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Zhao T, Zhang Q, Wen Q, Liu S, Niu Z, Qu Y, Wang Y, Ding Q, Wei P, Li L, Kong T, Fu P, Qian S, Wang K, Wu X, Zheng J. Characteristics of T-Cell Receptor Repertoire for Differential Response to Methotrexate Treatment for Rheumatoid Arthritis. Immunol Invest 2024; 53:1113-1124. [PMID: 39140790 DOI: 10.1080/08820139.2024.2381078] [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] [Indexed: 08/15/2024]
Abstract
BACKGROUND Methotrexate (MTX) serves as the initial treatment for rheumatoid arthritis (RA). However, a substantial proportion of RA patients, estimated between 30% and 50%, do not respond positively to MTX. While the T-cell receptor (TCR) is crucial for the immune response during RA, its role in differentiating MTX responsiveness has not been thoroughly investigated. METHODS This study used next-generation sequencing to analyze the TCR β-chain complementary determining region sequences in peripheral blood mononuclear cells obtained from RA patients before MTX treatment. This study aimed to compare the characteristics of the TCR repertoire between the MTX responder and non-responder groups. RESULTS The study identified a significant difference in the TRBV6-6 gene (p = .003) concerning MTX treatment response. Additionally, a significant difference was found in the number of "3" nucleotide deletions at the 5'Jdels site (p = .023) in the VDJ rearrangement. CONCLUSION These findings suggest distinct TCR repertoire characteristics between MTX responder and non-responder groups among RA patients. This discovery offers new insights into understanding the variable responses of RA patients to MTX therapy.
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MESH Headings
- Humans
- Arthritis, Rheumatoid/drug therapy
- Arthritis, Rheumatoid/immunology
- Arthritis, Rheumatoid/genetics
- Methotrexate/therapeutic use
- Male
- Female
- Middle Aged
- Antirheumatic Agents/therapeutic use
- Antirheumatic Agents/pharmacology
- Adult
- High-Throughput Nucleotide Sequencing
- Aged
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- Treatment Outcome
- Complementarity Determining Regions/genetics
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/metabolism
- Leukocytes, Mononuclear/immunology
- Leukocytes, Mononuclear/metabolism
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Affiliation(s)
- Taowa Zhao
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo, China
- Cixi Biomedical Research Institute, Wenzhou Medical University, Ningbo, China
| | - Qian Zhang
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo, China
| | - Qinwen Wen
- Department of Rheumatology and Immunology, Ningbo First Hospital, Ningbo, China
| | - Shuyin Liu
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo, China
- Cixi Biomedical Research Institute, Wenzhou Medical University, Ningbo, China
| | - Zitong Niu
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo, China
- Cixi Biomedical Research Institute, Wenzhou Medical University, Ningbo, China
| | - Yang Qu
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo, China
- Cixi Biomedical Research Institute, Wenzhou Medical University, Ningbo, China
| | - Yiting Wang
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo, China
| | - Qiaojiao Ding
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo, China
- Cixi Biomedical Research Institute, Wenzhou Medical University, Ningbo, China
| | - Pengyao Wei
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo, China
- Cixi Biomedical Research Institute, Wenzhou Medical University, Ningbo, China
| | - Lin Li
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo, China
| | - Tong Kong
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo, China
| | - Pan Fu
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo, China
| | - Sihua Qian
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo, China
| | - Kaizhe Wang
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo, China
| | - Xiudi Wu
- Department of Rheumatology and Immunology, Ningbo First Hospital, Ningbo, China
| | - Jianping Zheng
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences (CAS), Ningbo, China
- Cixi Biomedical Research Institute, Wenzhou Medical University, Ningbo, China
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2
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Yue M, Li J, Li J, Hu T, Feng S, Cao J, Tang R, Wang P, Zhu F, Han L, Wu J, Cui X, Liu R. Comparative analysis of the immune repertoire between peripheral blood and bone marrow fluids in those infected by EBV and immunodeficiency: A retrospective case study. Medicine (Baltimore) 2024; 103:e39501. [PMID: 39312313 PMCID: PMC11419465 DOI: 10.1097/md.0000000000039501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 08/08/2024] [Indexed: 09/25/2024] Open
Abstract
High-throughput immune repertoire (IR) sequencing provides direct insight into the diversity of B cell receptor (BCR) and T cell receptor (TCR), with great potential to revolutionize the diagnosis, monitoring, and prevention of immune system-related disorders. In this study, multiplex PCR was applied to amplify the complementarity-determining regions of BCR and TCR, followed by comprehensive analysis by high-throughput sequencing. We compare the TCR (BCR) of bone marrow fluid (BMF) and peripheral blood (PB) samples from 17 patients in the Epstein-Barr and immunodeficiency groups, respectively. Our study shows that the diversity of the IR of blood samples is very similar to that of bone marrow samples statistically. However, the distributions of the monoclonal genes are significantly different in these 2 samples of most patients. This suggests that the BMFs can be replaced by the PB samples in diversity detection of IR to monitor the immune status of the body, while the detection of the BMFs is unreplaceable when the monoclonal change occurs. We used high-throughput sequencing to assess the TCR and BCR of the patients and provide a basis for the clinical analysis of PB and bone marrow samples and selection of disease diagnosis and monitoring methods.
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Affiliation(s)
- Mei Yue
- Department of Hematology, Children’s Hospital of Capital Institute of Pediatrics, Beijing, China
| | - Juanjuan Li
- Department of Hematology, Children’s Hospital of Capital Institute of Pediatrics, Beijing, China
| | - Junhui Li
- Department of Hematology, Children’s Hospital of Capital Institute of Pediatrics, Beijing, China
| | - Tao Hu
- Department of Hematology, Children’s Hospital of Capital Institute of Pediatrics, Beijing, China
| | - Shunqiao Feng
- Department of Hematology, Children’s Hospital of Capital Institute of Pediatrics, Beijing, China
| | - Jing Cao
- Department of Hematology, Children’s Hospital of Capital Institute of Pediatrics, Beijing, China
| | - Ruihong Tang
- Department of Hematology, Children’s Hospital of Capital Institute of Pediatrics, Beijing, China
| | | | | | - Lu Han
- MyGenostics Inc, Beijing, China
| | - Jian Wu
- MyGenostics Inc, Beijing, China
| | - Xiaodai Cui
- Department of Key Laboratory, Children’s Hospital of Capital Institute of Pediatrics, Beijing, China
| | - Rong Liu
- Department of Hematology, Children’s Hospital of Capital Institute of Pediatrics, Beijing, China
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3
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Abu-Shmais AA, Vukovich MJ, Wasdin PT, Suresh YP, Marinov TM, Rush SA, Gillespie RA, Sankhala RS, Choe M, Joyce MG, Kanekiyo M, McLellan JS, Georgiev IS. Antibody sequence determinants of viral antigen specificity. mBio 2024:e0156024. [PMID: 39264172 DOI: 10.1128/mbio.01560-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 08/13/2024] [Indexed: 09/13/2024] Open
Abstract
Throughout life, humans experience repeated exposure to viral antigens through infection and vaccination, resulting in the generation of diverse, antigen-specific antibody repertoires. A paramount feature of antibodies that enables their critical contributions in counteracting recurrent and novel pathogens, and consequently fostering their utility as valuable targets for therapeutic and vaccine development, is the exquisite specificity displayed against their target antigens. Yet, there is still limited understanding of the determinants of antibody-antigen specificity, particularly as a function of antibody sequence. In recent years, experimental characterization of antibody repertoires has led to novel insights into fundamental properties of antibody sequences but has been largely decoupled from at-scale antigen specificity analysis. Here, using the LIBRA-seq technology, we generated a large data set mapping antibody sequence to antigen specificity for thousands of B cells, by screening the repertoires of a set of healthy individuals against 20 viral antigens representing diverse pathogens of biomedical significance. Analysis uncovered virus-specific patterns in variable gene usage, gene pairing, somatic hypermutation, as well as the presence of convergent antiviral signatures across multiple individuals, including the presence of public antibody clonotypes. Notably, our results showed that, for B-cell receptors originating from different individuals but leveraging an identical combination of heavy and light chain variable genes, there is a specific CDRH3 identity threshold above which B cells appear to exclusively share the same antigen specificity. This finding provides a quantifiable measure of the relationship between antibody sequence and antigen specificity and further defines experimentally grounded criteria for defining public antibody clonality.IMPORTANCEThe B-cell compartment of the humoral immune system plays a critical role in the generation of antibodies upon new and repeated pathogen exposure. This study provides an unprecedented level of detail on the molecular characteristics of antibody repertoires that are specific to each of the different target pathogens studied here and provides empirical evidence in support of a 70% CDRH3 amino acid identity threshold in pairs of B cells encoded by identical IGHV:IGL(K)V genes, as a means of defining public clonality and therefore predicting B-cell antigen specificity in different individuals. This is of exceptional importance when leveraging public clonality as a method to annotate B-cell receptor data otherwise lacking antigen specificity information. Understanding the fundamental rules of antibody-antigen interactions can lead to transformative new approaches for the development of antibody therapeutics and vaccines against current and emerging viruses.
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Affiliation(s)
- Alexandra A Abu-Shmais
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Matthew J Vukovich
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Perry T Wasdin
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Program in Chemical and Physical Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Yukthi P Suresh
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Toma M Marinov
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Computer Science, Vanderbilt University, Nashville, Tennessee, USA
| | - Scott A Rush
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Rebecca A Gillespie
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Rajeshwer S Sankhala
- Emerging Infectious Disease Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Misook Choe
- Emerging Infectious Disease Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - M Gordon Joyce
- Emerging Infectious Disease Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Jason S McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Ivelin S Georgiev
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Program in Chemical and Physical Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Computer Science, Vanderbilt University, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
- Program in Computational Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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4
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Kawakami N, Wekerle H. Life history of a brain autoreactive T cell: From thymus through intestine to blood-brain barrier and brain lesion. Neurotherapeutics 2024:e00442. [PMID: 39237437 DOI: 10.1016/j.neurot.2024.e00442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 08/21/2024] [Accepted: 08/21/2024] [Indexed: 09/07/2024] Open
Abstract
Brain antigen-specific autoreactive T cells seem to play a key role in inducing inflammation in the central nervous system (CNS), a characteristic feature of human multiple sclerosis (MS). These T cells are generated within the thymus, where they escape negative selection and become integrated into the peripheral immune repertoire of immune cells. Typically, these autoreactive T cells rest in the periphery without attacking the CNS. When autoimmune T cells enter gut-associated lymphatic tissue (GALT), they may be stimulated by the microbiota and its metabolites. After activation, the cells migrate into the CNS through the blood‒brain barrier, become reactivated upon interacting with local antigen-presenting cells, and induce inflammatory lesions within the brain parenchyma. This review describes how microbiota influence autoreactive T cells during their life, starting in the thymus, migrating through the periphery and inducing inflammation in their target organ, the CNS.
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Affiliation(s)
- Naoto Kawakami
- Institute of Clinical Neuroimmunology, University Hospital, LMU Munich and Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Germany.
| | - Hartmut Wekerle
- Institute of Clinical Neuroimmunology, University Hospital, LMU Munich and Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Germany; Emeritus Group Neuroimmunology, Max Planck Institute of Biological Intelligence, Germany.
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Jamaleddine H, Rogers D, Perreault G, Postat J, Patel D, Mandl JN, Khadra A. Chronic infection control relies on T cells with lower foreign antigen binding strength generated by N-nucleotide diversity. PLoS Biol 2024; 22:e3002465. [PMID: 38300945 PMCID: PMC10833529 DOI: 10.1371/journal.pbio.3002465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 12/08/2023] [Indexed: 02/03/2024] Open
Abstract
The breadth of pathogens to which T cells can respond is determined by the T cell receptors (TCRs) present in an individual's repertoire. Although more than 90% of the sequence diversity among TCRs is generated by terminal deoxynucleotidyl transferase (TdT)-mediated N-nucleotide addition during V(D)J recombination, the benefit of TdT-altered TCRs remains unclear. Here, we computationally and experimentally investigated whether TCRs with higher N-nucleotide diversity via TdT make distinct contributions to acute or chronic pathogen control specifically through the inclusion of TCRs with lower antigen binding strengths (i.e., lower reactivity to peptide-major histocompatibility complex (pMHC)). When T cells with high pMHC reactivity have a greater propensity to become functionally exhausted than those of low pMHC reactivity, our computational model predicts a shift toward T cells with low pMHC reactivity over time during chronic, but not acute, infections. This TCR-affinity shift is critical, as the elimination of T cells with lower pMHC reactivity in silico substantially increased the time to clear a chronic infection, while acute infection control remained largely unchanged. Corroborating an affinity-centric benefit for TCR diversification via TdT, we found evidence that TdT-deficient TCR repertoires possess fewer T cells with weaker pMHC binding strengths in vivo and showed that TdT-deficient mice infected with a chronic, but not an acute, viral pathogen led to protracted viral clearance. In contrast, in the case of a chronic fungal pathogen where T cells fail to clear the infection, both our computational model and experimental data showed that TdT-diversified TCR repertoires conferred no additional protection to the hosts. Taken together, our in silico and in vivo data suggest that TdT-mediated TCR diversity is of particular benefit for the eventual resolution of prolonged pathogen replication through the inclusion of TCRs with lower foreign antigen binding strengths.
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Affiliation(s)
| | - Dakota Rogers
- Department of Physiology, McGill University, Montreal, Quebec, Canada
- McGill University Research Centre on Complex Traits, Montreal, Quebec, Canada
| | - Geneviève Perreault
- McGill University Research Centre on Complex Traits, Montreal, Quebec, Canada
| | - Jérémy Postat
- Department of Physiology, McGill University, Montreal, Quebec, Canada
- McGill University Research Centre on Complex Traits, Montreal, Quebec, Canada
| | - Dhanesh Patel
- Department of Physiology, McGill University, Montreal, Quebec, Canada
- McGill University Research Centre on Complex Traits, Montreal, Quebec, Canada
| | - Judith N. Mandl
- Department of Physiology, McGill University, Montreal, Quebec, Canada
- McGill University Research Centre on Complex Traits, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Anmar Khadra
- Department of Physiology, McGill University, Montreal, Quebec, Canada
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6
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Fang Y, Shen B, Dai Q, Xie Q, Li X, Wu W, Wang M. Composition and diversity analysis of the TCR CDR3 repertoire in patients with idiopathic orbital inflammation using high-throughput sequencing. BMC Ophthalmol 2023; 23:491. [PMID: 38044453 PMCID: PMC10694961 DOI: 10.1186/s12886-023-03248-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 11/28/2023] [Indexed: 12/05/2023] Open
Abstract
BACKGROUND Idiopathic orbital inflammation (IOI) is a nonspecific orbital inflammatory disease with the third highest prevalence among orbital diseases, and its pathogenesis is associated with T-cell-mediated immune responses. This study aimed to investigate the differences in T-cell receptor (TCR) expression between IOI patients and healthy subjects by high-throughput sequencing and to characterize TCR expression in patients with IOI and with respect to glucocorticoid response. METHODS A total of 19 subjects were enrolled in this study and were divided into the idiopathic orbital inflammation group (IOI group, n = 13) and the healthy control group (HC group, n = 6), and within the IOI group were further divided into the glucocorticoid therapy sensitive group (IOI(EF) group, n = 6) and the glucocorticoid therapy ineffective group (IOI(IN) group, n = 7) based on the degree of effectiveness to glucocorticoid therapy. High-throughput TCR sequencing was performed on peripheral blood mononuclear cells of IOI patients and healthy control individuals using 5' RACE technology combined with Unique Identifier (UID) digital tag correction technology. The TCR CDR3 region diversity, sharing patterns, and differential sequences between the IOI and HC groups, and between the IOI(EF) and IOI(IN) groups were analyzed. RESULTS It was found that the diversity of TCR CDR3 in the IOI group was significantly lower than that in the HC group, and the frequency of V gene use was significantly different between groups. The diversity of TCR CDR3 in patients in the IOI(EF) group was significantly lower than that in patients in the IOI(IN) group, and the frequency of V and J gene use was significantly different between the IOI(EF) group and the IOI(IN) group. Additionally, we found 133 nucleotide sequences shared in all IOI samples and screened two sequences with higher expression from them. CONCLUSIONS Our results suggested that abnormal clonal expansion of specific T-cells exists in IOI patients and that TCR diversity may had an impact on the prognosis of glucocorticoid-treated IOI. This study may contribute to a better understanding of the immune status of IOI and provide new insights for T-cell -associated IOI pathogenesis, diagnosis and treatment prediction.
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Affiliation(s)
- Yenan Fang
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
- Department of Ophthalmology, Children's Hospital of Fudan University, National Children's Medical Center, No. 399 Wanyuan Road, Shanghai, 201102, China
| | - Bingyan Shen
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Qin Dai
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Qiqi Xie
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Xinyu Li
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Wencan Wu
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China.
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China.
| | - Min Wang
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China.
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China.
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Liu Y, Zhu E, Lei Y, Luo A, Yan Y, Cai M, Liu S, Huang Y, Guan H, Zhong M, Li W, Lin L, Hultstöm M, Lai E, Zheng Z, Liu X, Tang C. Diagnostic Values of METTL1-Related Genes and Immune Characteristics in Systemic Lupus Erythematosus. J Inflamm Res 2023; 16:5367-5383. [PMID: 38026241 PMCID: PMC10661937 DOI: 10.2147/jir.s431628] [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: 07/24/2023] [Accepted: 10/31/2023] [Indexed: 12/01/2023] Open
Abstract
Purpose Methyltransferase like 1 (METTL1) regulates epitranscriptomes via the m7G modification in mammalian mRNA and microRNA. Systemic lupus erythematosus (SLE) is caused by abnormal immune reactivity and has diverse clinical manifestations. RNA methylation as a mechanism to regulate gene expression is widely implicated in immune regulation. However, the role of m7G in immune response of SLE has not been extensively studied. Patients and Methods Expression of METTL1 was identified in the public dataset GSE122459 and validated in an independent cohort of SLE patients. We investigated the association between METTL1-expression and clinical manifestations of SLE. Subsequently, differentially expressed genes (DEG) that were correlated with METTL1-expression in GSE122459 were used for functional enrichment analysis. The correlation between infiltrating immune cells and METTL1, as well as candidate biomarkers identified to be correlated with either METTL1 or immune cell infiltration were assessed by single-sample GSEA. Potential mechanisms were explored with Gene ontology and KEGG pathway enrichment. Diagnostic performances of candidate biomarkers in SLE were analyzed. Results The mRNA and protein expression of METTL1 in SLE patients were significantly decreased in both datasets. METTL1-coexpressed DEGs were enriched in several key immune-related pathways. Activated CD8 T cells, activated CD4 T cells, memory B cells and type 2 helper T cells were different between patients with high and low METTL1 expression. Further, activated CD8 T-cells, activated CD4 T-cells, memory B-cells were correlated with METTL1. The genes of LAMP3, CD83, PDCD1LG2, IGKVD3D-20, IGKV5-2, IGKV2D-30, IGLV3-19 and IGLV4-60 were identified as candidate targets that were correlated with immune cell proportion. Moreover, LAMP3, CD83, and PDCD1LG2 expression were of diagnostic value in SLE as indicated by ROC analysis. Conclusion Our findings suggested that METTL1 and its candidate targets LAMP3, CD83, PDCD1LG2 may be used for diagnosing SLE and could be explored for developing targeted molecular therapy for SLE.
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Affiliation(s)
- Yu Liu
- Department of Nephrology, Center of Kidney and Urology, the Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, People’s Republic of China
| | - Enyi Zhu
- Department of Nephrology, Center of Kidney and Urology, the Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, People’s Republic of China
| | - Yan Lei
- Department of Nephrology, Center of Kidney and Urology, the Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, People’s Republic of China
| | - Ailing Luo
- Department of Hematology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, People’s Republic of China
| | - Yaping Yan
- Department of Hematology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, People’s Republic of China
| | - Mansi Cai
- Department of Hematology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, People’s Republic of China
| | - Shanshan Liu
- Department of Hematology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, People’s Republic of China
| | - Yan Huang
- The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, 421001, People’s Republic of China
| | - Hui Guan
- Department of Nephrology, Center of Kidney and Urology, the Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, People’s Republic of China
| | - Ming Zhong
- Department of Nephrology, Center of Kidney and Urology, the Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, People’s Republic of China
| | - Weinian Li
- Department of Rheumatology, Guangzhou First People’s Hospital, South China University of Technology, Guangzhou, 510623, People’s Republic of China
| | - Lian Lin
- Department of Nephrology, Center of Kidney and Urology, the Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, People’s Republic of China
| | - Michael Hultstöm
- Department of Surgical Sciences, Anesthesiology and Intensive Care, Uppsala University, Uppsala, Sweden
- Department of Medical Cell Biology, Unit for Integrative Physiology, Uppsala University, Uppsala, Sweden
| | - Enyin Lai
- Department of Physiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, 310058, People’s Republic of China
| | - Zhihua Zheng
- Department of Nephrology, Center of Kidney and Urology, the Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, People’s Republic of China
| | - Xiaoping Liu
- Department of Hematology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, 510623, People’s Republic of China
| | - Chun Tang
- Department of Nephrology, Center of Kidney and Urology, the Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, People’s Republic of China
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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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9
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Calonga-Solís V, Olbrich M, Ott F, Adelman Cipolla G, Malheiros D, Künstner A, Farias TD, Camargo CM, Petzl-Erler ML, Busch H, Fähnrich A, Augusto DG. The landscape of the immunoglobulin repertoire in endemic pemphigus foliaceus. Front Immunol 2023; 14:1189251. [PMID: 37575223 PMCID: PMC10421657 DOI: 10.3389/fimmu.2023.1189251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 07/05/2023] [Indexed: 08/15/2023] Open
Abstract
Introduction Primarily driven by autoreactive B cells, pemphigus foliaceus (PF) is an uncommon autoimmune blistering skin disease of sporadic occurrence worldwide. However, PF reaches a prevalence of 3% in the endemic areas of Brazil, the highest ever registered for any autoimmune disease, which indicates environmental factors influencing the immune response in susceptible individuals. We aimed to provide insights into the immune repertoire of patients with PF living in the endemic region of the disease, compared to healthy individuals from the endemic region and a non-endemic area. Methods We characterized the B-cell repertoire in i) nontreated patients (n=5); ii) patients under immunosuppressive treatment (n=5); iii) patients in remission without treatment (n=6); and two control groups iv) from the endemic (n=6) and v) non-endemic areas in Brazil (n=4). We used total RNA extracted from peripheral blood mononuclear cells and performed a comprehensive characterization of the variable region of immunoglobulin heavy chain (IGH) in IgG and IgM using next-generation sequencing. Results Compared to individuals from a different area, we observed remarkably lower clonotype diversity in the B-cell immune repertoire of patients and controls from the endemic area (p < 0.02), suggesting that the immune repertoire in the endemic area is under geographically specific and intense environmental pressure. Moreover, we observed longer CDR3 sequences in patients, and we identified differential disease-specific usage of IGHV segments, including increased IGHV3-30 and decreased IGHV3-23 in patients with active disease (p < 0.04). Finally, our robust network analysis discovered clusters of CDR3 sequences uniquely observed in patients with PF. Discussion Our results indicate that environmental factors, in addition to disease state, impact the characteristics of the repertoire. Our findings can be applied to further investigation of the environmental factors that trigger pemphigus and expand the knowledge for identifying new targeted and more effective therapies.
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Affiliation(s)
- Verónica Calonga-Solís
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
- Medical Systems Biology Group, Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Michael Olbrich
- Medical Systems Biology Group, Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Fabian Ott
- Medical Systems Biology Group, Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | | | - Danielle Malheiros
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Axel Künstner
- Medical Systems Biology Group, Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Ticiana D.J. Farias
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Carolina M. Camargo
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | | | - Hauke Busch
- Medical Systems Biology Group, Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Anke Fähnrich
- Medical Systems Biology Group, Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Danillo G. Augusto
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC, United States
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10
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Pelissier A, Luo S, Stratigopoulou M, Guikema JEJ, Rodríguez Martínez M. Exploring the impact of clonal definition on B-cell diversity: implications for the analysis of immune repertoires. Front Immunol 2023; 14:1123968. [PMID: 37138881 PMCID: PMC10150052 DOI: 10.3389/fimmu.2023.1123968] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/13/2023] [Indexed: 05/05/2023] Open
Abstract
The adaptive immune system has the extraordinary ability to produce a broad range of immunoglobulins that can bind a wide variety of antigens. During adaptive immune responses, activated B cells duplicate and undergo somatic hypermutation in their B-cell receptor (BCR) genes, resulting in clonal families of diversified B cells that can be related back to a common ancestor. Advances in high-throughput sequencing technologies have enabled the high-throughput characterization of B-cell repertoires, however, the accurate identification of clonally related BCR sequences remains a major challenge. In this study, we compare three different clone identification methods on both simulated and experimental data, and investigate their impact on the characterization of B-cell diversity. We observe that different methods lead to different clonal definitions, which affects the quantification of clonal diversity in repertoire data. Our analyses show that direct comparisons between clonal clusterings and clonal diversity of different repertoires should be avoided if different clone identification methods were used to define the clones. Despite this variability, the diversity indices inferred from the repertoires' clonal characterization across samples show similar patterns of variation regardless of the clonal identification method used. We find the Shannon entropy to be the most robust in terms of the variability of diversity rank across samples. Our analysis also suggests that the traditional germline gene alignment-based method for clonal identification remains the most accurate when the complete information about the sequence is known, but that alignment-free methods may be preferred for shorter sequencing read lengths. We make our implementation freely available as a Python library cdiversity.
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Affiliation(s)
- Aurelien Pelissier
- IBM Research Europe, Rüschlikon, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Siyuan Luo
- IBM Research Europe, Rüschlikon, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Maria Stratigopoulou
- Department of Pathology, Amsterdam University Medical Centers, location AMC, Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam, Netherlands
| | - Jeroen E. J. Guikema
- Department of Pathology, Amsterdam University Medical Centers, location AMC, Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam, Netherlands
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11
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Zornikova KV, Sheetikov SA, Rusinov AY, Iskhakov RN, Bogolyubova AV. Architecture of the SARS-CoV-2-specific T cell repertoire. Front Immunol 2023; 14:1070077. [PMID: 37020560 PMCID: PMC10067759 DOI: 10.3389/fimmu.2023.1070077] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 03/08/2023] [Indexed: 03/22/2023] Open
Abstract
The T cell response plays an indispensable role in the early control and successful clearance of SARS-CoV-2 infection. However, several important questions remain about the role of cellular immunity in COVID-19, including the shape and composition of disease-specific T cell repertoires across convalescent patients and vaccinated individuals, and how pre-existing T cell responses to other pathogens—in particular, common cold coronaviruses—impact susceptibility to SARS-CoV-2 infection and the subsequent course of disease. This review focuses on how the repertoire of T cell receptors (TCR) is shaped by natural infection and vaccination over time. We also summarize current knowledge regarding cross-reactive T cell responses and their protective role, and examine the implications of TCR repertoire diversity and cross-reactivity with regard to the design of vaccines that confer broader protection against SARS-CoV-2 variants.
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Affiliation(s)
- Ksenia V. Zornikova
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
| | - Saveliy A. Sheetikov
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Alexander Yu Rusinov
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Rustam N. Iskhakov
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Apollinariya V. Bogolyubova
- Laboratory of Transplantation Immunology, National Medical Research Center for Hematology, Moscow, Russia
- *Correspondence: Apollinariya V. Bogolyubova,
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12
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Gill K, Moore C, Nwogu O, Kroner JW, Chang WC, Stevens ML, kyzy AB, Biagini JM, Devonshire AL, Kottyan L, Schwartz JT, Assa’ad AH, Martin LJ, Andorf S, Hershey GKK, Roskin KM. B cell repertoire in children with skin barrier dysfunction supports altered IgE maturation associated with allergic food sensitization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.01.526538. [PMID: 36778284 PMCID: PMC9915585 DOI: 10.1101/2023.02.01.526538] [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: 02/09/2023]
Abstract
The skin is a major immune organ and skin barrier dysfunction is a major risk factor for the development of the inappropriate immune response seen in allergic disease. Skin barrier disruption alters the landscape of antigens experienced by the immune system and the downstream impacts on the antibody repertoire remain poorly characterized, particularly for the IgE isotype responsible for allergic specificity and in early life, when allergic disease is developing. In this study, we sequenced antibody gene repertoires from a large and well-characterized cohort of children with atopic dermatitis and found that food sensitization was associated with lower mutation frequencies in the IgE compartment. This trend was abrogated in children living with pets during the first year of life. These results elucidate potential molecular mechanisms underlying the protective effects of pet ownership and non-antiseptic environs reported for allergic disease, and the hygiene hypothesis more broadly. We also observed increased IgE diversity and increased isotype-switching to the IgE isotype, suggesting that B cell development, particularly isotype-switching, is heavily altered in the those with food allergen sensitizations relative to those without food allergen sensitizations. Unlike for food antigens, aeroallergen sensitization exhibited no effect on IgE mutation or diversity. Consistent patterns of antibody rearrangement were associated with food allergen sensitization in subjects with atopic dermatitis. Thus, we propose the Immune Repertoire in Atopic Disease (IRAD) score, to quantify this repertoire shift and to aid clinically in patient diagnosis and risk stratification.
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Affiliation(s)
- Kirandeep Gill
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
| | - Carolina Moore
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
| | - Onyekachi Nwogu
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
| | - John W. Kroner
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
| | - Wan-Chi Chang
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
| | - Mariana L. Stevens
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
| | - Asel Baatyrbek kyzy
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
| | - Jocelyn M. Biagini
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine; Cincinnati, Ohio, USA
| | - Ashley L. Devonshire
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine; Cincinnati, Ohio, USA
| | - Leah Kottyan
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine; Cincinnati, Ohio, USA
| | - Justin T. Schwartz
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine; Cincinnati, Ohio, USA
| | - Amal H. Assa’ad
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine; Cincinnati, Ohio, USA
| | - Lisa J. Martin
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine; Cincinnati, Ohio, USA
| | - Sandra Andorf
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
- Division of Biostatistics and Epidemiology, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine; Cincinnati, Ohio, USA
| | - Gurjit K. Khurana Hershey
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine; Cincinnati, Ohio, USA
| | - Krishna M. Roskin
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine; Cincinnati, Ohio, USA
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13
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Krechetov SP, Vtorushina VV, Inviyaeva EV, Gorodnova EA, Kolesnik SV, Kudlay DA, Borovikov PI, Krechetova LV, Dolgushina NV, Sukhikh GT. T-Cell Immunity in COVID-19-Recovered Individuals and Individuals Vaccinated with the Combined Vector Vaccine Gam-COVID-Vac. Int J Mol Sci 2023; 24:ijms24031930. [PMID: 36768254 PMCID: PMC9916700 DOI: 10.3390/ijms24031930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/13/2023] [Accepted: 01/15/2023] [Indexed: 01/21/2023] Open
Abstract
The COVID-19 pandemic has required extensive research on the new coronavirus SARS-CoV-2 and the creation of new highly effective vaccines. The presence of T-cells in the body that respond to virus antigens suggests adequate antiviral immunity. We investigated T-cell immunity in individuals who recovered from mild and moderate COVID-19 and in individuals vaccinated with the Gam-COVID-Vac combined vector vaccine. The ELISPOT method was used to determine the number of T-cells responding with IFN-γ synthesis to stimulation by peptides containing epitopes of the S-protein or N-, M-, ORF3, and ORF7 proteins, using peripheral blood mononuclear cells (PBMCs). At the same time, the multiplex method was used to determine the accumulation of IFN-γ and other cytokines in the culture medium. According to the data obtained, the proportion of positive conclusions about the T-cell immune response to SARS-CoV-2 antigens in control, recovered, and vaccinated individuals was 12%, 70%, and 52%, respectively. At the same time, more than half of the vaccinated individuals with a T-cell response were sensitized to the antigens of N-, M-, ORF3, and ORF7 proteins not produced by Gam-COVID-Vac, indicating a high likelihood of asymptomatic SARS-CoV-2 infection. Increased IFN-γ release by single sensitized T-cells in response to specific stimulation in recovered and vaccinated individuals did not result in the accumulation of this and other cytokines in the culture medium. These findings suggest a balance between cytokine production and utilization by immunocompetent cells as a prerequisite for providing a controlled cytokine signal and avoiding a "cytokine storm".
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Affiliation(s)
- Sergey Petrovich Krechetov
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I., Kulakov of the Ministry of Healthcare of Russian Federation, 117997 Moscow, Russia
| | - Valentina Valentinovna Vtorushina
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I., Kulakov of the Ministry of Healthcare of Russian Federation, 117997 Moscow, Russia
| | - Evgenia Vladimirovna Inviyaeva
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I., Kulakov of the Ministry of Healthcare of Russian Federation, 117997 Moscow, Russia
| | - Elena Aleksandrovna Gorodnova
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I., Kulakov of the Ministry of Healthcare of Russian Federation, 117997 Moscow, Russia
- Correspondence: ; Tel.: +7-(916)564-77-69
| | - Svetlana Vladimirovna Kolesnik
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I., Kulakov of the Ministry of Healthcare of Russian Federation, 117997 Moscow, Russia
| | - Dmitry Anatolievich Kudlay
- NRC Institute of Immunology FMBA of Russia, 115522 Moscow, Russia
- Department of Pharmacology, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia
| | - Pavel Igorevich Borovikov
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I., Kulakov of the Ministry of Healthcare of Russian Federation, 117997 Moscow, Russia
| | - Liubov Valentinovna Krechetova
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I., Kulakov of the Ministry of Healthcare of Russian Federation, 117997 Moscow, Russia
| | - Nataliya Vitalievna Dolgushina
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I., Kulakov of the Ministry of Healthcare of Russian Federation, 117997 Moscow, Russia
- Department of Obstetrics, Gynecology, Perinatology and Reproductology, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia
| | - Gennady Tikhonovich Sukhikh
- National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I., Kulakov of the Ministry of Healthcare of Russian Federation, 117997 Moscow, Russia
- Department of Obstetrics, Gynecology, Perinatology and Reproductology, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia
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14
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Luo S, Jing C, Ye AY, Kratochvil S, Cottrell CA, Koo JH, Chapdelaine Williams A, Francisco LV, Batra H, Lamperti E, Kalyuzhniy O, Zhang Y, Barbieri A, Manis JP, Haynes BF, Schief WR, Batista FD, Tian M, Alt FW. Humanized V(D)J-rearranging and TdT-expressing mouse vaccine models with physiological HIV-1 broadly neutralizing antibody precursors. Proc Natl Acad Sci U S A 2023; 120:e2217883120. [PMID: 36574685 PMCID: PMC9910454 DOI: 10.1073/pnas.2217883120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/22/2022] [Indexed: 12/28/2022] Open
Abstract
Antibody heavy chain (HC) and light chain (LC) variable region exons are assembled by V(D)J recombination. V(D)J junctional regions encode complementarity-determining-region 3 (CDR3), an antigen-contact region immensely diversified through nontemplated nucleotide additions ("N-regions") by terminal deoxynucleotidyl transferase (TdT). HIV-1 vaccine strategies seek to elicit human HIV-1 broadly neutralizing antibodies (bnAbs), such as the potent CD4-binding site VRC01-class bnAbs. Mice with primary B cells that express receptors (BCRs) representing bnAb precursors are used as vaccination models. VRC01-class bnAbs uniformly use human HC VH1-2 and commonly use human LCs Vκ3-20 or Vκ1-33 associated with an exceptionally short 5-amino-acid (5-aa) CDR3. Prior VRC01-class models had nonphysiological precursor levels and/or limited precursor diversity. Here, we describe VRC01-class rearranging mice that generate more physiological primary VRC01-class BCR repertoires via rearrangement of VH1-2, as well as Vκ1-33 and/or Vκ3-20 in association with diverse CDR3s. Human-like TdT expression in mouse precursor B cells increased LC CDR3 length and diversity and also promoted the generation of shorter LC CDR3s via N-region suppression of dominant microhomology-mediated Vκ-to-Jκ joins. Priming immunization with eOD-GT8 60mer, which strongly engages VRC01 precursors, induced robust VRC01-class germinal center B cell responses. Vκ3-20-based responses were enhanced by N-region addition, which generates Vκ3-20-to-Jκ junctional sequence combinations that encode VRC01-class 5-aa CDR3s with a critical E residue. VRC01-class-rearranging models should facilitate further evaluation of VRC01-class prime and boost immunogens. These new VRC01-class mouse models establish a prototype for the generation of vaccine-testing mouse models for other HIV-1 bnAb lineages that employ different HC or LC Vs.
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Affiliation(s)
- Sai Luo
- HHMI, Boston Children's Hospital, Boston, MA 02115
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Changbin Jing
- HHMI, Boston Children's Hospital, Boston, MA 02115
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Adam Yongxin Ye
- HHMI, Boston Children's Hospital, Boston, MA 02115
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Sven Kratochvil
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139
| | - Christopher A Cottrell
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, San Diego, CA 92037
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, San Diego, CA 92037
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, San Diego, CA 92037
| | - Ja-Hyun Koo
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139
| | - Aimee Chapdelaine Williams
- HHMI, Boston Children's Hospital, Boston, MA 02115
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Lucas Vieira Francisco
- HHMI, Boston Children's Hospital, Boston, MA 02115
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Himanshu Batra
- HHMI, Boston Children's Hospital, Boston, MA 02115
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Edward Lamperti
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139
| | - Oleksandr Kalyuzhniy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, San Diego, CA 92037
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, San Diego, CA 92037
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, San Diego, CA 92037
| | - Yuxiang Zhang
- HHMI, Boston Children's Hospital, Boston, MA 02115
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Alessandro Barbieri
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, MA 02115
| | - John P Manis
- Department of Laboratory Medicine, Boston Children's Hospital, Boston, MA 02115
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710
- Department of Immunology, Duke University School of Medicine, Durham, NC 27710
| | - William R Schief
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, San Diego, CA 92037
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, San Diego, CA 92037
- Center for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, San Diego, CA 92037
| | - Facundo D Batista
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139
- Department of Immunology, Harvard Medical School, Boston, MA 02115
- Department of Microbiology, Harvard Medical School, Boston, MA 02115
| | - Ming Tian
- HHMI, Boston Children's Hospital, Boston, MA 02115
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
- Department of Genetics, Harvard Medical School, Boston, MA 02115
| | - Frederick W Alt
- HHMI, Boston Children's Hospital, Boston, MA 02115
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
- Department of Genetics, Harvard Medical School, Boston, MA 02115
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15
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Zhong X, D’Antona AM. A potential antibody repertoire diversification mechanism through tyrosine sulfation for biotherapeutics engineering and production. Front Immunol 2022; 13:1072702. [PMID: 36569848 PMCID: PMC9774471 DOI: 10.3389/fimmu.2022.1072702] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 11/23/2022] [Indexed: 12/13/2022] Open
Abstract
The diversity of three hypervariable loops in antibody heavy chain and light chain, termed the complementarity-determining regions (CDRs), defines antibody's binding affinity and specificity owing to the direct contact between the CDRs and antigens. These CDR regions typically contain tyrosine (Tyr) residues that are known to engage in both nonpolar and pi stacking interaction with antigens through their complementary aromatic ring side chains. Nearly two decades ago, sulfotyrosine residue (sTyr), a negatively charged Tyr formed by Golgi-localized membrane-bound tyrosylprotein sulfotransferases during protein trafficking, were also found in the CDR regions and shown to play an important role in modulating antibody-antigen interaction. This breakthrough finding demonstrated that antibody repertoire could be further diversified through post-translational modifications, in addition to the conventional genetic recombination. This review article summarizes the current advances in the understanding of the Tyr-sulfation modification mechanism and its application in potentiating protein-protein interaction for antibody engineering and production. Challenges and opportunities are also discussed.
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16
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Luo S, Zhang J, Kreutzberger AJ, Eaton A, Edwards RJ, Jing C, Dai HQ, Sempowski GD, Cronin K, Parks R, Ye AY, Mansouri K, Barr M, Pishesha N, Williams AC, Vieira Francisco L, Saminathan A, Peng H, Batra H, Bellusci L, Khurana S, Alam SM, Montefiori DC, Saunders KO, Tian M, Ploegh H, Kirchhausen T, Chen B, Haynes BF, Alt FW. An antibody from single human V H-rearranging mouse neutralizes all SARS-CoV-2 variants through BA.5 by inhibiting membrane fusion. Sci Immunol 2022; 7:eadd5446. [PMID: 35951767 PMCID: PMC9407951 DOI: 10.1126/sciimmunol.add5446] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/03/2022] [Indexed: 12/14/2022]
Abstract
SARS-CoV-2 Omicron subvariants have generated a worldwide health crisis due to resistance to most approved SARS-CoV-2 neutralizing antibodies and evasion of vaccination-induced antibodies. To manage Omicron subvariants and prepare for new ones, additional means of isolating broad and potent humanized SARS-CoV-2 neutralizing antibodies are desirable. Here, we describe a mouse model in which the primary B cell receptor (BCR) repertoire is generated solely through V(D)J recombination of a human VH1-2 heavy chain (HC) and, substantially, a human Vκ1-33 light chain (LC). Thus, primary humanized BCR repertoire diversity in these mice derives from immensely diverse HC and LC antigen-contact CDR3 sequences generated by nontemplated junctional modifications during V(D)J recombination. Immunizing this mouse model with SARS-CoV-2 (Wuhan-Hu-1) spike protein immunogens elicited several VH1-2/Vκ1-33-based neutralizing antibodies that bound RBD in a different mode from each other and from those of many prior patient-derived VH1-2-based neutralizing antibodies. Of these, SP1-77 potently and broadly neutralized all SARS-CoV-2 variants through BA.5. Cryo-EM studies revealed that SP1-77 bound RBD away from the receptor-binding motif via a CDR3-dominated recognition mode. Lattice light-sheet microscopy-based studies showed that SP1-77 did not block ACE2-mediated viral attachment or endocytosis but rather blocked viral-host membrane fusion. The broad and potent SP1-77 neutralization activity and nontraditional mechanism of action suggest that it might have therapeutic potential. Likewise, the SP1-77 binding epitope may inform vaccine strategies. Last, the type of humanized mouse models that we have described may contribute to identifying therapeutic antibodies against future SARS-CoV-2 variants and other pathogens.
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Affiliation(s)
- Sai Luo
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Jun Zhang
- Division of Molecular Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Alex J.B. Kreutzberger
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Amanda Eaton
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert J. Edwards
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Changbin Jing
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Hai-Qiang Dai
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Gregory D. Sempowski
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kenneth Cronin
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert Parks
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Adam Yongxin Ye
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Katayoun Mansouri
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Maggie Barr
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Novalia Pishesha
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Aimee Chapdelaine Williams
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Lucas Vieira Francisco
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Anand Saminathan
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Hanqin Peng
- Division of Molecular Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Himanshu Batra
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Lorenza Bellusci
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration (FDA), Silver Spring, MD, USA
| | - Surender Khurana
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration (FDA), Silver Spring, MD, USA
| | - S. Munir Alam
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - David C. Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Surgery, Duke University, Durham, NC 27710, USA
| | - Kevin O. Saunders
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Surgery, Duke University, Durham, NC 27710, USA
- Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ming Tian
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Hidde Ploegh
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Tom Kirchhausen
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Bing Chen
- Division of Molecular Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Frederick W. Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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17
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Hartley GE, Edwards ESJ, O’Hehir RE, van Zelm MC. New insights into human immune memory from SARS-CoV-2 infection and vaccination. Allergy 2022; 77:3553-3566. [PMID: 36048132 PMCID: PMC9538469 DOI: 10.1111/all.15502] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/13/2022] [Accepted: 08/29/2022] [Indexed: 01/28/2023]
Abstract
Since early 2020, the world has been embroiled in an ongoing viral pandemic with SARS-CoV-2 and emerging variants resulting in mass morbidity and an estimated 6 million deaths globally. The scientific community pivoted rapidly, providing unique and innovative means to identify infected individuals, technologies to evaluate immune responses to infection and vaccination, and new therapeutic strategies to treat infected individuals. Never before has immunology been so critically at the forefront of combatting a global pandemic. It has now become evident that not just antibody responses, but formation and durability of immune memory cells following vaccination are associated with protection against severe disease from SARS-CoV-2 infection. Furthermore, the emergence of variants of concern (VoC) highlight the need for immunological markers to quantify the protective capacity of Wuhan-based vaccines. Thus, harnessing and modulating the immune response is key to successful vaccination and treatment of disease. We here review the latest knowledge about immune memory generation and durability following natural infection and vaccination, and provide insights into the attributes of immune memory that may protect from emerging variants.
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Affiliation(s)
- Gemma E. Hartley
- Allergy and Clinical Immunology Laboratory, Department of Immunology and Pathology, Central Clinical SchoolMonash UniversityMelbourneVictoriaAustralia
| | - Emily S. J. Edwards
- Allergy and Clinical Immunology Laboratory, Department of Immunology and Pathology, Central Clinical SchoolMonash UniversityMelbourneVictoriaAustralia
| | - Robyn E. O’Hehir
- Allergy and Clinical Immunology Laboratory, Department of Immunology and Pathology, Central Clinical SchoolMonash UniversityMelbourneVictoriaAustralia,Allergy, Asthma and Clinical Immunology ServiceAlfred HospitalMelbourneVictoriaAustralia
| | - Menno C. van Zelm
- Allergy and Clinical Immunology Laboratory, Department of Immunology and Pathology, Central Clinical SchoolMonash UniversityMelbourneVictoriaAustralia,Allergy, Asthma and Clinical Immunology ServiceAlfred HospitalMelbourneVictoriaAustralia
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18
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Collins AM, Watson CT, Breden F. Immunoglobulin genes, reproductive isolation and vertebrate speciation. Immunol Cell Biol 2022; 100:497-506. [PMID: 35781330 PMCID: PMC9545137 DOI: 10.1111/imcb.12567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/19/2022] [Accepted: 06/21/2022] [Indexed: 12/15/2022]
Abstract
Reproductive isolation drives the formation of new species, and many genes contribute to this through Dobzhansky–Muller incompatibilities (DMIs). These incompatibilities occur when gene divergence affects loci encoding interacting products such as receptors and their ligands. We suggest here that the nature of vertebrate immunoglobulin (IG) genes must make them prone to DMIs. The genes of these complex loci form functional genes through the process of recombination, giving rise to a repertoire of heterodimeric receptors of incredible diversity. This repertoire, within individuals and within species, must defend against pathogens but must also avoid pathogenic self‐reactivity. We suggest that this avoidance of autoimmunity is only achieved through a coordination of evolution between heavy‐ and light‐chain genes, and between these genes and the rest of the genome. Without coordinated evolution, the hybrid offspring of two diverging populations will carry a heavy burden of DMIs, resulting in a loss of fitness. Critical incompatibilities could manifest as incompatibilities between a mother and her divergent offspring. During fetal development, biochemical differences between the parents of hybrid offspring could make their offspring a target of the maternal immune system. This hypothesis was conceived in the light of recent insights into the population genetics of IG genes. This has suggested that antibody genes are probably as susceptible to evolutionary forces as other parts of the genome. Further repertoire studies in human and nonhuman species should now help determine whether antibody genes have been part of the evolutionary forces that drive the development of species.
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Affiliation(s)
- Andrew M Collins
- School of Biotechnology and Biomolecular Sciences University of New South Wales Sydney NSW Australia
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics University of Louisville School of Medicine Louisville KY USA
| | - Felix Breden
- Department of Biological Sciences Simon Fraser University Burnaby BC Canada
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19
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van der Weele L, Pollastro S, van Schaik BDC, van Kampen AHC, Niewold ITG, Kuijpers TW, Warnke C, Jensen PEH, Kramer D, Ryner M, Hermanrud C, Dönnes P, Pallardy M, Spindeldreher S, Deisenhammer F, Fogdell-Hahn A, de Vries N. Longitudinal analysis of anti-drug antibody development in multiple sclerosis patients treated with interferon beta-1a (Rebif™) using B cell receptor repertoire analysis. J Neuroimmunol 2022; 370:577932. [PMID: 35853357 DOI: 10.1016/j.jneuroim.2022.577932] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 05/16/2022] [Accepted: 07/10/2022] [Indexed: 10/17/2022]
Abstract
A significant proportion of multiple sclerosis (MS) patients treated with interferon beta-1a (Rebif™) develop anti-drug antibodies (ADA) with a negative impact on treatment efficacy. We hypothesized that high-throughput B-cell receptor (BCR) repertoire analysis could be used to predict and monitor ADA development. To study this we analyzed 228 peripheral blood samples from 68 longitudinally followed patients starting on interferon beta-1a. Our results show that whole blood BCR analysis does not reflect, and does not predict ADA development in MS patients treated with interferon beta-1a. We propose that BCR analysis of phenotypically selected cell subsets or tissues might be more informative.
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Affiliation(s)
- Linda van der Weele
- Department of Clinical Immunology & Rheumatology, Amsterdam Rheumatology and Immunology Centre (ARC), Amsterdam UMC228, Location AMC, University of Amsterdam, Amsterdam, the Netherlands; Department of Experimental Immunology, Amsterdam Infection & Immunity Institute (AIII), Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Sabrina Pollastro
- Department of Clinical Immunology & Rheumatology, Amsterdam Rheumatology and Immunology Centre (ARC), Amsterdam UMC228, Location AMC, University of Amsterdam, Amsterdam, the Netherlands; Department of Experimental Immunology, Amsterdam Infection & Immunity Institute (AIII), Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Barbera D C van Schaik
- Department of Clinical Epidemiology, Biostatistics, and Bioinformatics, Amsterdam Infection & Immunity Institute (AIII), Amsterdam Public Health Research Institute, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Antoine H C van Kampen
- Department of Clinical Epidemiology, Biostatistics, and Bioinformatics, Amsterdam Infection & Immunity Institute (AIII), Amsterdam Public Health Research Institute, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Ilse T G Niewold
- Department of Clinical Immunology & Rheumatology, Amsterdam Rheumatology and Immunology Centre (ARC), Amsterdam UMC228, Location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Taco W Kuijpers
- Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Emma Children's Hospital, Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Clemens Warnke
- Department of Neurology, Medical Faculty, University Hospital of Cologne, Germany
| | - Poul Erik H Jensen
- Danish Multiple Sclerosis Center, Department of Neurology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | | | - Malin Ryner
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Christina Hermanrud
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | | | - Marc Pallardy
- Université Paris-Saclay, INSERM, Inflammation Microbiome Immunopathologie, Faculté Pharmacie, Châtenay-Malabry, France
| | | | | | - Anna Fogdell-Hahn
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Niek de Vries
- Department of Clinical Immunology & Rheumatology, Amsterdam Rheumatology and Immunology Centre (ARC), Amsterdam UMC228, Location AMC, University of Amsterdam, Amsterdam, the Netherlands; Department of Experimental Immunology, Amsterdam Infection & Immunity Institute (AIII), Amsterdam UMC, Location AMC, University of Amsterdam, Amsterdam, the Netherlands.
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20
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Barmettler S, Sharapova SO, Milota T, Greif PA, Magg T, Hauck F. Genomics Driving Diagnosis and Treatment of Inborn Errors of Immunity With Cancer Predisposition. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2022; 10:1725-1736.e2. [PMID: 35364342 DOI: 10.1016/j.jaip.2022.03.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 12/14/2022]
Abstract
Inborn errors of immunity (IEI) are genetically and clinically heterogeneous disorders that, in addition to infection susceptibility and immune dysregulation, can have an enhanced cancer predisposition. The increasing availability of upfront next-generation sequencing diagnostics in immunology and oncology have uncovered substantial overlap of germline and somatic genetic conditions that can result in immunodeficiency and cancer. However, broad application of unbiased genetics in these neighboring disciplines still needs to be deployed, and joined therapeutic strategies guided by germline and somatic genetic risk factors are lacking. We illustrate the current difficulties encountered in clinical practice, summarize the historical development of pathophysiological concepts of cancer predisposition, and review select genetic, molecular, and cellular mechanisms of well-defined and illustrative disease entities such as DNA repair defects, combined immunodeficiencies with Epstein-Barr virus susceptibility, autoimmune lymphoproliferative syndromes, regulatory T-cell disorders, and defects in cell intrinsic immunity. We review genetic variants that, when present in the germline, cause IEI with cancer predisposition but, when arising as somatic variants, behave as oncogenes and cause specific cancer entities. We finally give examples of small molecular compounds that are developed and studied to target genetically defined cancers but might also proof useful to treat IEI.
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Affiliation(s)
- Sara Barmettler
- Allergy and Clinical Immunology Unit, Division of Rheumatology, Allergy, & Immunology, Massachusetts General Hospital, Boston, Mass
| | - Svetlana O Sharapova
- Research Department, Belarusian Research Center for Pediatric Oncology, Hematology and Immunology, Minsk, Belarus
| | - Tomas Milota
- Department of Immunology, Second Faculty of Medicine, Charles University Hospital and Motol University Hospital, Prague, Czechia
| | - Philipp A Greif
- Department of Medicine III, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany; German Cancer Consortium (DKTK), partner site Munich, 81377 Munich, Germany; German Cancer Research Center (DKFZ), 69121 Heidelberg, Germany
| | - Thomas Magg
- Division of Pediatric Immunology and Rheumatology, Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Fabian Hauck
- Division of Pediatric Immunology and Rheumatology, Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität München, Munich, Germany.
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21
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Szittner Z, Péter B, Kurunczi S, Székács I, Horváth R. Functional blood cell analysis by label-free biosensors and single-cell technologies. Adv Colloid Interface Sci 2022; 308:102727. [DOI: 10.1016/j.cis.2022.102727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/25/2022] [Accepted: 06/27/2022] [Indexed: 11/01/2022]
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22
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HLA Homozygosity and Likelihood of Sensitization in Kidney Transplant Candidates. Transplant Direct 2022; 8:e1312. [PMID: 35415215 PMCID: PMC8989785 DOI: 10.1097/txd.0000000000001312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 02/09/2022] [Indexed: 11/10/2022] Open
Abstract
Background. Homozygosity for HLAs has been associated with adverse outcomes after viral infection as well as pregnancy-induced HLA sensitization. We sought to assess the relationship between HLA locus homozygosity and the level of HLA antibody sensitization. Methods. We measured sensitization using the calculated panel reactive antibody value for a large cohort of 147 461 patients added to the US OPTN/United Network for Organ Sharing kidney transplant waitlist between December 2014 and December 2019. We used multinomial logistic modeling to compare 62 510 sensitized patients to 84 955 unsensitized controls. Results. We found that the number of homozygous HLA loci was strongly associated with the level of sensitization. Within mildly, highly, or extremely sensitized candidates, women displayed a higher relative abundance of HLA homozygosity at multiple HLA loci as compared with men, with attenuation of this effect in Black candidates. In a multivariable logistic model, the number of homozygous HLA loci interacted with female sex but not with other factors associated with sensitization, including recipient ethnicity and a history of prior kidney transplant. Conclusions. This study shows that HLA homozygosity is an innate genetic factor that affects the likelihood of HLA sensitization. Further research is needed to identify the immunologic mechanisms that underlie this observation.
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23
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Khalid Z, Chen Y, Yu D, Abbas M, Huan M, Naz Z, Mengist HM, Cao MJ, Jin T. IgNAR antibody: Structural features, diversity and applications. FISH & SHELLFISH IMMUNOLOGY 2022; 121:467-477. [PMID: 35077867 DOI: 10.1016/j.fsi.2022.01.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 01/15/2022] [Accepted: 01/16/2022] [Indexed: 06/14/2023]
Abstract
In response to the invasion of exogenous microorganisms, one of the defence strategies of the immune system is to produce antibodies. Cartilaginous fish is among those who evolved the earliest humoral immune system that utilizes immunoglobulin-type antibodies. The cartilaginous fish antibodies fall into three categories: IgW, IgM, and IgNAR. The shark Immunoglobulin Novel Antigen Receptor (IgNAR) constitutes disulfide-bonded dimers of two protein chains, similar to the heavy chain of mammalian IgGs. Shark IgNAR is the primary antibody of a shark's adaptive immune system with a serum concentration of 0.1-1.0 mg/mL. Its structure comprises of one variable (V) domain (VNAR) and five constant (C1 -C5) domains in the secretory form. VNARs are classified into several subclasses based on specific properties such as the quantity and position of additional non-canonical cysteine (Cys) residues in the VNAR. The VDJ recombination in IgNAR comprises various fragments; one variable component, three diverse sections, one joining portion, and a solitary arrangement of constant fragments framed in each IgNAR gene cluster. The re-arrangement happens just inside this gene cluster bringing about a VD1D2D3J segment. Therefore, four re-arrangement procedures create the entire VNAR space. IgNAR antibody can serve as an excellent diagnostic, therapeutic, and research tool because it has a smaller size, high specificity for antigen-binding, and perfect stability. The domain characterization, structural features, types, diversity and therapeutic applications of IgNAR molecules are highlighted in this review. It would be helpful for further research on IgNAR antibodies acting as an essential constituent of the adaptive immune system and a potential therapeutic agent.
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Affiliation(s)
- Zunera Khalid
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Yulei Chen
- College of Ocean Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Jimei University, Xiamen, Fujian, China
| | - Du Yu
- CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Misbah Abbas
- CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Ma Huan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Zara Naz
- CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Hylemariam Mihiretie Mengist
- CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Min-Jie Cao
- College of Ocean Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Jimei University, Xiamen, Fujian, China.
| | - Tengchuan Jin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China; CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230027, China; CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Science, Shanghai, 200031, China.
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24
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Tian G, Li M, Lv G. Analysis of T-Cell Receptor Repertoire in Transplantation: Fingerprint of T Cell-mediated Alloresponse. Front Immunol 2022; 12:778559. [PMID: 35095851 PMCID: PMC8790170 DOI: 10.3389/fimmu.2021.778559] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/22/2021] [Indexed: 11/13/2022] Open
Abstract
T cells play a key role in determining allograft function by mediating allogeneic immune responses to cause rejection, and recent work pointed their role in mediating tolerance in transplantation. The unique T-cell receptor (TCR) expressed on the surface of each T cell determines the antigen specificity of the cell and can be the specific fingerprint for identifying and monitoring. Next-generation sequencing (NGS) techniques provide powerful tools for deep and high-throughput TCR profiling, and facilitate to depict the entire T cell repertoire profile and trace antigen-specific T cells in circulation and local tissues. Tailing T cell transcriptomes and TCR sequences at the single cell level provides a full landscape of alloreactive T-cell clones development and biofunction in alloresponse. Here, we review the recent advances in TCR sequencing techniques and computational tools, as well as the recent discovery in overall TCR profile and antigen-specific T cells tracking in transplantation. We further discuss the challenges and potential of using TCR sequencing-based assays to profile alloreactive TCR repertoire as the fingerprint for immune monitoring and prediction of rejection and tolerance.
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Affiliation(s)
| | - Mingqian Li
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of Jilin University, Changchun, China
| | - Guoyue Lv
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of Jilin University, Changchun, China
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25
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Abstract
IgA mediates microbial homeostasis at the intestinal mucosa. Within the gut, IgA acts in a context-dependent manner to both prevent and promote bacterial colonization and to influence bacterial gene expression, thus providing exquisite control of the microbiota. IgA-microbiota interactions are highly diverse across individuals and populations, yet the factors driving this variation remain poorly understood. In this Review, we summarize evidence for the host, bacterial and environmental factors that influence IgA-microbiota interactions. Recent advances have helped to clarify the antigenic specificity and immune selection of intestinal IgA and have highlighted the importance of microbial glycan recognition. Furthermore, emerging evidence suggests that diet and nutrition play an important role in shaping IgA recognition of the microbiota. IgA-microbiota interactions are disrupted during both overnutrition and undernutrition and may be altered dynamically in response to diet, with potential implications for host health. We situate this research in the context of outstanding questions and future directions in order to better understand the fascinating paradigm of IgA-microbiota homeostasis.
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26
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Zhang Z, Jara CJ, Singh M, Xu H, Goodnow CC, Jackson KJ, Reed JH. Human transitional and IgM low mature naïve B cells preserve permissive B-cell receptors. Immunol Cell Biol 2021; 99:865-878. [PMID: 33988890 PMCID: PMC8453828 DOI: 10.1111/imcb.12478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/11/2021] [Accepted: 05/11/2021] [Indexed: 12/02/2022]
Abstract
The level of immunoglobulin M (IgM) displayed on the surface of peripheral blood B cells exhibits a broad dynamic range and has been associated with both development and selection. To determine whether IgM surface expression associates with distinct immunoglobulin heavy‐chain (IGH) repertoire properties, we performed deep IgM sequencing of peripheral blood transitional and mature naïve B cells in the upper and lower quartiles of surface IgM expression for 12 healthy donors. Mature naïve B cells within the lowest quartile for surface IgM expression displayed more diverse IGH features including increased complementarity‐determining region 3 length, IGHJ6 segment usage and aromatic amino acids compared with mature naïve B cells with high surface IgM. There were no differences between IGH repertoires for transitional B cells with high or low surface IgM. These findings suggest that a selection checkpoint during progression of transitional to mature naïve B cells reduces the breadth of the IGH repertoire among high surface IgM B cells but that diversity is preserved in B cells expressing low levels of surface IgM.
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Affiliation(s)
- Zhiguo Zhang
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Christopher J Jara
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,Faculty of Medicine, St. Vincent's Clinical School, UNSW, Sydney, NSW, Australia
| | - Mandeep Singh
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,Faculty of Medicine, St. Vincent's Clinical School, UNSW, Sydney, NSW, Australia
| | - Huji Xu
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Christopher C Goodnow
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,School of Medical Sciences and Cellular Genomics Futures Institute, UNSW, Sydney, NSW, Australia
| | | | - Joanne H Reed
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,Faculty of Medicine, St. Vincent's Clinical School, UNSW, Sydney, NSW, Australia
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27
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Bartneck M. Lipid nanoparticle formulations for targeting leukocytes with therapeutic RNA in liver fibrosis. Adv Drug Deliv Rev 2021; 173:70-88. [PMID: 33774114 DOI: 10.1016/j.addr.2021.03.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/27/2021] [Accepted: 03/11/2021] [Indexed: 02/08/2023]
Abstract
Obesity and low-grade inflammation are promoters of a multitude of diseases including liver fibrosis. Activation of the mobile leukocytes has a major impact on the outcome of inflammatory disease and can hence foster or mitigate liver fibrosis. This renders immunological targets valuable for directed interventions using nanomedicines. Particularly, RNA-based drugs formulated as lipid nanoparticles (LNP) can open new avenues for the personalized treatment of liver fibrosis both through specific interference and via the induction of the expression of functional and therapeutic proteins. Using microfluidics technology, all components, including lipid-anchored targeting ligands, are assembled in a single-step mixing process. A highlight is set to immunologically relevant liver cell types that are most vulnerable for being reached by LNP. A selection of LNP from other therapeutic fields applicable for reaching these cells in liver fbrosis is summarized. Furthermore, recent proceedings and major obstacles in the field of these targeted LNP are presented.
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28
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Weng R, Liu S, Gu X, Zhong Z. Characterization of the B cell receptor repertoire of patients with acute coronary syndrome. Genes Genomics 2021; 44:19-28. [PMID: 33974240 DOI: 10.1007/s13258-021-01110-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 04/29/2021] [Indexed: 01/01/2023]
Abstract
BACKGROUND Acute coronary syndrome (ACS) is a complex cardiovascular disease whose development involves the dysregulation of adaptive immune responses. Though it has been proven that T cells associate with inflammation in the development of ACS, the function of B cells in disease remains unclear. OBJECTIVE The aim of this study was to reveal the diversity of the B cell receptor (BCR) repertoire of patients with ACS. METHODS We conducted a pilot study to sequence the immune repertoire of peripheral blood mononuclear cells (PBMCs) from patients with ACS, including acute myocardial infarction (AMI) and unstable angina (UA), and quantitatively characterized BCR repertoires by bioinformatics analysis. RESULTS We found that patients with AMI and UA had lower BCR repertoire diversity compared with controls with normal coronary arteries (NCA). Lower percentages of productive unique BCR nt sequences and higher percentages of top 200 unique BCR sequences were identified in AMI and UA patients than NCA controls. Patients had various preferential usage of V and J genes from B cell clones in accordance with the disease severity of coronary arteries. AMI patients had distinct CDR3 amino acids, and their frequency differed among patients with ACS. CONCLUSIONS Our results indicate that differential BCR signatures represent an imprint of distinct repertoires among ACS patients. This study thereby opens up the prospect of studying disease-relevant B cells to better understand and treat ACS.
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Affiliation(s)
- Ruiqiang Weng
- Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, No. 63 Huangtang Road, Meijiang District, Meizhou, 514031, People's Republic of China
- Guangdong Provincial Engineering and Technological Research Center for Molecular Diagnostics of Cardiovascular Diseases, Meizhou, 514031, People's Republic of China
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, 514031, People's Republic of China
| | - Sudong Liu
- Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, No. 63 Huangtang Road, Meijiang District, Meizhou, 514031, People's Republic of China
- Guangdong Provincial Engineering and Technological Research Center for Molecular Diagnostics of Cardiovascular Diseases, Meizhou, 514031, People's Republic of China
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, 514031, People's Republic of China
| | - Xiaodong Gu
- Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, No. 63 Huangtang Road, Meijiang District, Meizhou, 514031, People's Republic of China
- Guangdong Provincial Engineering and Technological Research Center for Molecular Diagnostics of Cardiovascular Diseases, Meizhou, 514031, People's Republic of China
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, 514031, People's Republic of China
| | - Zhixiong Zhong
- Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, No. 63 Huangtang Road, Meijiang District, Meizhou, 514031, People's Republic of China.
- Guangdong Provincial Engineering and Technological Research Center for Molecular Diagnostics of Cardiovascular Diseases, Meizhou, 514031, People's Republic of China.
- Center for Cardiovascular Diseases, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, 514031, People's Republic of China.
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29
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Zhang W, Hawkins PG, He J, Gupta NT, Liu J, Choonoo G, Jeong SW, Chen CR, Dhanik A, Dillon M, Deering R, Macdonald LE, Thurston G, Atwal GS. A framework for highly multiplexed dextramer mapping and prediction of T cell receptor sequences to antigen specificity. SCIENCE ADVANCES 2021; 7:7/20/eabf5835. [PMID: 33990328 PMCID: PMC8121425 DOI: 10.1126/sciadv.abf5835] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/25/2021] [Indexed: 05/04/2023]
Abstract
T cell receptor (TCR) antigen-specific recognition is essential for the adaptive immune system. However, building a TCR-antigen interaction map has been challenging due to the staggering diversity of TCRs and antigens. Accordingly, highly multiplexed dextramer-TCR binding assays have been recently developed, but the utility of the ensuing large datasets is limited by the lack of robust computational methods for normalization and interpretation. Here, we present a computational framework comprising a novel method, ICON (Integrative COntext-specific Normalization), for identifying reliable TCR-pMHC (peptide-major histocompatibility complex) interactions and a neural network-based classifier TCRAI that outperforms other state-of-the-art methods for TCR-antigen specificity prediction. We further demonstrated that by combining ICON and TCRAI, we are able to discover novel subgroups of TCRs that bind to a given pMHC via different mechanisms. Our framework facilitates the identification and understanding of TCR-antigen-specific interactions for basic immunological research and clinical immune monitoring.
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Affiliation(s)
- Wen Zhang
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA.
| | - Peter G Hawkins
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Jing He
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Namita T Gupta
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Jinrui Liu
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Gabrielle Choonoo
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Se W Jeong
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Calvin R Chen
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Ankur Dhanik
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Myles Dillon
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Raquel Deering
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Lynn E Macdonald
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Gavin Thurston
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Gurinder S Atwal
- Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA.
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30
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Atlas of breast cancer infiltrated B-lymphocytes revealed by paired single-cell RNA-sequencing and antigen receptor profiling. Nat Commun 2021; 12:2186. [PMID: 33846305 PMCID: PMC8042001 DOI: 10.1038/s41467-021-22300-2] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 02/24/2021] [Indexed: 12/20/2022] Open
Abstract
To gain mechanistic insights into the functions and developmental dynamics of tumor-infiltrated immune cells, especially B-lymphocytes, here we combine single-cell RNA-sequencing and antigen receptor lineage analysis to characterize a large number of triple-negative breast cancer infiltrated immune cells and report a comprehensive atlas of tumor-infiltrated B-lymphocytes. The single-cell transcriptional profiles reveal significant heterogeneity in tumor-infiltrated B-cell subgroups. The single-cell antigen receptor analyses demonstrate that compared with those in peripheral blood, tumor-infiltrated B-cells have more mature and memory B-cell characteristics, higher clonality, more class switching recombination and somatic hypermutations. Combined analyses suggest local differentiation of infiltrated memory B-cells within breast tumors. The B-cell signatures based on the single-cell RNA-sequencing results are significantly associated with improved survival in breast tumor patients. Functional analyses of tumor-infiltrated B-cell populations suggest that mechanistically, B-cell subgroups may contribute to immunosurveillance through various pathways. Further dissection of tumor-infiltrated B-cell populations will provide valuable clues for tumor immunotherapy. Immune cells infiltrating the tumour microenvironment play critical roles in disease pathogenesis and the immune response. Here the authors present the characterisation of infiltrating B cells in breast tumours by the formation of an atlas created from paired RNA sequence and antigen receptor profiling.
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31
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A single donor is sufficient to produce a highly functional in vitro antibody library. Commun Biol 2021; 4:350. [PMID: 33742103 PMCID: PMC7979914 DOI: 10.1038/s42003-021-01881-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/19/2021] [Indexed: 01/31/2023] Open
Abstract
Antibody complementarity determining region diversity has been considered to be the most important metric for the production of a functional antibody library. Generally, the greater the antibody library diversity, the greater the probability of selecting a diverse array of high affinity leads. According to this paradigm, the primary means of elevating library diversity has been by increasing the number of donors. In the present study we explored the possibility of creating an in vitro antibody library from a single healthy individual, showing that the number of lymphocytes, rather than the number of donors, is the key criterion in the production of a diverse and functional antibody library. We describe the construction of a high-quality phage display library comprising 5 × 109 human antibodies by applying an efficient B cell extraction protocol from a single donor and a targeted V-gene amplification strategy favoring specific antibody families for their improved developability profiles. Each step of the library generation process was followed and validated by next generation sequencing to monitor the library quality and diversity. The functionality of the library was tested using several therapeutically relevant targets for which a vast number of different antibodies with desired biophysical properties were obtained.
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32
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Bilal S, Etayo A, Hordvik I. Immunoglobulins in teleosts. Immunogenetics 2021; 73:65-77. [PMID: 33439286 DOI: 10.1007/s00251-020-01195-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/18/2020] [Indexed: 02/06/2023]
Abstract
Immunoglobulins are glycoproteins which are produced as membrane-bound receptors on B-cells or in a secreted form, known as antibodies. In teleosts, three immunoglobulin isotypes, IgM, IgT, and IgD, are present, each comprising two identical heavy and two identical light polypeptide chains. The basic mechanisms for generation of immunoglobulin diversity are similar in teleosts and higher vertebrates. The B-cell pre-immune repertoire is diversified by VDJ recombination, junctional flexibility, addition of nucleotides, and combinatorial association of light and heavy chains, while the post-immune repertoire undergoes somatic hypermutation during clonal expansion. Typically, the teleost immunoglobulin heavy chain gene complex has a modified translocon arrangement where the Dτ-Jτ-Cτ cluster of IgT is generally located between the variable heavy chain (VH) region and the Dμ/δ-Jμ/δ-Cμ-Cδ gene segments, or within the set of VH gene segments. However, multiple genome duplication and deletion events and loss of some individual genes through evolution has complicated the IgH gene organization. The IgH gene arrangement allows the expression of either IgT or IgM/IgD. Alternative splicing is responsible for the regulation of IgM/IgD expression and the secreted versus transmembrane forms of IgT, IgD, and IgM. The overall structure of IgM and IgT is usually conserved across species, whereas IgD has a large variety of structures. IgM is the main effector molecule in both systemic and mucosal immunity and shows a broad range of concentrations in different teleost species. Although IgM is usually present in higher concentrations under normal conditions, IgT is considered the main mucosal Ig.
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Affiliation(s)
- Sumaira Bilal
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Angela Etayo
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Ivar Hordvik
- Department of Biological Sciences, University of Bergen, Bergen, Norway.
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33
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Raybould MIJ, Rees AR, Deane CM. Current strategies for detecting functional convergence across B-cell receptor repertoires. MAbs 2021; 13:1996732. [PMID: 34781829 PMCID: PMC8604390 DOI: 10.1080/19420862.2021.1996732] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 10/10/2021] [Accepted: 10/12/2021] [Indexed: 12/11/2022] Open
Abstract
Convergence across B-cell receptor (BCR) and antibody repertoires has become instrumental in prioritizing candidates in recent rapid therapeutic antibody discovery campaigns. It has also increased our understanding of the immune system, providing evidence for the preferential selection of BCRs to particular (immunodominant) epitopes post vaccination/infection. These important implications for both drug discovery and immunology mean that it is essential to consider the optimal way to combine experimental and computational technology when probing BCR repertoires for convergence signatures. Here, we discuss the theoretical basis for observing BCR repertoire functional convergence and explore factors of study design that can impact functional signal. We also review the computational arsenal available to detect antibodies with similar functional properties, highlighting opportunities enabled by recent clustering algorithms that exploit structural similarities between BCRs. Finally, we suggest future areas of development that should increase the power of BCR repertoire functional clustering.
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Affiliation(s)
- Matthew I. J. Raybould
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, UK
| | | | - Charlotte M. Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, UK
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34
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Greiff V, Yaari G, Cowell LG. Mining adaptive immune receptor repertoires for biological and clinical information using machine learning. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.coisb.2020.10.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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35
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Gastman B, Agarwal PK, Berger A, Boland G, Broderick S, Butterfield LH, Byrd D, Fecci PE, Ferris RL, Fong Y, Goff SL, Grabowski MM, Ito F, Lim M, Lotze MT, Mahdi H, Malafa M, Morris CD, Murthy P, Neves RI, Odunsi A, Pai SI, Prabhakaran S, Rosenberg SA, Saoud R, Sethuraman J, Skitzki J, Slingluff CL, Sondak VK, Sunwoo JB, Turcotte S, Yeung CC, Kaufman HL. Defining best practices for tissue procurement in immuno-oncology clinical trials: consensus statement from the Society for Immunotherapy of Cancer Surgery Committee. J Immunother Cancer 2020; 8:e001583. [PMID: 33199512 PMCID: PMC7670953 DOI: 10.1136/jitc-2020-001583] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2020] [Indexed: 12/11/2022] Open
Abstract
Immunotherapy is now a cornerstone for cancer treatment, and much attention has been placed on the identification of prognostic and predictive biomarkers. The success of biomarker development is dependent on accurate and timely collection of biospecimens and high-quality processing, storage and shipping. Tumors are also increasingly used as source material for the generation of therapeutic T cells. There have been few guidelines or consensus statements on how to optimally collect and manage biospecimens and source material being used for immunotherapy and related research. The Society for Immunotherapy of Cancer Surgery Committee has brought together surgical experts from multiple subspecialty disciplines to identify best practices and to provide consensus on how best to access and manage specific tissues for immuno-oncology treatments and clinical investigation. In addition, the committee recommends early integration of surgeons and other interventional physicians with expertise in biospecimen collection, especially in clinical trials, to optimize the quality of tissue and the validity of correlative clinical studies in cancer immunotherapy.
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Affiliation(s)
- Brian Gastman
- Department of Plastic Surgery, Cleveland Clinic, Cleveland, Ohio, USA
| | - Piyush K Agarwal
- Department of Surgery, University of Chicago, Chicago, Illinois, USA
| | - Adam Berger
- Division of Surgical Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - Genevieve Boland
- Department of Surgical Oncology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Stephen Broderick
- Oncology, Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
- Department of Surgery, Johns Hopkins Medicine, Baltimore, Maryland, USA
| | - Lisa H Butterfield
- Parker Institute for Cancer Immunotherapy, San Francisco, California, USA
- Microbiology and Immunology, University of California San Francisco, San Francisco, California, USA
| | - David Byrd
- Department of Surgery, University of Washington, Seattle, Washington, USA
| | - Peter E Fecci
- Department of Neurosurgery, Duke University School of Medicine, Durham, North Carolina, USA
| | - Robert L Ferris
- Departments of Otolaryngology, Immunology, and Radiation Oncology, University of Pittsburgh Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
| | - Yuman Fong
- Department of Surgery, City of Hope National Medical Center, Duarte, California, USA
| | | | - Matthew M Grabowski
- Department of Neurosurgery, Duke Center for Brain and Spine Metastasis, Durham, North Carolina, USA
| | - Fumito Ito
- Center for Immunotherapy, Department of Surgical Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Michael Lim
- Departments of Neurosurgery, Oncology, Radiation Oncology, and Otolaryngology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael T Lotze
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Haider Mahdi
- OBGYN and Women's Health Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Mokenge Malafa
- Department of Gastrointestinal Oncology, Moffitt Cancer Center, Tampa, Florida, USA
| | - Carol D Morris
- Division of Orthopaedic Oncology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Pranav Murthy
- Department of Surgery, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Rogerio I Neves
- Department of Surgery, Penn State Cancer Institute, Hershey, Pennsylvania, USA
| | - Adekunle Odunsi
- Departments of Immunology and Gynecologic Oncology, Roswell Park Cancer Institute, Buffalo, New York, USA
| | - Sara I Pai
- Department of Surgical Oncology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Sangeetha Prabhakaran
- Division of Surgical Oncology, Department of Surgery, UNM Comprehensive Cancer Center, University of New Mexico, Albuquerque, New Mexico, USA
| | | | - Ragheed Saoud
- Department of Surgery, University of Chicago Hospitals, Chicago, Illinois, United States
| | | | - Joseph Skitzki
- Departments of Surgical Oncology and Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Craig L Slingluff
- Department of Surgery, Division of Surgical Oncology, Breast and Melanoma Surgery, University of Virginia, Charlottesville, Virginia, USA
| | - Vernon K Sondak
- Department of Cutaneous Oncology, Moffitt Cancer Center, Tampa, Florida, USA
| | - John B Sunwoo
- Department of Otolaryngology, Stanford University School of Medicine, Stanford, California, USA
| | - Simon Turcotte
- Surgery Department, Centre Hospitalier de l'Universite de Montreal, Montreal, Quebec, Canada
| | - Cecilia Cs Yeung
- Department of Pathology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Howard L Kaufman
- Department of Surgical Oncology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Immuneering Corp, Cambridge, Massachusetts, USA
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36
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Han J, Lotze MT. The Adaptome as Biomarker for Assessing Cancer Immunity and Immunotherapy. Methods Mol Biol 2020; 2055:369-397. [PMID: 31502161 DOI: 10.1007/978-1-4939-9773-2_17] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In terms of diagnosing and treating diseases, our adaptive immune system is the "best doctor." It carries out these tasks with unmatched precision, with the help of both T and B cell receptors, our most diverse set of genes, distinguishing one individual from another. It does this by generating autologous extraordinary diversity in the receptors, ranging from 1015 to 1025 for each chain of the rearranged receptors. By combining multiplex PCR and next-generation sequencing (NGS), we have developed high throughput methods to study adaptive immunity. The adaptome is the sum-total of expressed T and B cell receptor genes in a sample, composed of seven chains, including the alpha/beta and gamma/delta chains for T cells, and heavy/lambda or kappa chains for B cells. Immune repertoire is the sum-total of the individual clonotypes within one chain, including individual complementarity-determining regions (CDR) 3 sequences. In order to reflect the breadth and depth of the true adaptome, the following criteria assessing any method needs to be ascertained: (1) Methods need to be inclusive and quantitative; (2) Analysis should consider what questions need to be addressed and whether bulk or single cell sequencing provide the best tools for assessing the underlying biology and addressing important questions; (3) Measures of clonal diversity are key to understand the underlying structure and providence of the repertoire; and (4) Convergent evolution may allow a surprising degree of homologous or identical CDR3s associated with individual disease entities, creating hope for novel diagnostics and/or disease burden assessments. Integrating studies of the peripheral blood, lymph nodes, and tumor allows dynamic interrogation of the alterations occurring with age, treatment, and response to emergent and established therapies.
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Affiliation(s)
- Jian Han
- iRepertoire, Inc., Huntsville, AL, USA.,Hudson Alpha Institute, Huntsville, AL, USA
| | - Michael T Lotze
- University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
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37
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Cagigi A, Misasi J, Ploquin A, Stanley DA, Ambrozak D, Tsybovsky Y, Mason RD, Roederer M, Sullivan NJ. Vaccine Generation of Protective Ebola Antibodies and Identification of Conserved B-Cell Signatures. J Infect Dis 2019; 218:S528-S536. [PMID: 30010811 DOI: 10.1093/infdis/jiy333] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
We recently identified a single potently neutralizing monoclonal antibody (mAb), mAb114, isolated from a human survivor of natural Zaire ebolavirus (EBOV) infection, which fully protects nonhuman primates (NHPs) against lethal EBOV challenge. To evaluate the ability of vaccination to generate mAbs such as mAb114, we cloned antibodies from NHPs vaccinated with vectors encoding the EBOV glycoprotein (GP). We identified 14 unique mAbs with potent binding to GP, 4 of which were neutralized and had the functional characteristics of mAb114. These vaccine-induced macaque mAbs share many sequence similarities with mAb114 and use the same mAb114 VH gene (ie, IGHV3-13) when classified using the macaque IMGT database. The antigen-specific VH-gene repertoire present after each immunization indicated that IGHV3-13 mAbs populate an EBOV-specific B-cell repertoire that appears to become more prominent with subsequent boosting. These findings will support structure-based vaccine design aimed at enhanced induction of antibodies such as mAb114.
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Affiliation(s)
- Alberto Cagigi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - John Misasi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland.,Division of Infectious Diseases, Boston Children's Hospital, Massachusetts
| | - Aurélie Ploquin
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Daphne A Stanley
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - David Ambrozak
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Maryland
| | - Rosemarie D Mason
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Nancy J Sullivan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
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38
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Di Lorenzo B, Ravens S, Silva-Santos B. High-throughput analysis of the human thymic Vδ1 + T cell receptor repertoire. Sci Data 2019; 6:115. [PMID: 31273218 PMCID: PMC6609709 DOI: 10.1038/s41597-019-0118-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 05/29/2019] [Indexed: 12/11/2022] Open
Abstract
γδ T cells are a relatively rare subset of lymphocytes in the human peripheral blood, but they play important roles at the interface between the innate and the adaptive immune systems. The γδ T cell lineage is characterized by a signature γδ T cell receptor (γδTCR) that displays extensive sequence variability originated by DNA rearrangement of the corresponding V(D)J loci. Human γδ T cells comprise Vγ9Vδ2 T cells, the major subset in the peripheral blood; and Vδ1+ T cells, the predominant subpopulation in the post-natal thymus and in peripheral tissues. While less studied, Vδ1+ T cells recently gathered significant attention due to their anti-cancer and anti-viral activities. In this study we applied next-generation sequencing (NGS) to analyse the γδTCR repertoire of highly (FACS-)purified Vδ1+ T cells from human thymic biopsies. Our analysis reveals unsuspected aspects of thymically rearranged and expressed (at the mRNA level) TRG and TRD genes, thus constituting a data resource that qualifies previous conclusions on the TCR repertoire of γδ T cells developing in the human thymus. Design Type(s) | transcription profiling design • cellular data analysis objective | Measurement Type(s) | gamma delta T-lymphocyte | Technology Type(s) | RNA sequencing | Factor Type(s) | sex • gene | Sample Characteristic(s) | Homo sapiens • thymus |
Machine-accessible metadata file describing the reported data (ISA-Tab format)
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Affiliation(s)
- Biagio Di Lorenzo
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.,Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Sarina Ravens
- Institute of Immunology, Hannover Medical School, Hannover, Germany.
| | - Bruno Silva-Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.
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39
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Artificial immunoglobulin light chain with potential to associate with a wide variety of immunoglobulin heavy chains. Biochem Biophys Res Commun 2019; 515:481-486. [PMID: 31167721 DOI: 10.1016/j.bbrc.2019.05.149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 05/24/2019] [Indexed: 12/13/2022]
Abstract
Immunoglobulins play important roles in antigen recognition during the immune response, and the complementarity-determining region (CDR) 3 of the heavy chain is considered as the critical antigen-binding site. We previously developed a statistical protocol for the extensive analysis of heavy chain variable region repertoires and the dynamics of their immune response using next-generation sequencing (NGS). The properties of important antibody heavy chains predicted in silico by the protocol were examined by gene synthesis and antibody protein expression; however, the corresponding light chain that matches with the heavy chain could not be predicted by our protocol. To understand the dynamics of the heavy chain and the effect of light chain pairing on it, we firstly tried to obtain an artificial light chain that pairs with a broad range of heavy chains and then analyzed its effect on the antigen binding of heavy chains upon pairing. During the pre-B cell stage, the surrogate light chain (SLC) could pair with the nascent immunoglobulin μ heavy chains (Ig-μH) and promote them to function in the periphery. On the basis of this property, we designed several versions of genetically engineered "common light chain" prototypes by modifying the SLC structure. Among them, the mouse-derived VpreB1λ5Cκ light chain showed acceptable matching property with several different heavy chains without losing specificity of the original heavy chains, though the antigen affinities were variable. The extent of matching depended on the heavy chain; surprisingly, a specific heavy chain (IGHV9-3) could match with two different conventional Vκs (IGKV3-2*01 and IGKV10-96*01) without losing the antigen affinities, whereas another heavy chain (IGHV1-72) completely lost its antigen affinities by the same matching. Thus, the results suggested that the antigen recognition of the heavy chain is variably affected by the paired light chain, and that the artificial light chain, Mm_VpreB1λ5Cκ, has the potential to be a "common light chain", providing a novel system to analyze the effects of light chains in antigen recognition of heavy chains.
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40
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Kirpach J, Colone A, Bürckert JP, Faison WJ, Dubois ARSX, Sinner R, Reye AL, Muller CP. Detection of a Low Level and Heterogeneous B Cell Immune Response in Peripheral Blood of Acute Borreliosis Patients With High Throughput Sequencing. Front Immunol 2019; 10:1105. [PMID: 31156648 PMCID: PMC6532064 DOI: 10.3389/fimmu.2019.01105] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 04/30/2019] [Indexed: 01/08/2023] Open
Abstract
The molecular diagnosis of acute Borreliosis is complicated and better strategies to improve the diagnostic processes are warranted. High Throughput Sequencing (HTS) of human B cell repertoires after e.g., Dengue virus infection or influenza vaccination revealed antigen-associated “CDR3 signatures” which may have the potential to support diagnosis in infectious diseases. The human B cell immune response to Borrelia burgdorferi sensu lato—the causative agent of Borreliosis—has mainly been studied at the antibody level, while less attention has been given to the cellular part of the humoral immune response. There are indications that Borrelia actively influence the B cell immune response and that it is therefore not directly comparable to responses induced by other infections. The main goal of this study was to identify B cell features that could be used to support diagnosis of Borreliosis. Therefore, we characterized the B cell immune response in these patients by combining multicolor flow cytometry, single Borrelia-reactive B cell receptor (BCR) sequencing, and B cell repertoire deep sequencing. Our phenotyping experiments showed, that there is no significant difference between B cell subpopulations of acute Borreliosis patients and controls. BCR sequences from individual epitope-reactive B cells had little in common between each other. HTS showed, however, a higher complementarity determining region 3 (CDR3) amino acid (aa) sequence overlap between samples from different timepoints in patients as compared to controls. This indicates, that HTS is sensitive enough to detect ongoing B cell immune responses in these patients. Although each individual's repertoire was dominated by rather unique clones, clustering of bulk BCR repertoire sequences revealed a higher overlap of IgG BCR repertoire sequences between acute patients than controls. Even if we have identified a few Borrelia-associated CDR3aa sequences, they seem to be rather unique for each patient and therefore not suitable as biomarkers.
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Affiliation(s)
- Josiane Kirpach
- Vaccinology and B Cell Immunology, Infectious Diseases Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Alessia Colone
- Vaccinology and B Cell Immunology, Infectious Diseases Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Jean-Philippe Bürckert
- Vaccinology and B Cell Immunology, Infectious Diseases Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - William J Faison
- Vaccinology and B Cell Immunology, Infectious Diseases Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Axel R S X Dubois
- Vaccinology and B Cell Immunology, Infectious Diseases Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Regina Sinner
- Vaccinology and B Cell Immunology, Infectious Diseases Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Anna L Reye
- Vaccinology and B Cell Immunology, Infectious Diseases Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Claude P Muller
- Vaccinology and B Cell Immunology, Infectious Diseases Research Unit, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
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41
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Deep targeted sequencing reveals the diversity of TRB-CDR3 repertoire in patients with preeclampsia. Hum Immunol 2019; 80:848-854. [PMID: 30965079 DOI: 10.1016/j.humimm.2019.04.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/03/2019] [Accepted: 04/06/2019] [Indexed: 12/12/2022]
Abstract
Preeclampsia (PE) is one of the major causes of maternal and perinatal mortality worldwide. This study aimed to determine the immunological characteristics of PE patients and normal pregnancy at the T cell receptor beta-chain (TRB) level by using high-throughput sequencing. High-throughput sequencing was performed to analyze the expression of TRB-CDR3 in circulating T cells. T cells were isolated from 36 healthy pregnant women, 24 patients with severe PE, and 18 patients with moderate PE. Rearranged mRNA sequences were assigned to their germline V, D, and J counterparts, and translated into proper amino acids by the IMGT database. In general, PE samples had more TRB-CDR3 reads and types than those of normal pregnant woman in the circulation, but the mean number of TRB-CDR3 reads and unique TRB-CDR3 reads in severe group was lower than that in the moderate group. In PE patients, the V7_9 and V20_1 gene loci were more prevalent than in healthy pregnant women. In addition, 4 kinds of TRB-CDR3 peptides were found to be highly relevant to the pathogenesis of PE. Of them, peptides matched to herpes simplex virus antigen-specific T cells were much lower in PE samples.
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42
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Miho E, Roškar R, Greiff V, Reddy ST. Large-scale network analysis reveals the sequence space architecture of antibody repertoires. Nat Commun 2019; 10:1321. [PMID: 30899025 PMCID: PMC6428871 DOI: 10.1038/s41467-019-09278-8] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 03/01/2019] [Indexed: 12/23/2022] Open
Abstract
The architecture of mouse and human antibody repertoires is defined by the sequence similarity networks of the clones that compose them. The major principles that define the architecture of antibody repertoires have remained largely unknown. Here, we establish a high-performance computing platform to construct large-scale networks from comprehensive human and murine antibody repertoire sequencing datasets (>100,000 unique sequences). Leveraging a network-based statistical framework, we identify three fundamental principles of antibody repertoire architecture: reproducibility, robustness and redundancy. Antibody repertoire networks are highly reproducible across individuals despite high antibody sequence dissimilarity. The architecture of antibody repertoires is robust to the removal of up to 50-90% of randomly selected clones, but fragile to the removal of public clones shared among individuals. Finally, repertoire architecture is intrinsically redundant. Our analysis provides guidelines for the large-scale network analysis of immune repertoires and may be used in the future to define disease-associated and synthetic repertoires.
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Affiliation(s)
- Enkelejda Miho
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland.,Institute of Medical Engineering and Medical Informatics, School of Life Sciences, FHNW University of Applied Sciences and Arts Northwestern Switzerland, 4132, Muttenz, Switzerland.,aiNET GmbH, c/o Switzerland Innovation Park Basel Area AG, Hochbergstrasse 60C, 4057, Basel, Switzerland
| | - Rok Roškar
- Research Informatics, Scientific IT Services, ETH Zürich, 8001, Zürich, Switzerland
| | - Victor Greiff
- Department of Immunology, University of Oslo, 0372, Oslo, Norway.
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland.
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43
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Taylor SA, Malladi P, Pan X, Wechsler JB, Hulse KE, Perlman H, Whitington PF. Oligoclonal immunoglobulin repertoire in biliary remnants of biliary atresia. Sci Rep 2019; 9:4508. [PMID: 30872727 PMCID: PMC6418100 DOI: 10.1038/s41598-019-41148-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 03/01/2019] [Indexed: 12/13/2022] Open
Abstract
Biliary atresia (BA) is a neonatal cholestatic liver disease that is the leading cause of pediatric liver transplantation, however, the mechanism of disease remains unknown. There are two major forms of BA: isolated BA (iBA) comprises the majority of cases and is thought to result from an aberrant immune response to an environmental trigger, whereas syndromic BA (BASM) has associated malformations and is thought to arise from a congenital insult. To determine whether B cells in BA biliary remnants are antigen driven, we examined the immunoglobulin (Ig) repertoire of diseased tissue from each BA group. Deep sequencing of the Ig chain DNA was performed on iBA and BASM biliary remnants and lymph nodes obtained from the Childhood Liver Disease Research Network (ChiLDReN) repository. Statistical analysis of the Ig repertoire provided measures of Ig clonality and the Ig phenotype. Our data demonstrate that B cells infiltrate diseased iBA and BASM biliary remnant tissue. The Ig repertoires of iBA and BASM disease groups were oligoclonal supporting a role for an antigen-driven immune response in both sub-types. These findings shift the current understanding of BA and suggest a role for antigen stimulation in early iBA and BASM disease pathogenesis.
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Affiliation(s)
- Sarah A Taylor
- Department of Pediatrics, Ann and Robert H Lurie Children's Hospital of Chicago, Chicago, Illinois, United States. .,Stanley Manne Children's Research Institute, Chicago, Illinois, United States.
| | - Padmini Malladi
- Stanley Manne Children's Research Institute, Chicago, Illinois, United States
| | - Xiaomin Pan
- Stanley Manne Children's Research Institute, Chicago, Illinois, United States
| | - Joshua B Wechsler
- Department of Pediatrics, Ann and Robert H Lurie Children's Hospital of Chicago, Chicago, Illinois, United States
| | - Kathryn E Hulse
- Department of Medicine, Northwestern University, Chicago, Illinois, United States
| | - Harris Perlman
- Department of Medicine, Northwestern University, Chicago, Illinois, United States
| | - Peter F Whitington
- Department of Pediatrics, Ann and Robert H Lurie Children's Hospital of Chicago, Chicago, Illinois, United States.,Stanley Manne Children's Research Institute, Chicago, Illinois, United States
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44
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Tang W, Dou Y, Qin T, Ding Y, Tang X, Zhao X, An Y. Skewed B cell receptor repertoire and reduced antibody avidity in patients with DOCK8 deficiency. Scand J Immunol 2019; 89:e12759. [PMID: 30793341 DOI: 10.1111/sji.12759] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/28/2019] [Accepted: 02/13/2019] [Indexed: 01/31/2023]
Abstract
DOCK8 immunodeficiency syndrome (DIDS) is a combined immunodeficiency characterized by recurrent viral infections, severe atopy and early onset malignancy. Immunological abnormalities include lymphopenia, CD8+ T-cell cytoskeleton dysfunction, defective B cell memory and variable serum immunoglobulin levels. Here, we analyse the B cell receptor repertoire (BCR) characteristics and antibody avidity of four DIDS patients, attempt to understand the dysregulated humoral immunity in DIDS patients with a normal antibody titre and suggest a scientific basis for intravenous immunoglobulin (IVIG) replacement therapy for these patients. We analysed BCR characteristics, including somatic hypermutation (SHM) frequency, using deep sequencing of multiplex PCR products derived from BCR heavy chain CDR3 regions from DIDS patients and controls. The antibody avidity of human tetanus and hemophilus influenza B antibodies was determined by ELISA using thiocyanate elution. IVIG replacement treatment and infection conditions were investigated retrospectively. We found skewing of the BCR repertoire and decreased antibody avidity in patients with DIDS. DIDS patients had fewer negatively charged amino acids than healthy controls. The SHM frequency of the IGHV3 gene was lower in patients with DIDS. Patients received regular IVIG therapy, resulting in fewer and less severe infections. We conclude that although IgG levels are normal in most DIDS patients, IVIG replacement therapy is still necessary.
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Affiliation(s)
- Wenjing Tang
- Division of Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Ying Dou
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China.,Division of Hematology and Oncology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Tao Qin
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Yuan Ding
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Xuemei Tang
- Division of Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaodong Zhao
- Division of Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Yunfei An
- Division of Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
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45
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Shah HB, Smith K, Wren JD, Webb CF, Ballard JD, Bourn RL, James JA, Lang ML. Insights From Analysis of Human Antigen-Specific Memory B Cell Repertoires. Front Immunol 2019; 9:3064. [PMID: 30697210 PMCID: PMC6340933 DOI: 10.3389/fimmu.2018.03064] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 12/11/2018] [Indexed: 12/17/2022] Open
Abstract
Memory B cells that are generated during an infection or following vaccination act as sentinels to guard against future infections. Upon repeat antigen exposure memory B cells differentiate into new antibody-secreting plasma cells to provide rapid and sustained protection. Some pathogens evade or suppress the humoral immune system, or induce memory B cells with a diminished ability to differentiate into new plasma cells. This leaves the host vulnerable to chronic or recurrent infections. Single cell approaches coupled with next generation antibody gene sequencing facilitate a detailed analysis of the pathogen-specific memory B cell repertoire. Monoclonal antibodies that are generated from antibody gene sequences allow a functional analysis of the repertoire. This review discusses what has been learned thus far from analysis of diverse pathogen-specific memory B cell compartments and describes major differences in their repertoires. Such information may illuminate ways to advance the goal of improving vaccine and therapeutic antibody design.
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Affiliation(s)
- Hemangi B Shah
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Kenneth Smith
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Jonathan D Wren
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States.,Department of Biochemistry and Molecular Biology and Geriatric Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Carol F Webb
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States.,Division of Rheumatology, Immunology and Allergy, Department of Cell Biology and Internal Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Jimmy D Ballard
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Rebecka L Bourn
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
| | - Judith A James
- Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States.,Department of Medicine and Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Mark L Lang
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
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46
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Maity PC, Datta M, Nicolò A, Jumaa H. Isotype Specific Assembly of B Cell Antigen Receptors and Synergism With Chemokine Receptor CXCR4. Front Immunol 2019. [PMID: 30619343 DOI: 10.3389/fimmu.2018.02988.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Expression of the membrane-bound form of the immunoglobulin (Ig) as part of the antigen receptor is indispensable for both the development and the effector function of B cells. Among five known isotypes, IgM and IgD are the common B cell antigen receptors (BCRs) that are co-expressed in naïve B cells. Despite having identical antigen specificity and being associated with the same signaling heterodimer Igα/Igβ (CD79a/CD79b), IgM and IgD-BCR isotypes functionally differ from each other in the manner of antigen binding, the formation of isolated nanoclusters and in their interaction with co-receptors such as CD19 and CXCR4 on the plasma membrane. With recent developments in experimental techniques, it is now possible to investigate the nanoscale organization of the BCR and better understand early events of BCR engagement. Interestingly, the cytoskeleton network beneath the membrane controls the BCR isotype-specific organization and its interaction with co-receptors. BCR triggering results in reorganization of the cytoskeleton network, which is further modulated by isotype-specific signals from co-receptors. For instance, IgD-BCR is closely associated with CXCR4 on mature B cells and this close proximity allows CXCR4 to employ the BCR machinery as signaling hub. In this review, we discuss the functional specificity and nanocluster assembly of BCR isotypes and the consequences of cross-talk between CXCR4 and IgD-BCR. Furthermore, given the role of BCR and CXCR4 signaling in the development and survival of leukemic B cells, we discuss the consequences of the cross-talk between CXCR4 and the BCR for controlling the growth of transformed B cells.
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Affiliation(s)
| | - Moumita Datta
- Institute of Immunology, Ulm University, Ulm, Germany
| | | | - Hassan Jumaa
- Institute of Immunology, Ulm University, Ulm, Germany
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47
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Maity PC, Datta M, Nicolò A, Jumaa H. Isotype Specific Assembly of B Cell Antigen Receptors and Synergism With Chemokine Receptor CXCR4. Front Immunol 2019; 9:2988. [PMID: 30619343 PMCID: PMC6305424 DOI: 10.3389/fimmu.2018.02988] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 12/04/2018] [Indexed: 12/20/2022] Open
Abstract
Expression of the membrane-bound form of the immunoglobulin (Ig) as part of the antigen receptor is indispensable for both the development and the effector function of B cells. Among five known isotypes, IgM and IgD are the common B cell antigen receptors (BCRs) that are co-expressed in naïve B cells. Despite having identical antigen specificity and being associated with the same signaling heterodimer Igα/Igβ (CD79a/CD79b), IgM and IgD-BCR isotypes functionally differ from each other in the manner of antigen binding, the formation of isolated nanoclusters and in their interaction with co-receptors such as CD19 and CXCR4 on the plasma membrane. With recent developments in experimental techniques, it is now possible to investigate the nanoscale organization of the BCR and better understand early events of BCR engagement. Interestingly, the cytoskeleton network beneath the membrane controls the BCR isotype-specific organization and its interaction with co-receptors. BCR triggering results in reorganization of the cytoskeleton network, which is further modulated by isotype-specific signals from co-receptors. For instance, IgD-BCR is closely associated with CXCR4 on mature B cells and this close proximity allows CXCR4 to employ the BCR machinery as signaling hub. In this review, we discuss the functional specificity and nanocluster assembly of BCR isotypes and the consequences of cross-talk between CXCR4 and IgD-BCR. Furthermore, given the role of BCR and CXCR4 signaling in the development and survival of leukemic B cells, we discuss the consequences of the cross-talk between CXCR4 and the BCR for controlling the growth of transformed B cells.
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Affiliation(s)
| | - Moumita Datta
- Institute of Immunology, Ulm University, Ulm, Germany
| | | | - Hassan Jumaa
- Institute of Immunology, Ulm University, Ulm, Germany
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48
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Collins AM, Watson CT. Immunoglobulin Light Chain Gene Rearrangements, Receptor Editing and the Development of a Self-Tolerant Antibody Repertoire. Front Immunol 2018; 9:2249. [PMID: 30349529 PMCID: PMC6186787 DOI: 10.3389/fimmu.2018.02249] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/10/2018] [Indexed: 11/13/2022] Open
Abstract
Discussion of the antibody repertoire usually emphasizes diversity, but a conspicuous feature of the light chain repertoire is its lack of diversity. The diversity of reported allelic variants of germline light chain genes is also limited, even in well-studied species. In this review, the implications of this lack of diversity are considered. We explore germline and rearranged light chain genes in a variety of species, with a particular focus on human and mouse genes. The importance of the number, organization and orientation of the genes for the control of repertoire development is discussed, and we consider how primary rearrangements and receptor editing together shape the expressed light chain repertoire. The resulting repertoire is dominated by just a handful of IGKV and IGLV genes. It has been hypothesized that an important function of the light chain is to guard against self-reactivity, and the role of secondary rearrangements in this process could explain the genomic organization of the light chain genes. It could also explain why the light chain repertoire is so limited. Heavy and light chain genes may have co-evolved to ensure that suitable light chain partners are usually available for each heavy chain that forms early in B cell development. We suggest that the co-evolved loci of the house mouse often became separated during the inbreeding of laboratory mice, resulting in new pairings of loci that are derived from different sub-species of the house mouse. A resulting vulnerability to self-reactivity could explain at least some mouse models of autoimmune disease.
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Affiliation(s)
- Andrew M. Collins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Corey T. Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States
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49
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Fuchs T, Hahn M, Ries L, Giesler S, Busch S, Wang C, Han J, Schulze TJ, Puellmann K, Beham AW, Kaminski WE, Neumaier M. Expression of combinatorial immunoglobulins in macrophages in the tumor microenvironment. PLoS One 2018; 13:e0204108. [PMID: 30240437 PMCID: PMC6150476 DOI: 10.1371/journal.pone.0204108] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 09/04/2018] [Indexed: 02/06/2023] Open
Abstract
Recent evidence indicates the presence of macrophage subpopulations that express the TCRαβ in chronic inflammatory diseases such as tuberculosis and atherosclerosis and in the tumor microenvironment. Here, we demonstrate that a second subpopulation of macrophages expresses rearranged heavy and light chain immunoglobulins. We identify immunoglobulin expression in human and murine monocytes, in ex vivo differentiated macrophages and macrophages from the tumor microenvironment of five randomly selected distinct human tumor entities. The immunoglobulin heavy and light chains are expressed in a small macrophage subfraction (~3-5%) as combinatorial and individual-specific immune receptors. Using Sanger sequencing and deep sequencing, we routinely find markedly restricted Ig repertoires in monocytes/macrophages compared to normal B cells. Furthermore, we report the complete Ig heavy and light chain sequences of a fully functional immunoglobulin from a single tumor-associated macrophage. These results demonstrate that Ig expression is a defining feature of monocytes and also macrophages in the tumor microenvironment and thus reveal an as yet unrecognized modus operandi of host defense in professional phagocytes.
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Affiliation(s)
- Tina Fuchs
- Institute for Clinical Chemistry, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Martin Hahn
- Institute for Clinical Chemistry, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Lukas Ries
- Institute for Clinical Chemistry, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Sophie Giesler
- Institute for Clinical Chemistry, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Svenja Busch
- Institute for Clinical Chemistry, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Chunlin Wang
- iRepertoire inc. Huntsville, AL, United States of America
| | - Jian Han
- iRepertoire inc. Huntsville, AL, United States of America
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States of America
| | - Torsten J. Schulze
- Institute of Transfusion Medicine and Immunology, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | | | | | - Wolfgang E. Kaminski
- Institute for Clinical Chemistry, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
- Bioscientia Institute for Medical Diagnostics, Ingelheim, Germany
| | - Michael Neumaier
- Institute for Clinical Chemistry, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
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Abstract
PURPOSE OF REVIEW A successful human immunodeficiency virus-type 1 (HIV-1) vaccine will require immunogens that induce protective immune responses. However, recent studies suggest that the response to HIV-1 and perhaps other viruses may be altered by immune system exposure to intestinal microbiota-antigens. This review will discuss select aspects of these studies. RECENT FINDINGS Naïve CD4 T and B cell repertoires can be imprinted by intestinal microbiota-antigens to respond to virus epitopes prior to virus infection. A multiclade envelope (Env) gp145 DNA prime, recombinant adenovirus type 5 boost vaccine tested in a HIV Vaccine Trials Network (HVTN) phase IIb human vaccine efficacy trial (HVTN 505) induced a dominant gp41-reactive antibody response that was non-neutralizing and cross-reactive with intestinal microbiota. This vaccine regimen also induced a dominant gp41-reactive, intestinal microbiota-cross-reactive gp41 antibody response in neonatal and adult Rhesus macaques. Studies of naïve CD4 T cells have demonstrated cross-reactivity to both HIV-1 and influenza peptides. SUMMARY HIV-1 Env vaccine-induced CD4 T and B cell responses can originate from a pool of intestinal microbiota-cross-reactive immune cells. Moreover, intestinal microbiota-cross-reactive HIV-1 Env antibodies are ineffective in protection against HIV-1 infection. Thus, intestinal microbiota-imprinting of the B cell repertoire may be one of several roadblocks to the induction of protective HIV-1 antibodies.
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