blood expression signatures of COVID-19. Severely ill or deceased patients are marked by various secondary infections, unique gene patterns, dysregulated innate response, and peripheral organ damage not otherwise found in the cohort. High-density transcriptomic data offers shared gene expression signatures, providing unique insights into the immune system and individualized signatures of patients that could be used to understand the patient’s clinical condition. Whole blood transcriptomics provides patient-level insights for immune activation, immune repertoire, and secondary infections that can further guide precision treatment.
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Affiliation(s)
- Jeremy W Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States.,Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, United States
| | - Nicholas L Hartog
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States.,Allergy & Immunology, Spectrum Health, Grand Rapids, MI, United States
| | - Dave Chesla
- Office of Research, Spectrum Health, Grand Rapids, MI, United States.,Department of Obstetrics, Gynecology and Reproductive Biology, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - William Faber
- Physical Sciences, Grand Rapids Community College, Grand Rapids, MI, United States
| | - Chanise P Love
- Office of Research, Spectrum Health, Grand Rapids, MI, United States
| | | | | | | | - Li Teng
- Ambry Genetics, Aliso Viejo, CA, United States
| | | | - Mara L Leimanis
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States.,Pediatric Intensive Care Unit, Helen DeVos Children's Hospital, Grand Rapids, MI, United States
| | - B Keith English
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Amanda Holsworth
- Allergy & Immunology, Spectrum Health, Grand Rapids, MI, United States
| | - Austin Frisch
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Jacob Bauss
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Nathisha Kalpage
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Aram Derbedrossian
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Ryan M Pinti
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Nicole Hale
- The Department of Chemistry and Biochemistry, Calvin University, Grand Rapids, MI, United States
| | - Joshua Mills
- Department of Biology, Grand Valley State University, Allendale, MI, United States
| | - Alexandra Eby
- Department of Science, Davenport University, Grand Rapids, MI, United States
| | | | - Spencer C Pageau
- Office of Research, Spectrum Health, Grand Rapids, MI, United States
| | - Rama Shankar
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States.,Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, United States
| | - Bin Chen
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States.,Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, United States
| | - Joseph A Carcillo
- Department of Critical Care Medicine and Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Dominic Sanfilippo
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States.,Pediatric Intensive Care Unit, Helen DeVos Children's Hospital, Grand Rapids, MI, United States
| | - Rosemary Olivero
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States.,Infectious Disease, Helen DeVos Children's Hospital, Grand Rapids, MI, United States
| | - Caleb P Bupp
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States.,Medical Genetics, Spectrum Health Medical Genetics, Grand Rapids, MI, United States
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States.,Office of Research, Spectrum Health, Grand Rapids, MI, United States.,Pediatric Intensive Care Unit, Helen DeVos Children's Hospital, Grand Rapids, MI, United States
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Bieberich F, Vazquez-Lombardi R, Yermanos A, Ehling RA, Mason DM, Wagner B, Kapetanovic E, Di Roberto RB, Weber CR, Savic M, Rudolf F, Reddy ST. A Single-Cell Atlas of Lymphocyte Adaptive Immune Repertoires and Transcriptomes Reveals Age-Related Differences in Convalescent COVID-19 Patients. Front Immunol 2021; 12:701085. [PMID: 34322127 PMCID: PMC8312723 DOI: 10.3389/fimmu.2021.701085] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/24/2021] [Indexed: 01/23/2023] Open
Abstract
COVID-19 disease outcome is highly dependent on adaptive immunity from T and B lymphocytes, which play a critical role in the control, clearance and long-term protection against SARS-CoV-2. To date, there is limited knowledge on the composition of the T and B cell immune receptor repertoires [T cell receptors (TCRs) and B cell receptors (BCRs)] and transcriptomes in convalescent COVID-19 patients of different age groups. Here, we utilize single-cell sequencing (scSeq) of lymphocyte immune repertoires and transcriptomes to quantitatively profile the adaptive immune response in COVID-19 patients of varying age. We discovered highly expanded T and B cells in multiple patients, with the most expanded clonotypes coming from the effector CD8+ T cell population. Highly expanded CD8+ and CD4+ T cell clones show elevated markers of cytotoxicity (CD8: PRF1, GZMH, GNLY; CD4: GZMA), whereas clonally expanded B cells show markers of transition into the plasma cell state and activation across patients. By comparing young and old convalescent COVID-19 patients (mean ages = 31 and 66.8 years, respectively), we found that clonally expanded B cells in young patients were predominantly of the IgA isotype and their BCRs had incurred higher levels of somatic hypermutation than elderly patients. In conclusion, our scSeq analysis defines the adaptive immune repertoire and transcriptome in convalescent COVID-19 patients and shows important age-related differences implicated in immunity against SARS-CoV-2.
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Affiliation(s)
- Florian Bieberich
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | - Alexander Yermanos
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,Institute of Microbiology and Immunology, Department of Biology, ETH Zurich, Zurich, Switzerland.,Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland.,Botnar Research Centre for Child Health, Basel, Switzerland
| | - Roy A Ehling
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Derek M Mason
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,deepCDR Biologics AG, Basel, Switzerland
| | - Bastian Wagner
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Edo Kapetanovic
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | - Cédric R Weber
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,deepCDR Biologics AG, Basel, Switzerland
| | - Miodrag Savic
- Department of Biomedical Engineering, University of Basel, Allschwil, Switzerland.,Department of Surgery, Oral and Cranio-Maxillofacial Surgery, University Hospital Basel, Basel, Switzerland.,Department of Health, Economics and Health Directorate, Canton Basel-Landschaft, Switzerland
| | - Fabian Rudolf
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,Botnar Research Centre for Child Health, Basel, Switzerland
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Yan D, Yang J, Ji Z, Wang J, Lu X, Huang Y, Zhong C, Li L. Profiling T cell receptor β-chain in responders after immunization with recombinant hepatitis B vaccine. J Gene Med 2021; 23:e3367. [PMID: 34048625 DOI: 10.1002/jgm.3367] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 05/22/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND T cells with edited T cell receptor β-chain variable (TRBV) are involved in the immune response to recombinant hepatitis B surface antigen (rHBsAg) vaccine and the production of hepatitis B surface antibody (HBsAb). The immune repertoire (IR) profile and mechanism of vaccination positive responders (VPR) with rHBsAg are not fully understood. METHODS The IR of six VPRs (HBsAb+, HbsAg-) with rHBsAg vaccination was established by the high throughput sequencing technique and bioinformatics analysis and compared with those in five vaccination negative responders (VNRs) (HbsAb-, HbsAg-) who were also inoculated with rHBsAg. The repertoire features of the BV, BJ and V (CDR3) J genes and immune diversity in peripheral blood mononuclear cells, respectively, were analyzed for each subject. RESULTS There was no significant difference in sequencing amplification indices of each sample. However, TRBV15/BJ2-3 demonstrated significantly high expression levels in VPR compared to those in the VNR group (both p < 0.05). Further results showed that the BV15/BJ2-5 level was significantly increased for VPR compared to that of VNR group. Interestingly, the motif of CDR3 in TRBV15/BJ2-5 was mostly expressed as "GGETQ" or "GETQ". Additionally, there was no remarkable difference between the two groups of distribution with respect to the different clone expression levels of V (CDR3) J. CONCLUSIONS The features of IR in the VPR and VNR will contribute to the exploration of the mechanism of the positive response to rHBsAg, and also contribute to development of optimized hepatitis B vaccine, in addition to providing a partial interpretation of the VNR who has a relatively low infection with HBV.
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Affiliation(s)
- Dong Yan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; National Clinical Research Center for Infectious Diseases; the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiezuan Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; National Clinical Research Center for Infectious Diseases; the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhongkang Ji
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; National Clinical Research Center for Infectious Diseases; the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ju Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; National Clinical Research Center for Infectious Diseases; the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoqing Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; National Clinical Research Center for Infectious Diseases; the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yandi Huang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; National Clinical Research Center for Infectious Diseases; the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chengli Zhong
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; National Clinical Research Center for Infectious Diseases; the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; National Clinical Research Center for Infectious Diseases; the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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40
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De Sanctis JB, García AH, Moreno D, Hajduch M. Coronavirus infection: An immunologists' perspective. Scand J Immunol 2021; 93:e13043. [PMID: 33783027 PMCID: PMC8250184 DOI: 10.1111/sji.13043] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/15/2021] [Accepted: 03/25/2021] [Indexed: 02/06/2023]
Abstract
Coronavirus infections are frequent viral infections in several species. As soon as the severe acute respiratory syndrome (SARS) appeared in the early 2000s, most of the research focused on pulmonary disease. However, disorders in immune response and organ dysfunctions have been documented. Elderly individuals with comorbidities exhibit worse outcomes in all the coronavirus that cause SARS. Disease severity in SARS-CoV-2 infection is related to severe inflammation and tissue injury, and effective immune response against the virus is still under analysis. ACE2 receptor expression and polymorphism, age, gender and immune genetics are factors that also play an essential role in patients' clinical features and immune responses and have been partially discussed. The present report aims to review the physiopathology of SARS-CoV-2 infection and propose new research topics to understand the complex mechanisms of viral infection and viral clearance.
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Affiliation(s)
- Juan Bautista De Sanctis
- Institute of Molecular and Translational MedicineFaculty of Medicine and DentistryPalacky UniversityOlomoucCzech Republic
- Institute of ImmunologyFaculty of MedicineUniversidad Central de VenezuelaCaracasVenezuela
| | - Alexis Hipólito García
- Institute of ImmunologyFaculty of MedicineUniversidad Central de VenezuelaCaracasVenezuela
| | - Dolores Moreno
- Chair of General Pathology and PathophysiologyFaculty of MedicineCentral University of VenezuelaCaracasVenezuela
| | - Marián Hajduch
- Institute of Molecular and Translational MedicineFaculty of Medicine and DentistryPalacky UniversityOlomoucCzech Republic
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41
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Montague Z, Lv H, Otwinowski J, DeWitt WS, Isacchini G, Yip GK, Ng WW, Tsang OTY, Yuan M, Liu H, Wilson IA, Peiris JSM, Wu NC, Nourmohammad A, Mok CKP. Dynamics of B cell repertoires and emergence of cross-reactive responses in patients with different severities of COVID-19. Cell Rep 2021; 35:109173. [PMID: 33991510 PMCID: PMC8106887 DOI: 10.1016/j.celrep.2021.109173] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 04/05/2021] [Accepted: 05/04/2021] [Indexed: 02/06/2023] Open
Abstract
Individuals with the 2019 coronavirus disease (COVID-19) show varying severity of the disease, ranging from asymptomatic to requiring intensive care. Although monoclonal antibodies specific to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been identified, we still lack an understanding of the overall landscape of B cell receptor (BCR) repertoires in individuals with COVID-19. We use high-throughput sequencing of bulk and plasma B cells collected at multiple time points during infection to characterize signatures of the B cell response to SARS-CoV-2 in 19 individuals. Using principled statistical approaches, we associate differential features of BCRs with different disease severity. We identify 38 significantly expanded clonal lineages shared among individuals as candidates for responses specific to SARS-CoV-2. Using single-cell sequencing, we verify the reactivity of BCRs shared among individuals to SARS-CoV-2 epitopes. Moreover, we identify the natural emergence of a BCR with cross-reactivity to SARS-CoV-1 and SARS-CoV-2 in some individuals. Our results provide insights important for development of rational therapies and vaccines against COVID-19.
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Affiliation(s)
- Zachary Montague
- Department of Physics, University of Washington, 3910 15th Ave. Northeast, Seattle, WA 98195, USA
| | - Huibin Lv
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Jakub Otwinowski
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Göttingen, Germany
| | - William S DeWitt
- Department of Genome Sciences, University of Washington, 3720 15th Ave. NE, Seattle, WA 98195, USA; Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA 98109, USA
| | - Giulio Isacchini
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Göttingen, Germany; Laboratoire de physique de l'ecole normale supérieure (PSL University), CNRS, Sorbonne Université, and Université de Paris, 75005 Paris, France
| | - Garrick K Yip
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Wilson W Ng
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Owen Tak-Yin Tsang
- Infectious Diseases Centre, Princess Margaret Hospital, Hospital Authority of Hong Kong, Hong Kong SAR, China
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hejun Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - J S Malik Peiris
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Nicholas C Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Armita Nourmohammad
- Department of Physics, University of Washington, 3910 15th Ave. Northeast, Seattle, WA 98195, USA; Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Göttingen, Germany; Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA 98109, USA.
| | - Chris Ka Pun Mok
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China; The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR, China.
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42
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Chang CM, Feng PH, Wu TH, Alachkar H, Lee KY, Chang WC. Profiling of T Cell Repertoire in SARS-CoV-2-Infected COVID-19 Patients Between Mild Disease and Pneumonia. J Clin Immunol 2021; 41:1131-1145. [PMID: 33950324 PMCID: PMC8096628 DOI: 10.1007/s10875-021-01045-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/14/2021] [Indexed: 01/01/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a public health emergency. The most common symptoms of COVID-19 are fever, cough, and fatigue. While most patients with COVID-19 present with mild illness, some patients develop pneumonia, an important risk factor for mortality, at early stage of viral infection, putting these patients at increased risk of death. So far, little has been known about differences in the T cell repertoires between COVID-19 patients with and without pneumonia during SARS-CoV-2 infection. Herein, we aimed to investigate T cell receptor (TCR) repertoire profiles and patient-specific SARS-CoV-2-associated TCR clusters between COVID-19 patients with mild disease (no sign of pneumonia) and pneumonia. The TCR sequencing was conducted to characterize the peripheral TCR repertoire profile and diversity. The TCR clustering and CDR3 annotation were exploited to further discover groups of patient-specific TCR clonotypes with potential SARS-CoV-2 antigen specificities. Our study indicated a slight decrease in the TCR repertoire diversity and a skewed CDR3 length usage in patients with pneumonia compared to those with mild disease. The SARS-CoV-2-associated TCR clusters enriched in patients with mild disease exhibited significantly higher TCR generation probabilities and most of which were highly shared among patients, compared with those from pneumonia patients. Importantly, using similarity network-based clustering followed by the sequence conservation analysis, we found different patterns of CDR3 sequence motifs between mild disease- and pneumonia-specific SARS-CoV-2-associated public TCR clusters. Our results showed that characteristics of overall TCR repertoire and SARS-CoV-2-associated TCR clusters/clonotypes were divergent between COVID-19 patients with mild disease and patients with pneumonia. These findings provide important insights into the correlation between the TCR repertoire and disease severity in COVID-19 patients.
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Affiliation(s)
- Che-Mai Chang
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Po-Hao Feng
- Division of Pulmonary Medicine, Department of Internal Medicine, Taipei Medical University-Shuang Ho Hospital, No. 291, Zhongzheng Rd., Zhonghe Dist., New Taipei City, 235, Taiwan
- Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Tsung-Hsun Wu
- Master Program in Clinical Pharmacogenomics and Pharmacoproteomics, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Houda Alachkar
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | - Kang-Yun Lee
- Division of Pulmonary Medicine, Department of Internal Medicine, Taipei Medical University-Shuang Ho Hospital, No. 291, Zhongzheng Rd., Zhonghe Dist., New Taipei City, 235, Taiwan.
- Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.
| | - Wei-Chiao Chang
- Master Program in Clinical Pharmacogenomics and Pharmacoproteomics, School of Pharmacy, Taipei Medical University, Taipei, Taiwan.
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, No. 250, Wuxing St., Xinyi Dist., Taipei, 110, Taiwan.
- Department of Pharmacy, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan.
- Integrative Research Center for Critical Care, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan.
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Montague Z, Lv H, Otwinowski J, DeWitt WS, Isacchini G, Yip GK, Ng WW, Tsang OTY, Yuan M, Liu H, Wilson IA, Peiris JSM, Wu NC, Nourmohammad A, Mok CKP. Dynamics of B-cell repertoires and emergence of cross-reactive responses in COVID-19 patients with different disease severity. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2020.07.13.20153114. [PMID: 32699862 PMCID: PMC7373151 DOI: 10.1101/2020.07.13.20153114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
COVID-19 patients show varying severity of the disease ranging from asymptomatic to requiring intensive care. Although a number of SARS-CoV-2 specific monoclonal antibodies have been identified, we still lack an understanding of the overall landscape of B-cell receptor (BCR) repertoires in COVID-19 patients. Here, we used high-throughput sequencing of bulk and plasma B-cells collected over multiple time points during infection to characterize signatures of B-cell response to SARS-CoV-2 in 19 patients. Using principled statistical approaches, we determined differential features of BCRs associated with different disease severity. We identified 38 significantly expanded clonal lineages shared among patients as candidates for specific responses to SARS-CoV-2. Using single-cell sequencing, we verified reactivity of BCRs shared among individuals to SARS-CoV-2 epitopes. Moreover, we identified natural emergence of a BCR with cross-reactivity to SARS-CoV-1 and SARS-CoV-2 in a number of patients. Our results provide important insights for development of rational therapies and vaccines against COVID-19.
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Affiliation(s)
- Zachary Montague
- Department of Physics, University of Washington, 3910 15th Ave Northeast, Seattle, WA 98195, USA
| | - Huibin Lv
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Jakub Otwinowski
- Max Planck Institute for Dynamics and Self-organization, Am Faßberg 17, 37077 Göttingen, Germany
| | - William S. DeWitt
- Department of Genome Sciences, University of Washington, 3720 15th Ave NE, Seattle, WA 98195, USA
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Giulio Isacchini
- Max Planck Institute for Dynamics and Self-organization, Am Faßberg 17, 37077 Göttingen, Germany
- Laboratoire de physique de l’ecole normale supérieure (PSL University), CNRS, Sorbonne Université, and Université de Paris, 75005 Paris, France
| | - Garrick K. Yip
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Wilson W. Ng
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Owen Tak-Yin Tsang
- Infectious Diseases Centre, Princess Margaret Hospital, Hospital Authority of Hong Kong
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hejun Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - J. S. Malik Peiris
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Nicholas C. Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Armita Nourmohammad
- Department of Physics, University of Washington, 3910 15th Ave Northeast, Seattle, WA 98195, USA
- Max Planck Institute for Dynamics and Self-organization, Am Faßberg 17, 37077 Göttingen, Germany
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Chris Ka Pun Mok
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
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Arnaout RA, Prak ETL, Schwab N, Rubelt F. The Future of Blood Testing Is the Immunome. Front Immunol 2021; 12:626793. [PMID: 33790897 PMCID: PMC8005722 DOI: 10.3389/fimmu.2021.626793] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 01/19/2021] [Indexed: 12/13/2022] Open
Abstract
It is increasingly clear that an extraordinarily diverse range of clinically important conditions—including infections, vaccinations, autoimmune diseases, transplants, transfusion reactions, aging, and cancers—leave telltale signatures in the millions of V(D)J-rearranged antibody and T cell receptor [TR per the Human Genome Organization (HUGO) nomenclature but more commonly known as TCR] genes collectively expressed by a person’s B cells (antibodies) and T cells. We refer to these as the immunome. Because of its diversity and complexity, the immunome provides singular opportunities for advancing personalized medicine by serving as the substrate for a highly multiplexed, near-universal blood test. Here we discuss some of these opportunities, the current state of immunome-based diagnostics, and highlight some of the challenges involved. We conclude with a call to clinicians, researchers, and others to join efforts with the Adaptive Immune Receptor Repertoire Community (AIRR-C) to realize the diagnostic potential of the immunome.
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Affiliation(s)
- Ramy A Arnaout
- Department of Pathology and Division of Clinical Informatics, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, United States.,Department of Pathology, Harvard Medical School, Boston, MA, United States
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Nicholas Schwab
- Department of Neurology and Institute of Translational Neurology, University of Muenster, Muenster, Germany
| | - Florian Rubelt
- Roche Sequencing Solutions, Pleasanton, CA, United States
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Hartog N, Faber W, Frisch A, Bauss J, Bupp CP, Rajasekaran S, Prokop JW. SARS-CoV-2 infection: molecular mechanisms of severe outcomes to suggest therapeutics. Expert Rev Proteomics 2021; 18:105-118. [PMID: 33779460 PMCID: PMC8022340 DOI: 10.1080/14789450.2021.1908894] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/22/2021] [Indexed: 02/06/2023]
Abstract
Introduction:The year 2020 was defined by the 29,903 base pairs of RNA that codes for the SARS-CoV-2 genome. SARS-CoV-2 infects humans to cause COVID-19, spreading from patient-to-patient yet impacts patients very divergently.Areas covered: Within this review, we address the known molecular mechanisms and supporting data for COVID-19 clinical course and pathology, clinical risk factors and molecular signatures, therapeutics of severe COVID-19, and reinfection/vaccination. Literature and published datasets were reviewed using PubMed, Google Scholar, and NCBI SRA tools. The combination of exaggerated cytokine signaling, pneumonia, NETosis, pyroptosis, thrombocytopathy, endotheliopathy, multiple organ dysfunction syndrome (MODS), and acute respiratory distress syndrome (ARDS) create a positive feedback loop of severe damage in patients with COVID-19 that impacts the entire body and may persist for months following infection. Understanding the molecular pathways of severe COVID-19 opens the door for novel therapeutic design. We summarize the current insights into pathology, risk factors, secondary infections, genetics, omics, and drugs being tested to treat severe COVID-19.Expert opinion: A growing level of support suggests the need for stronger integration of biomarkers and precision medicine to guide treatment strategies of severe COVID-19, where each patient has unique outcomes and thus require guided treatment.
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Affiliation(s)
- Nicholas Hartog
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
- Allergy & Immunology, Spectrum Health, Grand Rapids, MI, USA
| | - William Faber
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
- Department of Chemistry, Grand Rapids Community College, Grand Rapids, MI, USA
| | - Austin Frisch
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - Jacob Bauss
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - Caleb P Bupp
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
- Spectrum Health Medical Genetics, Grand Rapids, MI, USA
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
- Pediatric Intensive Care Unit, Helen DeVos Children’s Hospital, Grand Rapids, MI, USA
- Office of Research, Office of Research, Spectrum Health, Grand Rapids, MI, USA
| | - Jeremy W Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, USA
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Giroux NS, Ding S, McClain MT, Burke TW, Petzold E, Chung HA, Palomino GR, Wang E, Xi R, Bose S, Rotstein T, Nicholson BP, Chen T, Henao R, Sempowski GD, Denny TN, Ko ER, Ginsburg GS, Kraft BD, Tsalik EL, Woods CW, Shen X. Chromatin remodeling in peripheral blood cells reflects COVID-19 symptom severity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.12.04.412155. [PMID: 33300002 PMCID: PMC7724678 DOI: 10.1101/2020.12.04.412155] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
SARS-CoV-2 infection triggers highly variable host responses and causes varying degrees of illness in humans. We sought to harness the peripheral blood mononuclear cell (PBMC) response over the course of illness to provide insight into COVID-19 physiology. We analyzed PBMCs from subjects with variable symptom severity at different stages of clinical illness before and after IgG seroconversion to SARS-CoV-2. Prior to seroconversion, PBMC transcriptomes did not distinguish symptom severity. In contrast, changes in chromatin accessibility were associated with symptom severity. Furthermore, single-cell analyses revealed evolution of the chromatin accessibility landscape and transcription factor motif occupancy for individual PBMC cell types. The most extensive remodeling occurred in CD14+ monocytes where sub-populations with distinct chromatin accessibility profiles were associated with disease severity. Our findings indicate that pre-seroconversion chromatin remodeling in certain innate immune populations is associated with divergence in symptom severity, and the identified transcription factors, regulatory elements, and downstream pathways provide potential prognostic markers for COVID-19 subjects.
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Affiliation(s)
- Nicholas S. Giroux
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Shengli Ding
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Micah T. McClain
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC, USA
- Durham Veterans Affairs Health Care System, Durham, NC, USA
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - Thomas W. Burke
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC, USA
| | - Elizabeth Petzold
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC, USA
| | - Hong A. Chung
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Grecia R. Palomino
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Ergang Wang
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Rui Xi
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Shree Bose
- Department of Pharmacology and Cancer Biology, School of Medicine, Duke University, Durham, NC, USA
| | - Tomer Rotstein
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | | | - Tianyi Chen
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, USA
| | - Ricardo Henao
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC, USA
| | - Gregory D. Sempowski
- Duke Human Vaccine Institute and Department of Medicine, School of Medicine, Duke University, Durham, NC, USA
| | - Thomas N. Denny
- Duke Human Vaccine Institute and Department of Medicine, School of Medicine, Duke University, Durham, NC, USA
| | - Emily R. Ko
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC, USA
| | - Geoffrey S. Ginsburg
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC, USA
| | - Bryan D. Kraft
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC, USA
- Durham Veterans Affairs Health Care System, Durham, NC, USA
| | - Ephraim L. Tsalik
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC, USA
- Durham Veterans Affairs Health Care System, Durham, NC, USA
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - Christopher W. Woods
- Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC, USA
- Durham Veterans Affairs Health Care System, Durham, NC, USA
- Division of Infectious Diseases, Duke University Medical Center, Durham, NC, USA
| | - Xiling Shen
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
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