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Jing Z, Galbo P, Ovando L, Demouth M, Welte S, Park R, Chandran K, Wu Y, MacCarthy T, Zheng D, Fooksman D. Fine-tuning spatial-temporal dynamics and surface receptor expression support plasma cell-intrinsic longevity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.02.15.527913. [PMID: 36891288 PMCID: PMC9994177 DOI: 10.1101/2023.02.15.527913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Durable serological memory following vaccination is critically dependent on the production and survival of long-lived plasma cells (LLPCs). Yet, the factors that control LLPC specification and survival remain poorly resolved. Using intra-vital two-photon imaging, we find that in contrast to most plasma cells in the bone marrow, LLPCs are uniquely sessile and organized into clusters that are dependent on April, an important survival factor. Using deep, bulk RNA sequencing, and surface protein flow-based phenotyping, we find that LLPCs express a unique transcriptome and proteome compared to bulk PCs, fine tuning expression of key cell surface molecules, CD93, CD81, CXCR4, CD326, CD44 and CD48, important for adhesion and homing, and phenotypically label LLPCs within mature PC pool. Conditional deletion of Cxcr4 in PCs following immunization leads to rapid mobilization from the BM, reduced survival of antigen-specific PCs, and ultimately accelerated decay of antibody titer. In naive mice, the endogenous LLPCs BCR repertoire exhibits reduced diversity, reduced somatic mutations, and increased public clones and IgM isotypes, particularly in young mice, suggesting LLPC specification is non-random. As mice age, the BM PC compartment becomes enriched in LLPCs, which may outcompete and limit entry of new PC into the LLPC niche and pool.
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Shingai M, Iida S, Kawai N, Kawahara M, Sekiya T, Ohno M, Nomura N, Handabile C, Kawakita T, Omori R, Yamagishi J, Sano K, Ainai A, Suzuki T, Ohnishi K, Ito K, Kida H. Extraction of the CDRH3 sequence of the mouse antibody repertoire selected upon influenza virus infection by subtraction of the background antibody repertoire. J Virol 2024; 98:e0199523. [PMID: 38323813 PMCID: PMC10949447 DOI: 10.1128/jvi.01995-23] [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: 12/19/2023] [Accepted: 01/14/2024] [Indexed: 02/08/2024] Open
Abstract
Historically, antibody reactivity to pathogens and vaccine antigens has been evaluated using serological measurements of antigen-specific antibodies. However, it is difficult to evaluate all antibodies that contribute to various functions in a single assay, such as the measurement of the neutralizing antibody titer. Bulk antibody repertoire analysis using next-generation sequencing is a comprehensive method for analyzing the overall antibody response; however, it is unreliable for estimating antigen-specific antibodies due to individual variation. To address this issue, we propose a method to subtract the background signal from the repertoire of data of interest. In this study, we analyzed changes in antibody diversity and inferred the heavy-chain complementarity-determining region 3 (CDRH3) sequences of antibody clones that were selected upon influenza virus infection in a mouse model using bulk repertoire analysis. A decrease in the diversity of the antibody repertoire was observed upon viral infection, along with an increase in neutralizing antibody titers. Using kernel density estimation of sequences in a high-dimensional sequence space with background signal subtraction, we identified several clusters of CDRH3 sequences induced upon influenza virus infection. Most of these repertoires were detected more frequently in infected mice than in uninfected control mice, suggesting that infection-specific antibody sequences can be extracted using this method. Such an accurate extraction of antigen- or infection-specific repertoire information will be a useful tool for vaccine evaluation in the future. IMPORTANCE As specific interactions between antigens and cell-surface antibodies trigger the proliferation of B-cell clones, the frequency of each antibody sequence in the samples reflects the size of each clonal population. Nevertheless, it is extremely difficult to extract antigen-specific antibody sequences from the comprehensive bulk antibody sequences obtained from blood samples due to repertoire bias influenced by exposure to dietary antigens and other infectious agents. This issue can be addressed by subtracting the background noise from the post-immunization or post-infection repertoire data. In the present study, we propose a method to quantify repertoire data from comprehensive repertoire data. This method allowed subtraction of the background repertoire, resulting in more accurate extraction of expanded antibody repertoires upon influenza virus infection. This accurate extraction of antigen- or infection-specific repertoire information is a useful tool for vaccine evaluation.
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Affiliation(s)
- Masashi Shingai
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- Division of Vaccine Immunology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Sayaka Iida
- Division of Bioinformatics, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Naoko Kawai
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Mamiko Kawahara
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Toshiki Sekiya
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Marumi Ohno
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Naoki Nomura
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
| | - Chimuka Handabile
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
| | - Tomomi Kawakita
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- Division of Vaccine Immunology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Ryosuke Omori
- Division of Bioinformatics, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Junya Yamagishi
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Kaori Sano
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Akira Ainai
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kazuo Ohnishi
- Department of Immunology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kimihito Ito
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Division of Bioinformatics, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Hiroshi Kida
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
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Simons BD, Karin O. Tuning of plasma cell lifespan by competition explains the longevity and heterogeneity of antibody persistence. Immunity 2024; 57:600-611.e6. [PMID: 38447570 DOI: 10.1016/j.immuni.2024.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 01/12/2024] [Accepted: 02/07/2024] [Indexed: 03/08/2024]
Abstract
Plasma cells that emerge after infection or vaccination exhibit heterogeneous lifespans; most survive for days to months, whereas others persist for decades, providing antigen-specific long-term protection. We developed a mathematical framework to explore the dynamics of plasma cell removal and its regulation by survival factors. Analyses of antibody persistence following hepatitis A and B and HPV vaccination revealed specific patterns of longevity and heterogeneity within and between responses, implying that this process is fine-tuned near a critical "flat" state between two dynamic regimes. This critical state reflects the tuning of rates of the underlying regulatory network and is highly sensitive to variation in parameters, which amplifies lifespan differences between cells. We propose that fine-tuning is the generic outcome of competition over shared survival signals, with a competition-based mechanism providing a unifying explanation for a wide range of experimental observations, including the dynamics of plasma cell accumulation and the effects of survival factor deletion. Our theory is testable, and we provide specific predictions.
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Affiliation(s)
- Benjamin D Simons
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge CB3 0WA, UK; Wellcome Trust, Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Wellcome Trust-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | - Omer Karin
- Department of Mathematics, Imperial College London, London SW7 2AZ, UK.
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Fooksman DR, Jing Z, Park R. New insights into the ontogeny, diversity, maturation and survival of long-lived plasma cells. Nat Rev Immunol 2024:10.1038/s41577-024-00991-0. [PMID: 38332373 DOI: 10.1038/s41577-024-00991-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/08/2024] [Indexed: 02/10/2024]
Abstract
Plasma cells are unique immune effectors, capable of producing large amounts of high-affinity antibodies that protect against pathogenic infections. Although most plasma cells have short lifespans, certain conditions or vaccinations can give rise to long-lived plasma cells (LLPCs) that provide individuals with lifelong protection against pathogen exposure. The nature of these LLPCs is poorly understood; however, recent studies have shed new light on the ontogeny, diversity, maturation and survival of these unique cells. Whereas LLPCs had been thought to arise preferentially from germinal centres, novel genetic tools have revealed that they can originate from various stages throughout the humoral response. Furthermore, new single-cell analyses have shown that mouse and human plasma cells are heterogeneous and may undergo further maturation in situ in the bone marrow niche. Finally, plasma cells were previously considered to be sessile cells maintained in fixed survival niches, but new data show that plasma cell subsets can differentially migrate and organize into clusters that may be associated with survival niches. These descriptive findings provide new insights into how cell-intrinsic programmes and extrinsic factors may regulate the longevity of plasma cells in various contexts, which suggest new research avenues for their functional validation.
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Affiliation(s)
- David R Fooksman
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA.
| | - Zhixin Jing
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Rosa Park
- Department of Pathology, Albert Einstein College of Medicine, Bronx, NY, USA
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Keppeke GD, Diogenes L, Gomes K, Andrade LEC. "Untargeting" autoantibodies using genome editing, a proof-of-concept study. Clin Immunol 2023; 251:109343. [PMID: 37094742 DOI: 10.1016/j.clim.2023.109343] [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: 01/28/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 04/26/2023]
Abstract
Autoantibodies (AAbs) are useful biomarkers and many have direct pathogenic role. Current standard therapies for elimination of specific B/plasma-cell clones are not fully efficient. We apply CRISPR/Cas9 genome-editing to knockout V(D)J rearrangements that produce pathogenic AAbs in vitro. HEK293T cell-lines were established stably expressing a humanized anti-dsDNA Ab (clone 3H9) and a human-derived anti-nAChR-α1 Ab (clone B12L). For each clone, five CRISPR/Cas9 heavy-chain's CDR2/3-targeting guided-RNAs (T-gRNAs) were designed. Non-Target-gRNA (NT-gRNA) was control. After editing, levels of secreted Abs were evaluated, as well as 3H9 anti-dsDNA and B12L anti-AChR reactivities. T-gRNAs editing decreased expression of heavy-chain genes to ~50-60%, compared to >90% in NT-gRNA, although secreted Abs levels and reactivity to their respective antigens in T-gRNAs decreased ~90% and ~ 95% compared with NT-gRNA for 3H9 and B12L, respectively. Sequencing indicated indels at Cas9 cut-site, which could lead to codon jam, and consequently, knockout. Additionally, remaining secreted 3H9-Abs presented variable dsDNA reactivity among the five T-gRNA, suggesting the exact Cas9 cut-site and indels further interfere with antibody-antigen interaction. CRISPR/Cas9 genome-editing was very effective to knockout the Heavy-Chain-IgG genes, considerably affecting AAbs secretion and binding capacity, fostering application of this concept to in vivo models as a potential novel therapeutic approach for AAb-mediated diseases.
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Affiliation(s)
| | - Larissa Diogenes
- Rheumatology Division, Department of Medicine, Federal University of Sao Paulo, Brazil
| | - Kethellen Gomes
- Rheumatology Division, Department of Medicine, Federal University of Sao Paulo, Brazil
| | - Luis Eduardo Coelho Andrade
- Rheumatology Division, Department of Medicine, Federal University of Sao Paulo, Brazil; Immunology Division, Fleury Laboratory, Sao Paulo, Brazil
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Ulbricht C, Cao Y, Niesner RA, Hauser AE. In good times and in bad: How plasma cells resolve stress for a life-long union with the bone marrow. Front Immunol 2023; 14:1112922. [PMID: 37033993 PMCID: PMC10080396 DOI: 10.3389/fimmu.2023.1112922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/14/2023] [Indexed: 04/11/2023] Open
Affiliation(s)
- Carolin Ulbricht
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Immune Dynamics, Deutsches Rheuma-Forschungszentrum (DRFZ), A Leibniz Institute, Berlin, Germany
| | - Yu Cao
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Immune Dynamics, Deutsches Rheuma-Forschungszentrum (DRFZ), A Leibniz Institute, Berlin, Germany
| | - Raluca A. Niesner
- Biophysical Analysis, Deutsches Rheuma-Forschungszentrum (DRFZ), A Leibniz Institute, Berlin, Germany
- Dynamic and Functional in vivo Imaging, Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Anja E. Hauser
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Immune Dynamics, Deutsches Rheuma-Forschungszentrum (DRFZ), A Leibniz Institute, Berlin, Germany
- *Correspondence: Anja E. Hauser,
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Musso N, Romano A, Bonacci PG, Scandura G, Pandino C, Camarda M, Russo GI, Di Raimondo F, Cacciola E, Cacciola R. Label-Free Enrichment of Circulating Tumor Plasma Cells: Future Potential Applications of Dielectrophoresis in Multiple Myeloma. Int J Mol Sci 2022; 23:ijms231912052. [PMID: 36233350 PMCID: PMC9569623 DOI: 10.3390/ijms231912052] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/23/2022] [Accepted: 09/28/2022] [Indexed: 12/05/2022] Open
Abstract
In multiple myeloma (MM), circulating tumor plasma cells (CTPCs) are an emerging prognostic factor, offering a promising and minimally invasive means for longitudinal patient monitoring. Recent advances highlight the complex biology of plasma cell trafficking, highlighting the phenotypic and genetic signatures of intra- and extra-medullary MM onset, making CTPC enumeration and characterization a new frontier of precision medicine for MM patients, requiring novel technological platforms for their standardized and harmonized detection. Dielectrophoresis (DEP) is an emerging label-free cell manipulation technique to separate cancer cells from healthy cells in peripheral blood samples, based on phenotype and membrane capacitance that could be successfully tested to enumerate and isolate CTPCs. Herein, we summarize preclinical data on DEP development for CTPC detection, as well as their clinical and research potential.
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Affiliation(s)
- Nicolò Musso
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, 95125 Catania, Italy
- StLab SRL, 95126 Catania, Italy
| | - Alessandra Romano
- Department of General Surgery and Surgical Medical Specialties, University of Catania, 95125 Catania, Italy
- Correspondence: ; Tel.: +39-095-378-2971
| | - Paolo Giuseppe Bonacci
- Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, 95125 Catania, Italy
| | - Grazia Scandura
- Department of General Surgery and Surgical Medical Specialties, University of Catania, 95125 Catania, Italy
| | - Clarissa Pandino
- Department of General Surgery and Surgical Medical Specialties, University of Catania, 95125 Catania, Italy
| | | | - Giorgio Ivan Russo
- Urology Section, University of Catania, Via S. Sofia 78, 95125 Catania, Italy
| | - Francesco Di Raimondo
- Department of General Surgery and Surgical Medical Specialties, University of Catania, 95125 Catania, Italy
| | - Emma Cacciola
- Department of Medical, Surgical Sciences and Advanced Technologies “G.F. Ingrassia”, University of Catania, 95123 Catania, Italy
- Hemostasis/Hematology Unit, A.O.U. Policlinico “G. Rodolico-San Marco”, 95123 Catania, Italy
| | - Rossella Cacciola
- Hemostasis/Hematology Unit, A.O.U. Policlinico “G. Rodolico-San Marco”, 95123 Catania, Italy
- Department of Clinical and Experimental Medicine, University of Catania, 95123 Catania, Italy
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Afonina IS, Hoffmann E. Infection and immunity: ‘There Are Things Out There You (Don't) Need To Know About’. FEBS J 2022; 289:3920-3925. [DOI: 10.1111/febs.16569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Inna S. Afonina
- Unit of Molecular Signal Transduction in Inflammation VIB‐UGent Center for Inflammation Research Ghent Belgium
- Department of Biomedical Molecular Biology Ghent University Belgium
| | - Eik Hoffmann
- Institute Pasteur Lille Center for Infection and Immunity of Lille (CIIL) France
- European Regimen Accelerator for Tuberculosis (ERA4TB), Innovative Medicines Initiative 2 Joint Undertaking (JU no. 853989)
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