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Funakoshi Y, Yakushijin K, Ohji G, Matsutani T, Hojo W, Sakai H, Matsumoto S, Watanabe M, Kitao A, Saito Y, Kawamoto S, Yamamoto K, Koyama T, Nagatani Y, Kimbara S, Imamura Y, Kiyota N, Ito M, Minami H. Response to mRNA SARS-CoV-2 vaccination evaluated by B-cell receptor repertoire after tixagevimab/cilgavimab administration. Br J Haematol 2023; 202:504-516. [PMID: 37349876 DOI: 10.1111/bjh.18932] [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: 03/22/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/24/2023]
Abstract
The use of anti-SARS-CoV-2 antibody products like tixagevimab/cilgavimab represents an important strategy to protect immunocompromised patients with haematological malignancies from COVID-19. Although patients who receive these agents should still be vaccinated, the use of tixagevimab/cilgavimab can mask the production of anti-spike antibody after vaccination, making it hard to assess vaccine response. We have newly established a quantification method to assess the response to SARS-CoV-2 vaccination at the mRNA level using B-cell receptor (BCR) repertoire assay and the Coronavirus Antibody Database (CoV-AbDab). Repeated blood samples before and after vaccination were analysed for the BCR repertoire, and BCR sequences were searched in the database. We analysed the number and percentage frequency of matched sequences. We found that the number of matched sequences increased 2 weeks after the first vaccination and quickly decreased. Meanwhile, the number of matched sequences more rapidly increased after the second vaccination. These results show that the postvaccine immune response can be assessed at the mRNA level by analysing the fluctuation in matching sequences. Finally, BCR repertoire analysis with CoV-AbDab clearly demonstrated the response to mRNA SARS-CoV-2 vaccination even after tixagevimab/cilgavimab administration in haematological malignancy patients who underwent allogeneic haematopoietic stem cell transplantation.
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Affiliation(s)
- Yohei Funakoshi
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan
| | - Kimikazu Yakushijin
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan
| | - Goh Ohji
- Division of Infection Disease Therapeutics, Department of Microbiology and Infectious Diseases, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan
| | - Takaji Matsutani
- Research & Development Department, Repertoire Genesis Inc., Ibaraki, Japan
| | | | | | - Sakuya Matsumoto
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan
| | - Marika Watanabe
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan
| | - Akihito Kitao
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan
| | - Yasuyuki Saito
- Division of Molecular and Cellular Signaling, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Shinichiro Kawamoto
- Department of Transfusion Medicine and Cell Therapy, Kobe University Hospital, Kobe, Japan
| | - Katsuya Yamamoto
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan
| | - Taiji Koyama
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan
| | - Yoshiaki Nagatani
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan
| | - Shiro Kimbara
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan
| | - Yoshinori Imamura
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan
| | - Naomi Kiyota
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan
- Cancer Center, Kobe University Hospital, Kobe, Japan
| | - Mitsuhiro Ito
- Division of Medical Biophysics, Kobe University Graduate School of Health Sciences, Kobe, Japan
| | - Hironobu Minami
- Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan
- Cancer Center, Kobe University Hospital, Kobe, Japan
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Zhou H, Xu M, Hu P, Li Y, Ren C, Li M, Pan Y, Wang S, Liu X. Identifying hub genes and common biological pathways between COVID-19 and benign prostatic hyperplasia by machine learning algorithms. Front Immunol 2023; 14:1172724. [PMID: 37426635 PMCID: PMC10328422 DOI: 10.3389/fimmu.2023.1172724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 06/07/2023] [Indexed: 07/11/2023] Open
Abstract
Background COVID-19, a serious respiratory disease that has the potential to affect numerous organs, is a serious threat to the health of people around the world. The objective of this article is to investigate the potential biological targets and mechanisms by which SARS-CoV-2 affects benign prostatic hyperplasia (BPH) and related symptoms. Methods We downloaded the COVID-19 datasets (GSE157103 and GSE166253) and the BPH datasets (GSE7307 and GSE132714) from the Gene Expression Omnibus (GEO) database. In GSE157103 and GSE7307, differentially expressed genes (DEGs) were found using the "Limma" package, and the intersection was utilized to obtain common DEGs. Further analyses followed, including those using Protein-Protein Interaction (PPI), Gene Ontology (GO) function enrichment analysis, and the Kyoto Encyclopedia of Genes and Genomes (KEGG). Potential hub genes were screened using three machine learning methods, and they were later verified using GSE132714 and GSE166253. The CIBERSORT analysis and the identification of transcription factors, miRNAs, and drugs as candidates were among the subsequent analyses. Results We identified 97 common DEGs from GSE157103 and GSE7307. According to the GO and KEGG analyses, the primary gene enrichment pathways were immune-related pathways. Machine learning methods were used to identify five hub genes (BIRC5, DNAJC4, DTL, LILRB2, and NDC80). They had good diagnostic properties in the training sets and were validated in the validation sets. According to CIBERSORT analysis, hub genes were closely related to CD4 memory activated of T cells, T cells regulatory and NK cells activated. The top 10 drug candidates (lucanthone, phytoestrogens, etoposide, dasatinib, piroxicam, pyrvinium, rapamycin, niclosamide, genistein, and testosterone) will also be evaluated by the P value, which is expected to be helpful for the treatment of COVID-19-infected patients with BPH. Conclusion Our findings reveal common signaling pathways, possible biological targets, and promising small molecule drugs for BPH and COVID-19. This is crucial to understand the potential common pathogenic and susceptibility pathways between them.
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Affiliation(s)
- Hang Zhou
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Mingming Xu
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Ping Hu
- Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, China
| | - Yuezheng Li
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Congzhe Ren
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Muwei Li
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Yang Pan
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Shangren Wang
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Xiaoqiang Liu
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
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Gao H, Yu L, Yan F, Zheng Y, Huang H, Zhuang X, Zeng Y. Landscape of B Cell Receptor Repertoires in COVID-19 Patients Revealed Through CDR3 Sequencing of Immunoglobulin Heavy and Light Chains. Immunol Invest 2022; 51:1994-2008. [PMID: 35797435 DOI: 10.1080/08820139.2022.2092407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The outbreak and persistence of coronavirus disease 2019 (COVID-19) threaten human health. B cells play a vital role in fighting the infections caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Despite many studies on the immune responses in COVID-19 patients, it is still unclear how B cell receptor (BCR) constituents, including immunoglobulin heavy (IGHs) and light chains (IGLs), respond to SARS-CoV-2 in patients with varying symptoms. In this study, we conducted complementarity-determining region 3 (CDR3) sequencing of BCR IGHs and IGLs from the peripheral blood of COVID-19 patients and healthy donors. The results showed significantly reduced clonal diversity, more expanded clones, and longer CDR3 lengths of IGH and IGL in COVID-19 patients than those in healthy individuals. The IGLs had a much higher percentage of VJ skew usage (47.83% IGLV and 42.86% IGLJ were significantly regulated) than the IGHs (12.09% IGHV and 0% IGHJ) between the healthy individuals and patients, which indicated the importance of BCR light chains. Furthermore, we found a largely expanded IGLV3-25 gene cluster mostly pairing with IGLJ1 and ILGJ2 in COVID-19 patients and a newly identified upregulated IGLJ1 gene and IGLJ2+IGLV13-21 recombination, both of which are potential sources of SARS-CoV-2-targeting antibodies. Our findings on specific immune B-cell signatures associated with COVID-19 have clinical implications for vaccine and biomarker development for disease diagnosis.
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Affiliation(s)
- Hongzhi Gao
- Central Laboratory, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China.,Department of Respiratory Medicine, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Liying Yu
- Central Laboratory, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Furong Yan
- Central Laboratory, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Youxian Zheng
- Department of Microbiology, Quanzhou Municipal Center for Disease Control and Prevention, Fujian Province, Quanzhou, China
| | - Hongbo Huang
- Department of Pulmonary and Critical Care Medicine, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, Fujian Province, China
| | - Xibin Zhuang
- Department of Pulmonary and Critical Care Medicine, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, Fujian Province, China
| | - Yiming Zeng
- Department of Respiratory Medicine, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
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Wong MK, Liu JT, Budylowksi P, Yue FY, Li Z, Rini JM, Carlyle JR, Zia A, Ostrowski M, Martin A. Convergent CDR3 homology amongst Spike-specific antibody responses in convalescent COVID-19 subjects receiving the BNT162b2 vaccine. Clin Immunol 2022; 237:108963. [PMID: 35259543 PMCID: PMC8897198 DOI: 10.1016/j.clim.2022.108963] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/25/2022] [Accepted: 03/01/2022] [Indexed: 01/04/2023]
Abstract
Convalescent coronavirus disease 2019 (COVID-19) subjects who receive BNT162b2 develop robust antibody responses against SARS-CoV-2. However, our understanding of the clonal B cell response pre- and post-vaccination in such individuals is limited. Here we characterized B cell phenotypes and the BCR repertoire after BNT162b2 immunization in two convalescent COVID-19 subjects. BNT162b2 stimulated many B cell clones that were under-represented during SARS-CoV-2 infection. In addition, the vaccine generated B cell clusters with >65% similarity in CDR3 VH and VL region consensus sequences both within and between subjects. This result suggests that the CDR3 region plays a dominant role adjacent to heavy and light chain V/J pairing in the recognition of the SARS-CoV-2 spike protein. Antigen-specific B cell populations with homology to published SARS-CoV-2 antibody sequences from the CoV-AbDab database were observed in both subjects. These results point towards the development of convergent antibody responses against the virus in different individuals.
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Affiliation(s)
- Matthew K Wong
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Jun T Liu
- Department of Laboratory Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Patrick Budylowksi
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Feng Yun Yue
- Department of Laboratory Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Zhijie Li
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - James M Rini
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - James R Carlyle
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Amin Zia
- dYcode Bio, Toronto, Ontario, Canada
| | - Mario Ostrowski
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada; Department of Medicine, University of Toronto; Toronto, ON, Canada; Keenan Research Centre for Biomedical Science of St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada.
| | - Alberto Martin
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada.
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