1
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Cooper L, Xu H, Polmear J, Kealy L, Szeto C, Pang ES, Gupta M, Kirn A, Taylor JJ, Jackson KJL, Broomfield BJ, Nguyen A, Gago da Graça C, La Gruta N, Utzschneider DT, Groom JR, Martelotto L, Parish IA, O'Keeffe M, Scharer CD, Gras S, Good-Jacobson KL. Type I interferons induce an epigenetically distinct memory B cell subset in chronic viral infection. Immunity 2024; 57:1037-1055.e6. [PMID: 38593796 PMCID: PMC11096045 DOI: 10.1016/j.immuni.2024.03.016] [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: 03/08/2023] [Revised: 11/02/2023] [Accepted: 03/15/2024] [Indexed: 04/11/2024]
Abstract
Memory B cells (MBCs) are key providers of long-lived immunity against infectious disease, yet in chronic viral infection, they do not produce effective protection. How chronic viral infection disrupts MBC development and whether such changes are reversible remain unknown. Through single-cell (sc)ATAC-seq and scRNA-seq during acute versus chronic lymphocytic choriomeningitis viral infection, we identified a memory subset enriched for interferon (IFN)-stimulated genes (ISGs) during chronic infection that was distinct from the T-bet+ subset normally associated with chronic infection. Blockade of IFNAR-1 early in infection transformed the chromatin landscape of chronic MBCs, decreasing accessibility at ISG-inducing transcription factor binding motifs and inducing phenotypic changes in the dominating MBC subset, with a decrease in the ISG subset and an increase in CD11c+CD80+ cells. However, timing was critical, with MBCs resistant to intervention at 4 weeks post-infection. Together, our research identifies a key mechanism to instruct MBC identity during viral infection.
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Affiliation(s)
- Lucy Cooper
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Hui Xu
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Jack Polmear
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Liam Kealy
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Christopher Szeto
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Ee Shan Pang
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Mansi Gupta
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Alana Kirn
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Justin J Taylor
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Benjamin J Broomfield
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia; Division of Immunology, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Angela Nguyen
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Catarina Gago da Graça
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Nicole La Gruta
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Daniel T Utzschneider
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Joanna R Groom
- Division of Immunology, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Luciano Martelotto
- Adelaide Centre for Epigenetics and the South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia; University of Melbourne Centre for Cancer Research, Victoria Comprehensive Cancer Centre, Melbourne, VIC, Australia
| | - Ian A Parish
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia; John Curtin School of Medical Research, ANU, Canberra, ACT, Australia
| | - Meredith O'Keeffe
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Christopher D Scharer
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA, USA
| | - Stephanie Gras
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia
| | - Kim L Good-Jacobson
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia; Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
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2
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Henderson R, Anasti K, Manne K, Stalls V, Saunders C, Bililign Y, Williams A, Bubphamala P, Montani M, Kachhap S, Li J, Jaing C, Newman A, Cain D, Lu X, Venkatayogi S, Berry M, Wagh K, Korber B, Saunders KO, Tian M, Alt F, Wiehe K, Acharya P, Alam SM, Haynes BF. Engineering immunogens that select for specific mutations in HIV broadly neutralizing antibodies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.15.571700. [PMID: 38168268 PMCID: PMC10760096 DOI: 10.1101/2023.12.15.571700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Vaccine development targeting rapidly evolving pathogens such as HIV-1 requires induction of broadly neutralizing antibodies (bnAbs) with conserved paratopes and mutations, and, in some cases, the same Ig-heavy chains. The current trial-and-error search for immunogen modifications that improve selection for specific bnAb mutations is imprecise. To precisely engineer bnAb boosting immunogens, we used molecular dynamics simulations to examine encounter states that form when antibodies collide with the HIV-1 Envelope (Env). By mapping how bnAbs use encounter states to find their bound states, we identified Env mutations that were predicted to select for specific antibody mutations in two HIV-1 bnAb B cell lineages. The Env mutations encoded antibody affinity gains and selected for desired antibody mutations in vivo. These results demonstrate proof-of-concept that Env immunogens can be designed to directly select for specific antibody mutations at residue-level precision by vaccination, thus demonstrating the feasibility of sequential bnAb-inducing HIV-1 vaccine design.
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Affiliation(s)
- Rory Henderson
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Kara Anasti
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Kartik Manne
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Victoria Stalls
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Carrie Saunders
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Yishak Bililign
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Ashliegh Williams
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Pimthada Bubphamala
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Maya Montani
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Sangita Kachhap
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Jingjing Li
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Chuancang Jaing
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Amanda Newman
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Derek Cain
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Xiaozhi Lu
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Sravani Venkatayogi
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Madison Berry
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Kshitij Wagh
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- The New Mexico Consortium, Los Alamos, NM, 87544 USA
| | - Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- The New Mexico Consortium, Los Alamos, NM, 87544 USA
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
| | - Ming Tian
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, 02115
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Fred Alt
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, 02115
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Surgery, Duke University Medical Center, Durham, NC 27710, USA
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | - S Munir Alam
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
- Department of Pathology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
- Department of Immunology, Duke University Medical Center, Durham, NC 27710, USA
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3
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Quirk GE, Schoenle MV, Peyton KL, Uhrlaub JL, Lau B, Burgess JL, Ellingson K, Beitel S, Romine J, Lutrick K, Fowlkes A, Britton A, Tyner HL, Caban-Martinez AJ, Naleway A, Gaglani M, Yoon S, Edwards L, Olsho L, Dake M, LaFleur BJ, Nikolich JŽ, Sprissler R, Worobey M, Bhattacharya D. Determinants of de novo B cell responses to drifted epitopes in post-vaccination SARS-CoV-2 infections. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.12.23295384. [PMID: 37745498 PMCID: PMC10516057 DOI: 10.1101/2023.09.12.23295384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Vaccine-induced immunity may impact subsequent de novo responses to drifted epitopes in SARS-CoV-2 variants, but this has been difficult to quantify due to the challenges in recruiting unvaccinated control groups whose first exposure to SARS-CoV-2 is a primary infection. Through local, statewide, and national SARS-CoV-2 testing programs, we were able to recruit cohorts of individuals who had recovered from either primary or post-vaccination infections by either the Delta or Omicron BA.1 variants. Regardless of variant, we observed greater Spike-specific and neutralizing antibody responses in post-vaccination infections than in those who were infected without prior vaccination. Through analysis of variant-specific memory B cells as markers of de novo responses, we observed that Delta and Omicron BA.1 infections led to a marked shift in immunodominance in which some drifted epitopes elicited minimal responses, even in primary infections. Prior immunity through vaccination had a small negative impact on these de novo responses, but this did not correlate with cross-reactive memory B cells, arguing against competitive inhibition of naïve B cells. We conclude that dampened de novo B cell responses against drifted epitopes are mostly a function of altered immunodominance hierarchies that are apparent even in primary infections, with a more modest contribution from pre-existing immunity, perhaps due to accelerated antigen clearance.
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Affiliation(s)
- Grace E Quirk
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Marta V Schoenle
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Kameron L Peyton
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Jennifer L Uhrlaub
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Branden Lau
- University of Arizona Genomics Core and the Arizona Research Labs, University of Arizona Genetics Core, University of Arizona, Tucson, AZ, USA
| | - Jefferey L Burgess
- Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, Arizona, USA
| | - Katherine Ellingson
- Department of Epidemiology and Biostatistics, Zuckerman College of Public Health, University of Arizona, Tucson
| | - Shawn Beitel
- Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, Arizona, USA
| | - James Romine
- Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, Arizona, USA
| | - Karen Lutrick
- College of Medicine-Tucson, University of Arizona, Tucson, Arizona, USA
| | - Ashley Fowlkes
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA
| | - Amadea Britton
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA
| | - Harmony L Tyner
- St. Luke's Regional Health Care System, Duluth, Minnesota, USA
| | | | - Allison Naleway
- Kaiser Permanente Northwest Center for Health Research, Portland, Oregon, USA
| | - Manjusha Gaglani
- Baylor Scott & White Health and Texas A&M University College of Medicine, Temple, Texas, USA
| | - Sarang Yoon
- Rocky Mountain Center for Occupational and Environmental Health, Department of Family and Preventive Medicine, University of Utah Health, Salt Lake City, Utah, USA
| | | | | | - Michael Dake
- Office of the Senior Vice-President for Health Sciences, University of Arizona, Tucson, AZ, USA
| | | | - Janko Ž Nikolich
- BIO5 Institute, University of Arizona, Tucson, AZ, USA
- University of Arizona Center on Aging, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Ryan Sprissler
- University of Arizona Genomics Core and the Arizona Research Labs, University of Arizona Genetics Core, University of Arizona, Tucson, AZ, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
- BIO5 Institute, University of Arizona, Tucson, AZ, USA
| | - Deepta Bhattacharya
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, AZ, USA
- BIO5 Institute, University of Arizona, Tucson, AZ, USA
- Department of Surgery, University of Arizona College of Medicine, Tucson, AZ, USA
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4
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Luo W, Conter L, Elsner RA, Smita S, Weisel F, Callahan D, Wu S, Chikina M, Shlomchik M. IL-21R signal reprogramming cooperates with CD40 and BCR signals to select and differentiate germinal center B cells. Sci Immunol 2023; 8:eadd1823. [PMID: 36800413 PMCID: PMC10206726 DOI: 10.1126/sciimmunol.add1823] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 01/26/2023] [Indexed: 02/19/2023]
Abstract
Both B cell receptor (BCR) and CD40 signaling are rewired in germinal center (GC) B cells (GCBCs) to synergistically induce c-MYC and phosphorylated S6 ribosomal protein (p-S6), markers of positive selection. How interleukin-21 (IL-21), a key T follicular helper (TFH)-derived cytokine, affects GCBCs is unclear. Like BCR and CD40 signals, IL-21 receptor (IL-21R) plus CD40 signals also synergize to induce c-MYC and p-S6 in GCBCs. However, IL-21R plus CD40 stimulation differentially affects GCBC fate compared with BCR plus CD40 ligation-engaging unique molecular mechanisms-as revealed by bulk RNA sequencing (RNA-seq), single-cell RNA-seq, and flow cytometry of GCBCs in vitro and in vivo. Whereas both signal pairs induced BLIMP1 in some GCBCs, only the IL-21R/CD40 combination induced IRF4hi/CD138+ cells, indicative of plasma cell differentiation, along with CCR6+/CD38+ memory B cell precursors. These findings reveal a second positive selection pathway in GCBCs, document rewired IL-21R signaling in GCBCs, and link specific TFH- and Ag-derived signals to GCBC differentiation.
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Affiliation(s)
- Wei Luo
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
- These authors contributed equally
- Present address: Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Laura Conter
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
- These authors contributed equally
| | - Rebecca A. Elsner
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
- These authors contributed equally
| | - Shuchi Smita
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Florian Weisel
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Derrick Callahan
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Shuxian Wu
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Maria Chikina
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Mark Shlomchik
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
- Lead contact
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5
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Bhattacharya D. Instructing durable humoral immunity for COVID-19 and other vaccinable diseases. Immunity 2022; 55:945-964. [PMID: 35637104 PMCID: PMC9085459 DOI: 10.1016/j.immuni.2022.05.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/02/2022] [Accepted: 05/05/2022] [Indexed: 11/29/2022]
Abstract
Many aspects of SARS-CoV-2 have fully conformed with the principles established by decades of viral immunology research, ultimately leading to the crowning achievement of highly effective COVID-19 vaccines. Nonetheless, the pandemic has also exposed areas where our fundamental knowledge is thinner. Some key unknowns are the duration of humoral immunity post-primary infection or vaccination and how long booster shots confer protection. As a corollary, if protection does not last as long as desired, what are some ways it can be improved? Here, I discuss lessons from other infections and vaccines that point to several key features that influence durable antibody production and the perseverance of immunity. These include (1) the specific innate sensors that are initially triggered, (2) the kinetics of antigen delivery and persistence, (3) the starting B cell receptor (BCR) avidity and antigen valency, and (4) the memory B cell subsets that are recalled by boosters. I further highlight the fundamental B cell-intrinsic and B cell-extrinsic pathways that, if understood better, would provide a rational framework for vaccines to reliably provide durable immunity.
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Affiliation(s)
- Deepta Bhattacharya
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, AZ 85724, USA.
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6
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Vaidehi Narayanan H, Hoffmann A. From Antibody Repertoires to Cell-Cell Interactions to Molecular Networks: Bridging Scales in the Germinal Center. Front Immunol 2022; 13:898078. [PMID: 35603162 PMCID: PMC9114758 DOI: 10.3389/fimmu.2022.898078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/08/2022] [Indexed: 01/02/2023] Open
Abstract
Antibody-mediated adaptive immunity must provide effective long-term protection with minimal adverse effects, against rapidly mutating pathogens, in a human population with diverse ages, genetics, and immune histories. In order to grasp and leverage the complexities of the antibody response, we advocate for a mechanistic understanding of the multiscale germinal center (GC) reaction - the process by which precursor B-cells evolve high-affinity antigen-specific antibodies, forming an effector repertoire of plasma and memory cells for decades-long protection. The regulatory dynamics of B-cells within the GC are complex, and unfold across multiple interacting spatial and temporal scales. At the organism scale, over weeks to years, the antibody sequence repertoire formed by various B-cell clonal lineages modulates antibody quantity and quality over time. At the tissue and cellular scale, over hours to weeks, B-cells undergo selection via spatially distributed interactions with local stroma, antigen, and helper T-cells. At the molecular scale, over seconds to days, intracellular signaling, transcriptional, and epigenetic networks modulate B-cell fates and shape their clonal lineages. We summarize our current understanding within each of these scales, and identify missing links in connecting them. We suggest that quantitative multi-scale mathematical models of B-cell and GC reaction dynamics provide predictive frameworks that can apply basic immunological knowledge to practical challenges such as rational vaccine design.
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Affiliation(s)
- Haripriya Vaidehi Narayanan
- Signaling Systems Laboratory, Department of Microbiology, Immunology, and Molecular Genetics, and Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA, United States
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7
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Ovchinnikov V, Karplus M. A Coarse-Grained Model of Affinity Maturation Indicates the Importance of B-Cell Receptor Avidity in Epitope Subdominance. Front Immunol 2022; 13:816634. [PMID: 35371013 PMCID: PMC8971376 DOI: 10.3389/fimmu.2022.816634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/24/2022] [Indexed: 12/02/2022] Open
Abstract
The elicitation of broadly neutralizing antibodies (bnAbs) is a major goal in the design of vaccines against rapidly-mutating viruses. In the case of influenza, many bnAbs that target conserved epitopes on the stem of the hemagglutinin protein (HA) have been discovered. However, these antibodies are rare, are not boosted well upon reinfection, and often have low neutralization potency, compared to strain-specific antibodies directed to the HA head. Different hypotheses have been proposed to explain this phenomenon. We use a coarse-grained computational model of the germinal center reaction to investigate how B-cell receptor binding valency affects the growth and affinity maturation of competing B-cells. We find that receptors that are unable to bind antigen bivalently, and also those that do not bind antigen cooperatively, have significantly slower rates of growth, memory B-cell production, and, under certain conditions, rates of affinity maturation. The corresponding B-cells are predicted to be outcompeted by B-cells that bind bivalently and cooperatively. We use the model to explore strategies for a universal influenza vaccine, e.g., how to boost the concentrations of the slower growing cross-reactive antibodies directed to the stem. The results suggest that, upon natural reinfections subsequent to vaccination, the protectiveness of such vaccines would erode, possibly requiring regular boosts. Collectively, our results strongly support the importance of bivalent antibody binding in immunodominance, and suggest guidelines for developing a universal influenza vaccine.
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Affiliation(s)
- Victor Ovchinnikov
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, United States
- *Correspondence: Victor Ovchinnikov, ; ; Martin Karplus,
| | - Martin Karplus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, United States
- Laboratoire de Chimie Biophysique, ISIS, Université de Strasbourg, Strasbourg, France
- *Correspondence: Victor Ovchinnikov, ; ; Martin Karplus,
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8
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Lindsly S, Gupta M, Stansbury C, Rajapakse I. Understanding memory B cell selection. J Theor Biol 2021; 531:110905. [PMID: 34543633 DOI: 10.1016/j.jtbi.2021.110905] [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: 12/22/2020] [Revised: 09/12/2021] [Accepted: 09/14/2021] [Indexed: 11/18/2022]
Abstract
The mammalian adaptive immune system has evolved over millions of years to become an incredibly effective defense against foreign antigens. The adaptive immune system's humoral response creates plasma B cells and memory B cells, each with their own immunological objectives. The affinity maturation process is widely viewed as a heuristic to solve the global optimization problem of finding B cells with high affinity to the antigen. However, memory B cells appear to be purposely selected earlier in the affinity maturation process and have lower affinity. We propose that this memory B cell selection process may be an approximate solution to two optimization problems: optimizing for affinity to similar antigens in the future despite mutations or other minor differences, and optimizing to warm start the generation of plasma B cells in the future. We use simulations to provide evidence for our hypotheses, taking into account data showing that certain B cell mutations are more likely than others. Our findings are consistent with memory B cells having high-affinity to mutated antigens, but do not provide strong evidence that memory B cells will be more useful than selected naive B cells for seeding the secondary germinal centers.
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Affiliation(s)
- Stephen Lindsly
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States
| | - Maya Gupta
- Google Research, Mountain View, CA, United States.
| | - Cooper Stansbury
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States
| | - Indika Rajapakse
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States; Department of Mathematics, University of Michigan, Ann Arbor, United States.
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9
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Thobe K, Konrath F, Chapuy B, Wolf J. Patient-Specific Modeling of Diffuse Large B-Cell Lymphoma. Biomedicines 2021; 9:biomedicines9111655. [PMID: 34829885 PMCID: PMC8615565 DOI: 10.3390/biomedicines9111655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/30/2021] [Accepted: 11/05/2021] [Indexed: 11/16/2022] Open
Abstract
Personalized medicine aims to tailor treatment to patients based on their individual genetic or molecular background. Especially in diseases with a large molecular heterogeneity, such as diffuse large B-cell lymphoma (DLBCL), personalized medicine has the potential to improve outcome and/or to reduce resistance towards treatment. However, integration of patient-specific information into a computational model is challenging and has not been achieved for DLBCL. Here, we developed a computational model describing signaling pathways and expression of critical germinal center markers. The model integrates the regulatory mechanism of the signaling and gene expression network and covers more than 50 components, many carrying genetic lesions common in DLBCL. Using clinical and genomic data of 164 primary DLBCL patients, we implemented mutations, structural variants and copy number alterations as perturbations in the model using the CoLoMoTo notebook. Leveraging patient-specific genotypes and simulation of the expression of marker genes in specific germinal center conditions allows us to predict the consequence of the modeled pathways for each patient. Finally, besides modeling how genetic perturbations alter physiological signaling, we also predicted for each patient model the effect of rational inhibitors, such as Ibrutinib, that are currently discussed as possible DLBCL treatments, showing patient-dependent variations in effectiveness and synergies.
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Affiliation(s)
- Kirsten Thobe
- Mathematical Modelling of Cellular Processes, Max Delbrück Center for Molecular Medicine, 13125 Berlin-Buch, Germany; (K.T.); (F.K.)
| | - Fabian Konrath
- Mathematical Modelling of Cellular Processes, Max Delbrück Center for Molecular Medicine, 13125 Berlin-Buch, Germany; (K.T.); (F.K.)
| | - Björn Chapuy
- Department of Hematology and Medical Oncology, University of Göttingen, 37075 Göttingen, Germany;
- Department of Hematology, Oncology and Cancer Immunology, Berlin Medical Center Charité, 12203 Berlin, Germany
| | - Jana Wolf
- Mathematical Modelling of Cellular Processes, Max Delbrück Center for Molecular Medicine, 13125 Berlin-Buch, Germany; (K.T.); (F.K.)
- Department of Mathematics and Computer Science, Free University Berlin, Arnimallee 14, 14195 Berlin, Germany
- Correspondence:
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10
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Elsner RA, Shlomchik MJ. Germinal Center and Extrafollicular B Cell Responses in Vaccination, Immunity, and Autoimmunity. Immunity 2021; 53:1136-1150. [PMID: 33326765 DOI: 10.1016/j.immuni.2020.11.006] [Citation(s) in RCA: 205] [Impact Index Per Article: 68.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/19/2020] [Accepted: 11/11/2020] [Indexed: 02/07/2023]
Abstract
Activated B cells participate in either extrafollicular (EF) or germinal center (GC) responses. Canonical responses are composed of a short wave of plasmablasts (PBs) arising from EF sites, followed by GC producing somatically mutated memory B cells (MBC) and long-lived plasma cells. However, somatic hypermutation (SHM) and affinity maturation can take place at both sites, and a substantial fraction of MBC are produced prior to GC formation. Infection responses range from GC responses that persist for months to persistent EF responses with dominant suppression of GCs. Here, we review the current understanding of the functional output of EF and GC responses and the molecular switches promoting them. We discuss the signals that regulate the magnitude and duration of these responses, and outline gaps in knowledge and important areas of inquiry. Understanding such molecular switches will be critical for vaccine development, interpretation of vaccine efficacy and the treatment for autoimmune diseases.
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Affiliation(s)
- Rebecca A Elsner
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15216, USA
| | - Mark J Shlomchik
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15216, USA.
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11
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Abstract
As one of the most important weapons against infectious diseases, vaccines have saved countless lives since their first use in the late eighteenth century. Antibodies produced by effector B cells upon vaccination play a critical role in mediating protection. The past several decades of research have led to a revolution in our understanding of B cell response to vaccination. Vaccines against SARS-CoV-2 coronavirus were developed at an unprecedented speed to power our global fight against COVID-19 pandemic. Nevertheless, we still face many challenges in the development of vaccines against many other deadly viruses, such as human immunodeficiency virus (HIV) and influenza virus. In this review, we summarize the latest findings on B cell response to vaccination and pathogen infection. We also discuss the current challenges in the field and the potential strategies targeting B cell response to improve vaccine efficacy.Key abbreviations box: BCR: B cell receptor; bNAb: broadly neutralizing antibody; DC: dendritic cells; DZ: dark zone; EF response: extrafollicular response; FDC: follicular dendritic cell; GC: germinal center; HIV: human immunodeficiency virus; IC: immune complex; LLPC: long-lived plasma cell; LZ: light zone; MBC: memory B cell; SLPB: short-lived plasmablast; TFH: T follicular helper cells; TLR: Toll-like receptor.
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Affiliation(s)
- Wei Luo
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Qian Yin
- Institute for Immunity, Transplantation & Infection, Stanford University School of Medicine, Stanford, California, USA
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12
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Helmold Hait S, Hogge CJ, Rahman MA, Hunegnaw R, Mushtaq Z, Hoang T, Robert-Guroff M. T FH Cells Induced by Vaccination and Following SIV Challenge Support Env-Specific Humoral Immunity in the Rectal-Genital Tract and Circulation of Female Rhesus Macaques. Front Immunol 2021; 11:608003. [PMID: 33584682 PMCID: PMC7876074 DOI: 10.3389/fimmu.2020.608003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/07/2020] [Indexed: 11/13/2022] Open
Abstract
T follicular helper (TFH) cells are pivotal in lymph node (LN) germinal center (GC) B cell affinity maturation. Circulating CXCR5+ CD4+ T (cTFH) cells have supported memory B cell activation and broadly neutralizing antibodies in HIV controllers. We investigated the contribution of LN SIV-specific TFH and cTFH cells to Env-specific humoral immunity in female rhesus macaques following a mucosal Ad5hr-SIV recombinant priming and SIV gp120 intramuscular boosting vaccine regimen and following SIV vaginal challenge. TFH and B cells were characterized by flow cytometry. B cell help was evaluated in TFH-B cell co-cultures and by real-time PCR. Vaccination induced Env-specific TFH and Env-specific memory (ESM) B cells in LNs. LN Env-specific TFH cells post-priming and GC ESM B cells post-boosting correlated with rectal Env-specific IgA titers, and GC B cells at the same timepoints correlated with vaginal Env-specific IgG titers. Vaccination expanded cTFH cell responses, including CD25+ Env-specific cTFH cells that correlated negatively with vaginal Env-specific IgG titers but positively with rectal Env-specific IgA titers. Although cTFH cells post-2nd boost positively correlated with viral-loads following SIV challenge, cTFH cells of SIV-infected and protected macaques supported maturation of circulating B cells into plasma cells and IgA release in co-culture. Additionally, cTFH cells of naïve macaques promoted upregulation of genes associated with B cell proliferation, BCR engagement, plasma cell maturation, and antibody production, highlighting the role of cTFH cells in blood B cell maturation. Vaccine-induced LN TFH and GC B cells supported anti-viral mucosal immunity while cTFH cells provided B cell help in the periphery during immunization and after SIV challenge. Induction of TFH responses in blood and secondary lymphoid organs is likely desirable for protective efficacy of HIV vaccines.
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Affiliation(s)
- Sabrina Helmold Hait
- Immune Biology of Retroviral Infection Section, Vaccine Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Christopher James Hogge
- Immune Biology of Retroviral Infection Section, Vaccine Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Mohammad Arif Rahman
- Immune Biology of Retroviral Infection Section, Vaccine Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Ruth Hunegnaw
- Immune Biology of Retroviral Infection Section, Vaccine Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Zuena Mushtaq
- Immune Biology of Retroviral Infection Section, Vaccine Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Tanya Hoang
- Immune Biology of Retroviral Infection Section, Vaccine Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Marjorie Robert-Guroff
- Immune Biology of Retroviral Infection Section, Vaccine Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
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13
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Stavropoulou E, Kantartzi K, Tsigalou C, Konstantinidis T, Voidarou C, Konstantinidis T, Bezirtzoglou E. Unraveling the Interconnection Patterns Across Lung Microbiome, Respiratory Diseases, and COVID-19. Front Cell Infect Microbiol 2021; 10:619075. [PMID: 33585285 PMCID: PMC7876344 DOI: 10.3389/fcimb.2020.619075] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/11/2020] [Indexed: 01/07/2023] Open
Abstract
Albeit the lungs were thought to be sterile, recent scientific data reported a microbial microbiota in the lungs of healthy individuals. Apparently, new developments in technological approachesincluding genome sequencing methodologies contributed in the identification of the microbiota and shed light on the role of the gut and lung microbiomes in the development of respiratory diseases. Moreover, knowledge of the human microbiome in health may act as a tool for evaluating characteristic shifts in the case of disease. This review paper discusses the development of respiratory disease linked to the intestinal dysbiosis which influences the lung immunity and microbiome. The gastrointestinal-lung dialogue provides interesting aspects in the pathogenesis of the respiratory diseases. Lastly, we were further interested on the role of this interconnection in the progression and physiopathology of newly emergedCOVID-19.
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Affiliation(s)
- Elisavet Stavropoulou
- CHUV (Centre HospitalierUniversitaire Vaudois), Lausanne, Switzerland,Department of Infectious Diseases, Central Institute, Valais Hospital, Sion, Switzerland,*Correspondence: Elisavet Stavropoulou,
| | - Konstantia Kantartzi
- Nephrology Clinic, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Christina Tsigalou
- Laboratory of Microbiology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Theocharis Konstantinidis
- Laboratory of Microbiology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | | | - Theodoros Konstantinidis
- Laboratory of Hygiene and Environmental Protection, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Eugenia Bezirtzoglou
- Laboratory of Hygiene and Environmental Protection, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
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14
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Verheijen M, Rane S, Pearson C, Yates AJ, Seddon B. Fate Mapping Quantifies the Dynamics of B Cell Development and Activation throughout Life. Cell Rep 2020; 33:108376. [PMID: 33207189 PMCID: PMC8622872 DOI: 10.1016/j.celrep.2020.108376] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 07/29/2020] [Accepted: 10/21/2020] [Indexed: 01/10/2023] Open
Abstract
Follicular mature (FM) and germinal center (GC) B cells underpin humoral immunity, but the dynamics of their generation and maintenance are not clearly defined. Here, we exploited a fate-mapping system in mice that tracks B cells as they develop into peripheral subsets, together with a cell division fate reporter mouse and mathematical models. We find that FM cells are kinetically homogeneous, recirculate freely, are continually replenished from transitional populations, and self-renew rarely. In contrast, GC B cell lineages persist for weeks with rapid turnover and site-specific dynamics. Those in the spleen derive from transitional cells and are kinetically homogeneous, while those in lymph nodes derive from FM B cells and comprise both transient and persistent clones. These differences likely derive from the nature of antigen exposure at the different sites. Our integrative approach also reveals how the host environment drives cell-extrinsic, age- related changes in B cell homeostasis. Verheijen and Rane et al. combine fate mapping and mathematical models to quantify the development and dynamics of follicular mature B cells and germinal center B cells in spleen and lymph nodes, and show how these processes vary across the mouse lifespan.
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Affiliation(s)
- Melissa Verheijen
- Institute of Immunity and Transplantation, Division of Infection and Immunity, UCL, Royal Free Hospital, Rowland Hill Street, London NW3 2PF, UK
| | - Sanket Rane
- Department of Pathology and Cell Biology, Columbia University Medical Center, 701 West 168th Street, New York, NY 10032, USA
| | - Claire Pearson
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Andrew J Yates
- Department of Pathology and Cell Biology, Columbia University Medical Center, 701 West 168th Street, New York, NY 10032, USA.
| | - Benedict Seddon
- Institute of Immunity and Transplantation, Division of Infection and Immunity, UCL, Royal Free Hospital, Rowland Hill Street, London NW3 2PF, UK.
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15
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Wong R, Belk JA, Govero J, Uhrlaub JL, Reinartz D, Zhao H, Errico JM, D'Souza L, Ripperger TJ, Nikolich-Zugich J, Shlomchik MJ, Satpathy AT, Fremont DH, Diamond MS, Bhattacharya D. Affinity-Restricted Memory B Cells Dominate Recall Responses to Heterologous Flaviviruses. Immunity 2020; 53:1078-1094.e7. [PMID: 33010224 DOI: 10.1016/j.immuni.2020.09.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 06/11/2020] [Accepted: 09/04/2020] [Indexed: 02/06/2023]
Abstract
Memory B cells (MBCs) can respond to heterologous antigens either by molding new specificities through secondary germinal centers (GCs) or by selecting preexisting clones without further affinity maturation. To distinguish these mechanisms in flavivirus infections and immunizations, we studied recall responses to envelope protein domain III (DIII). Conditional deletion of activation-induced cytidine deaminase (AID) between heterologous challenges of West Nile, Japanese encephalitis, Zika, and dengue viruses did not affect recall responses. DIII-specific MBCs were contained mostly within the plasma-cell-biased CD80+ subset, and few GCs arose following heterologous boosters, demonstrating that recall responses are confined by preexisting clonal diversity. Measurement of monoclonal antibody (mAb) binding affinity to DIII proteins, timed AID deletion, single-cell RNA sequencing, and lineage tracing experiments point to selection of relatively low-affinity MBCs as a mechanism to promote diversity. Engineering immunogens to avoid this MBC diversity may facilitate flavivirus-type-specific vaccines with minimized potential for infection enhancement.
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Affiliation(s)
- Rachel Wong
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Immunobiology, University of Arizona, Tucson, AZ 85724, USA
| | - Julia A Belk
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jennifer Govero
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Jennifer L Uhrlaub
- Department of Immunobiology, University of Arizona, Tucson, AZ 85724, USA
| | - Dakota Reinartz
- Department of Immunobiology, University of Arizona, Tucson, AZ 85724, USA
| | - Haiyan Zhao
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - John M Errico
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Lucas D'Souza
- Department of Immunobiology, University of Arizona, Tucson, AZ 85724, USA
| | - Tyler J Ripperger
- Department of Immunobiology, University of Arizona, Tucson, AZ 85724, USA
| | | | - Mark J Shlomchik
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Daved H Fremont
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Michael S Diamond
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA; Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
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16
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Abbott RK, Crotty S. Factors in B cell competition and immunodominance. Immunol Rev 2020; 296:120-131. [PMID: 32483855 PMCID: PMC7641103 DOI: 10.1111/imr.12861] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/20/2020] [Accepted: 04/27/2020] [Indexed: 02/06/2023]
Abstract
The majority of all vaccines work by inducing protective antibody responses. The mechanisms by which the B cells responsible for producing protective antibodies are elicited to respond are not well understood. Interclonal B cell competition to complex antigens, particularly in germinal centers, has emerged as an important hurdle in designing effective vaccines. This review will focus on recent advances in understanding the roles of B cell precursor frequency, B cell receptor affinity for antigen, antigen avidity, and other factors that can substantially alter the outcomes of B cell responses to complex antigens. Understanding the interdependence of these fundamental factors that affect B cell responses can inform current vaccine design efforts for pathogens with complex proteins as candidate immunogens such as HIV, influenza, and coronaviruses.
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Affiliation(s)
- Robert K. Abbott
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037 USA
- Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
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17
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Preite S, Gomez-Rodriguez J, Cannons JL, Schwartzberg PL. T and B-cell signaling in activated PI3K delta syndrome: From immunodeficiency to autoimmunity. Immunol Rev 2020; 291:154-173. [PMID: 31402502 DOI: 10.1111/imr.12790] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 05/30/2019] [Indexed: 12/15/2022]
Abstract
Phosphatidylinositol 3 kinases (PI3K) are a family of lipid kinases that are activated by a variety of cell-surface receptors, and regulate a wide range of downstream readouts affecting cellular metabolism, growth, survival, differentiation, adhesion, and migration. The importance of these lipid kinases in lymphocyte signaling has recently been highlighted by genetic analyses, including the recognition that both activating and inactivating mutations of the catalytic subunit of PI3Kδ, p110δ, lead to human primary immunodeficiencies. In this article, we discuss how studies on the human genetic disorder "Activated PI3K-delta syndrome" and mouse models of this disease (Pik3cdE1020K/+ mice) have provided fundamental insight into pathways regulated by PI3Kδ in T and B cells and their contribution to lymphocyte function and disease, including responses to commensal bacteria and the development of autoimmunity and tumors. We highlight critical roles of PI3Kδ in T follicular helper cells and the orchestration of the germinal center reaction, as well as in CD8+ T-cell function. We further present data demonstrating the ability of the AKT-resistant FOXO1AAA mutant to rescue IgG1 class switching defects in Pik3cdE1020K/+ B cells, as well as data supporting a role for PI3Kδ in promoting multiple T-helper effector cell lineages.
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Affiliation(s)
- Silvia Preite
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland.,National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Julio Gomez-Rodriguez
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland.,National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Jennifer L Cannons
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland.,National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Pamela L Schwartzberg
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland.,National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
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18
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Zhu J, Hay AN, Potter AA, Richwine MW, Sproule T, LeRoith T, Wilson J, Hasham MG, Roopenian DC, Leeth CM. Abrogated AID Function Prolongs Survival and Diminishes Renal Pathology in the BXSB Mouse Model of Systemic Lupus Erythematosus. THE JOURNAL OF IMMUNOLOGY 2020; 204:1091-1100. [PMID: 31988182 DOI: 10.4049/jimmunol.1900501] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 12/22/2019] [Indexed: 12/31/2022]
Abstract
Almost a decade has passed since the approval of belimumab, an mAb directed against B lymphocyte stimulation and the first targeted therapy approved for systemic lupus erythematous (SLE) in over 50 y. Although well tolerated, the efficacy of belimumab remains limited and is not labeled for patients suffering from nephritis, the leading cause of patient mortality. We sought to explore alternative targets of autoreactive B lymphocytes through manipulation of affinity maturation. The BXSB/MpJ mouse, a well-established model of human SLE, develops elevated antinuclear Abs and immune complex-mediated nephritis along with other manifestations of SLE-like disease. To limit interfering with critical background genetics, we used CRISPR-Cas9 to disrupt activation-induced cytidine deaminase (AID; Aicda) directly in BXSB zygotes. Homozygous null mice demonstrated significantly prolonged survival compared with wild-type. Although mice continued to develop plasma cells, splenic follicular structure was restored, and renal pathology was reduced. Mice developed expanded germinal center B lymphocyte populations as in other models of AID deficiency as well as increased populations of CD73+ B lymphocytes. Treatment with the small molecule inhibitor of RAD51, 4,4'-diisothiocyano-2,2'-stilbenedisulfonic acid, resulted in minimal changes in disease markers in BXSB mice. The prolonged survival in AID-deficient BXSB mice appears attributed primarily to the reduced renal pathology, warranting further exploration, as current therapeutics targeting lupus nephritis are limited and, thus, in great demand.
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Affiliation(s)
- Jing Zhu
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Alayna N Hay
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Ashley A Potter
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - Madison W Richwine
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | | | - Tanya LeRoith
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061
| | - John Wilson
- The Jackson Laboratory, Bar Harbor, ME 04609; and
| | | | | | - Caroline M Leeth
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061;
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19
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Shlomchik MJ, Luo W, Weisel F. Linking signaling and selection in the germinal center. Immunol Rev 2019; 288:49-63. [PMID: 30874353 DOI: 10.1111/imr.12744] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 01/24/2019] [Indexed: 12/24/2022]
Abstract
Germinal centers (GC) are sites of rapid B-cell proliferation in response to certain types of immunization. They arise in about 1 week and can persist for several months. In GCs, B cells differentiate in a unique way and begin to undergo somatic mutation of the Ig V regions at a high rate. GC B cells (GCBC) thus undergo clonal diversification that can affect the affinity of the newly mutant B-cell receptor (BCR) for its driving antigen. Through processes that are still poorly understood, GCBC with higher affinity are selectively expanded while those with mutations that inactivate the BCR are lost. In addition, at various times during the extended GC reaction, some GCBC undergo differentiation into either long-lived memory B cells (MBC) or plasma cells. The cellular and molecular signals that govern these fate decisions are not well-understood, but are an active area of research in multiple laboratories. In this review, we cover both the history of this field and focus on recent work that has helped to elucidate the signals and molecules, such as key transcription factors, that coordinate both positive selection as well as differentiation of GCBC.
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Affiliation(s)
- Mark J Shlomchik
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Wei Luo
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Florian Weisel
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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20
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Schwartz GW, Shauli T, Linial M, Hershberg U. Serine substitutions are linked to codon usage and differ for variable and conserved protein regions. Sci Rep 2019; 9:17238. [PMID: 31754132 PMCID: PMC6872785 DOI: 10.1038/s41598-019-53452-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 11/01/2019] [Indexed: 11/11/2022] Open
Abstract
Serine is the only amino acid that is encoded by two disjoint codon sets (TCN & AGY) so that a tandem substitution of two nucleotides is required to switch between the two sets. We show that these codon sets underlie distinct substitution patterns at positions subject to purifying and diversifying selections. We found that in humans, positions that are conserved among ~100 vertebrates, and thus subjected to purifying selection, are enriched for substitutions involving serine (TCN, denoted S'), proline, and alanine, (S'PA). In contrast, the less conserved positions are enriched for serine encoded with AGY codons (denoted S″), glycine and asparagine, (GS″N). We tested this phenomenon in the HIV envelope glycoprotein (gp120), and the V-gene that encodes B-cell receptors/antibodies. These fast evolving proteins both have hypervariable positions, which are under diversifying selection, closely adjacent to highly conserved structural regions. In both instances, we identified an opposite abundance of two groups of serine substitutions, with enrichment of S'PA in the conserved positions, and GS″N in the hypervariable regions. Finally, we analyzed the substitutions across 60,000 individual human exomes to show that, when serine has a specific functional constraint of phosphorylation capability, S' codons are 32-folds less prone than S″ to substitutions to Threonine or Tyrosine that could potentially retain the phosphorylation site capacity. Combined, our results, that cover evolutionary signals at different temporal scales, demonstrate that through its encoding by two codon sets, serine allows for the existence of alternating substitution patterns within positions of functional maintenance versus sites of rapid diversification.
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Affiliation(s)
- Gregory W Schwartz
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, USA
| | - Tair Shauli
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Michal Linial
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Uri Hershberg
- Drexel School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, USA.
- Department of Microbiology and Immunology, Drexel College of Medicine, Drexel University, Philadelphia, USA.
- Department of Human Biology, Faculty of Science, University of Haifa, Haifa, Israel.
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21
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Faro J, von Haeften B, Gardner R, Faro E. A Sensitivity Analysis Comparison of Three Models for the Dynamics of Germinal Centers. Front Immunol 2019; 10:2038. [PMID: 31543878 PMCID: PMC6729701 DOI: 10.3389/fimmu.2019.02038] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 08/12/2019] [Indexed: 01/25/2023] Open
Abstract
Germinal centers (GCs) are transient anatomical microenvironments where antibody affinity maturation and memory B cells generation takes place. In the past, models of Germinal Center (GC) dynamics have focused on understanding antibody affinity maturation rather than on the main mechanism(s) driving their rise-and-fall dynamics. Here, based on a population dynamics model core, we compare three mechanisms potentially responsible for this GC biphasic behavior dependent on follicular dendritic cell (FDC) maturation, follicular T helper (Tfh) cell maturation, and antigen depletion. Analyzing the kinetics of B and T cells, as well as its parameter sensitivities, we found that only the FDC-maturation-based model could describe realistic GC dynamics, whereas the simple Tfh-maturation and antigen-depletion mechanisms, as implemented here, could not. We also found that in all models the processes directly related to Tfh cell kinetics have the highest impact on GC dynamics. This suggests the existence of some still unknown mechanism(s) tuning GC dynamics by affecting Tfh cell response to proliferation-inducing stimuli.
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Affiliation(s)
- Jose Faro
- Area of Immunology, Faculty of Biology, CINBIO (Biomedical Research Center), University of Vigo, Vigo, Spain
- Instituto Biomédico de Vigo, Vigo, Spain
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Bernardo von Haeften
- Departamento de Física, FCEyN, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - Rui Gardner
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Emilio Faro
- Department of Applied Mathematics II, University of Vigo, Vigo, Spain
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22
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Multi-type Galton–Watson Processes with Affinity-Dependent Selection Applied to Antibody Affinity Maturation. Bull Math Biol 2018; 81:830-868. [DOI: 10.1007/s11538-018-00548-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 11/30/2018] [Indexed: 01/18/2023]
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23
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Woodruff MC, Kim EH, Luo W, Pulendran B. B Cell Competition for Restricted T Cell Help Suppresses Rare-Epitope Responses. Cell Rep 2018; 25:321-327.e3. [PMID: 30304673 PMCID: PMC6235168 DOI: 10.1016/j.celrep.2018.09.029] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 07/26/2018] [Accepted: 09/07/2018] [Indexed: 12/21/2022] Open
Abstract
The immune system responds preferentially to particular antigenic-epitopes contained within complex immunogens, such as proteins or microbes. This poorly understood phenomenon, termed "immunodominance," remains an obstacle to achieving polyvalent immune responses against multiple antigenic-epitopes through vaccination. We observed profound suppression in the hapten-specific antibody response in mice immunized with hapten-protein conjugate, mixed with an excess of protein, relative to that in mice immunized with hapten-protein alone. The suppression was robust (100-fold and 10-fold with a 10- or 2-fold excess of protein, respectively), stable over a 6-log range in antigen dose, observed within 10 days of vaccination, and resistant to boosting and adjuvants. Furthermore, there were reduced frequencies of antigen-specific germinal-center B cells and long-lived bone-marrow plasma cells. The mechanism of this "antigen-competition" was mediated largely by early access to T-helper cells. These results offer mechanistic insights into B cell competition during an immune response and suggest vaccination strategies against HIV, influenza, and dengue.
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Affiliation(s)
| | - Eui Ho Kim
- Emory Vaccine Center, Emory University, Atlanta, GA 30329, USA; Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Wei Luo
- Institute for Immunity, Transplantation and Infection, Department of Pathology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Department of Pathology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA.
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24
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Yaari G, Flajnik M, Hershberg U. Questions of Stochasticity and Control in Immune Repertoires. Trends Immunol 2018; 39:859-861. [PMID: 30243818 DOI: 10.1016/j.it.2018.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 09/04/2018] [Accepted: 09/04/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Gur Yaari
- Bioengineering, Faculty of Engineering, Bar-Ilan University, Ramat Gan 5290002, Israel.
| | - Martin Flajnik
- Department of Microbiology and Immunology, University of Maryland, Suite 380, 685 West Baltimore Street, Baltimore, MD 21201, USA
| | - Uri Hershberg
- Department of Human Biology, Faculty of Sciences, University of Haifa, Haifa, 3498838, Israel; School of Biomedical Engineering, Science and Health Systems and Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, PA 19104, USA.
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25
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Krishna V, Bachman KE. A mechanism of T cell dependent selection of antigen engaged Germinal Center B cells. PLoS One 2018; 13:e0200241. [PMID: 30138347 PMCID: PMC6107130 DOI: 10.1371/journal.pone.0200241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 06/24/2018] [Indexed: 11/25/2022] Open
Abstract
A model of B cell affinity selection is proposed, and an explanation of peripheral tolerance mechanisms through antibody repertoire editing is presented. We show that affinity discrimination between B cells is driven by a competition between obtaining T cell help and removal of B cells from the light zone, either through apoptosis or by a return to the dark zone of germinal centers. We demonstrate that this mechanism also allows for the negative selection of self reactive B cells and maintenance of B cell tolerance during the Germinal Center reaction. Finally, we demonstrate that clonal expansion upon return to the Germinal Center dark zone amplifies differences in the antigen affinity of B cells that survive the light zone.
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Affiliation(s)
- Vinod Krishna
- Computational Biology, Discovery Sciences, Janssen Research and Development LLC., 1400 McKean Road, Spring House, PA, United States of America
- * E-mail:
| | - Kurtis E. Bachman
- Computational Biology, Discovery Sciences, Janssen Research and Development LLC., 1400 McKean Road, Spring House, PA, United States of America
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26
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Firl DJ, Degn SE, Padera T, Carroll MC. Capturing change in clonal composition amongst single mouse germinal centers. eLife 2018; 7:33051. [PMID: 30066671 PMCID: PMC6070335 DOI: 10.7554/elife.33051] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 07/01/2018] [Indexed: 01/09/2023] Open
Abstract
Understanding cellular processes occurring in vivo on time scales of days to weeks requires repeatedly interrogating the same tissue without perturbing homeostasis. We describe a novel setup for longitudinal intravital imaging of murine peripheral lymph nodes (LNs). The formation and evolution of single germinal centers (GCs) was visualized over days to weeks. Naïve B cells encounter antigen and form primary foci, which subsequently seed GCs. These experience widely varying rates of homogenizing selection, even within closely confined spatial proximity. The fluidity of GCs is greater than previously observed with large shifts in clonality over short time scales; and loss of GCs is a rare, observable event. The observation of contemporaneous, congruent shifts in clonal composition between GCs within the same animal suggests inter-GC trafficking of memory B cells. This tool refines approaches to resolving immune dynamics in peripheral LNs with high temporospatial resolution and minimal perturbation of homeostasis.
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Affiliation(s)
- Daniel J Firl
- Cleveland Clinic Lerner College of Medicine, Cleveland, United States.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, United States.,Howard Hughes Medical Institute, Maryland, United States
| | - Soren E Degn
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, United States.,Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Timothy Padera
- Edwin L. Steele Laboratories for Tumor Biology, Department of Radiation Oncology, Massachusetts General Hospital, Boston, United States
| | - Michael C Carroll
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, United States.,Department of Pediatrics, Harvard Medical School, Boston, United States
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27
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Rosenfeld AM, Meng W, Chen DY, Zhang B, Granot T, Farber DL, Hershberg U, Luning Prak ET. Computational Evaluation of B-Cell Clone Sizes in Bulk Populations. Front Immunol 2018; 9:1472. [PMID: 30008715 PMCID: PMC6034424 DOI: 10.3389/fimmu.2018.01472] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 06/13/2018] [Indexed: 12/27/2022] Open
Abstract
B cell clones expand and contract during adaptive immune responses and can persist or grow uncontrollably in lymphoproliferative disorders. One way to monitor and track B cell clones is to perform large-scale sampling of bulk cell populations, amplifying, and sequencing antibody gene rearrangements by next-generation sequencing (NGS). Here, we describe a series of computational approaches for estimating B cell clone size in NGS immune repertoire profiling data of antibody heavy chain gene rearrangements. We define three different measures of B cell clone size-copy numbers, instances, and unique sequences-and show how these measures can be used to rank clones, analyze their diversity, and study their distribution within and between individuals. We provide a detailed, step-by-step procedure for performing these analyses using two different data sets of spleen samples from human organ donors. In the first data set, 19 independently generated biological replicates from a single individual are analyzed for B cell clone size, diversity and sampling sufficiency for clonal overlap analysis. In the second data set, B cell clones are compared in eight different organ donors. We comment upon frequently encountered pitfalls and offer practical advice with alternative approaches. Overall, we provide a series of pragmatic analytical approaches and show how different clone size measures can be used to study the clonal landscape in bulk B cell immune repertoire profiling data.
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Affiliation(s)
- Aaron M. Rosenfeld
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, United States
| | - Wenzhao Meng
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Dora Y. Chen
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Bochao Zhang
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, United States
| | - Tomer Granot
- Columbia Center for Translational Immunology, Columbia University, New York, NY, United States
| | - Donna L. Farber
- Columbia Center for Translational Immunology, Columbia University, New York, NY, United States
| | - Uri Hershberg
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA, United States
- Department of Microbiology and Immunology, Drexel College of Medicine, Drexel University, Philadelphia, PA, United States
| | - Eline T. Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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28
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Roh KH, Song HW, Pradhan P, Bai K, Bohannon CD, Dale G, Leleux J, Jacob J, Roy K. A synthetic stroma-free germinal center niche for efficient generation of humoral immunity ex vivo. Biomaterials 2018; 164:106-120. [PMID: 29500990 DOI: 10.1016/j.biomaterials.2018.02.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 02/16/2018] [Accepted: 02/19/2018] [Indexed: 01/22/2023]
Abstract
B cells play a major role in the adaptive immune response by producing antigen-specific antibodies against pathogens and imparting immunological memory. Following infection or vaccination, antibody-secreting B cells and memory B cells are generated in specialized regions of lymph nodes and spleens, called germinal centers. Here, we report a fully synthetic ex-vivo system that recapitulates the generation of antigen-specific germinal-center (GC) like B cells using material-surface driven polyvalent signaling. This synthetic germinal center (sGC) reaction was effectively induced using biomaterial-based artificial "follicular T helper cells (TFH)" that provided both natural CD40-CD40L ligation as well as crosslinking of CD40 and by mimicking artificial "follicular dendritic cells (FDC)" to provide efficient, polyvalent antigen presentation. The artificial sGC reaction resulted in efficient B cell expansion, immunoglobulin (Ig) class switching, and expression of germinal center phenotypes. Antigen presentation during sGC reaction selectively enhanced the antigen-specific B cell population and induced somatic hyper-mutations for potential affinity maturation. The resulting B cell population consisted primarily of GC-like B cells (centrocytes) as well as some plasma-like B cells expressing CD138. With concurrent cell sorting, we successfully created highly enriched populations of antigen-specific B cells. Adoptive transfer of these GC-like B cells into non-irradiated isogeneic or non-lethally irradiated congenic recipient mice showed successful engraftment and survival of the donor cells for the 4 week test period. We show that this material-surface driven sGC reaction can be successfully applied to not only splenic B cells but also B cells isolated from more therapeutically relevant sources such as peripheral blood mononuclear cells (PBMCs), thus making our current work an exciting prospect in the new era of personalized medicine and custom-immunotherapy.
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Affiliation(s)
- Kyung-Ho Roh
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Hannah W Song
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Pallab Pradhan
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Kevin Bai
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Caitlin D Bohannon
- Division of Microbiology and Immunology, Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Gordon Dale
- Division of Microbiology and Immunology, Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jardin Leleux
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Joshy Jacob
- Division of Microbiology and Immunology, Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Krishnendu Roy
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA.
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29
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Escape from thymic deletion and anti-leukemic effects of T cells specific for hematopoietic cell-restricted antigen. Nat Commun 2018; 9:225. [PMID: 29335408 PMCID: PMC5768767 DOI: 10.1038/s41467-017-02665-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 12/18/2017] [Indexed: 12/17/2022] Open
Abstract
Whether hematopoietic cell-restricted distribution of antigens affects the degree of thymic negative selection has not been investigated in detail. Here, we show that T cells specific for hematopoietic cell-restricted antigens (HRA) are not completely deleted in the thymus, using the mouse minor histocompatibility antigen H60, the expression of which is restricted to hematopoietic cells. As a result, low avidity T cells escape from thymic deletion. This incomplete thymic deletion occurs to the T cells developing de novo in the thymus of H60-positive recipients in H60-mismatched bone marrow transplantation (BMT). H60-specific thymic deletion escapee CD8+ T cells exhibit effector differentiation potentials in the periphery and contribute to graft-versus-leukemia effects in the recipients of H60-mismatched BMT, regressing H60+ hematological tumors. These results provide information essential for understanding thymic negative selection and developing a strategy to treat hematological tumors.
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30
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Amitai A, Mesin L, Victora GD, Kardar M, Chakraborty AK. A Population Dynamics Model for Clonal Diversity in a Germinal Center. Front Microbiol 2017; 8:1693. [PMID: 28955307 PMCID: PMC5600966 DOI: 10.3389/fmicb.2017.01693] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 08/22/2017] [Indexed: 12/21/2022] Open
Abstract
Germinal centers (GCs) are micro-domains where B cells mature to develop high affinity antibodies. Inside a GC, B cells compete for antigen and T cell help, and the successful ones continue to evolve. New experimental results suggest that, under identical conditions, a wide spectrum of clonal diversity is observed in different GCs, and high affinity B cells are not always the ones selected. We use a birth, death and mutation model to study clonal competition in a GC over time. We find that, like all evolutionary processes, diversity loss is inherently stochastic. We study two selection mechanisms, birth-limited and death limited selection. While death limited selection maintains diversity and allows for slow clonal homogenization as affinity increases, birth limited selection results in more rapid takeover of successful clones. Finally, we qualitatively compare our model to experimental observations of clonal selection in mice.
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Affiliation(s)
- Assaf Amitai
- Chemical Engineering, Massachusetts Institute of TechnologyCambridge, MA, United States.,Institute for Medical Engineering and Science, Massachusetts Institute of TechnologyCambridge, MA, United States.,Ragon Institute of MGH, MIT and HarvardCambridge, MA, United States
| | - Luka Mesin
- Laboratory of Lymphocyte Dynamics, Rockefeller UniversityNew York, NY, United States
| | - Gabriel D Victora
- Laboratory of Lymphocyte Dynamics, Rockefeller UniversityNew York, NY, United States
| | - Mehran Kardar
- Physics, Massachusetts Institute of TechnologyCambridge, MA, United States
| | - Arup K Chakraborty
- Chemical Engineering, Massachusetts Institute of TechnologyCambridge, MA, United States.,Institute for Medical Engineering and Science, Massachusetts Institute of TechnologyCambridge, MA, United States.,Ragon Institute of MGH, MIT and HarvardCambridge, MA, United States.,Biological Engineering and Chemistry, Massachusetts Institute of TechnologyCambridge, MA, United States
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31
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Zabel F, Fettelschoss A, Vogel M, Johansen P, Kündig TM, Bachmann MF. Distinct T helper cell dependence of memory B-cell proliferation versus plasma cell differentiation. Immunology 2017; 150:329-342. [PMID: 27861835 DOI: 10.1111/imm.12688] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 11/02/2016] [Accepted: 11/03/2016] [Indexed: 02/03/2023] Open
Abstract
Several memory B-cell subclasses with distinct functions have been described, of which the most effective is the class-switched (CS) memory B-cell population. We have previously shown, using virus-like particles (VLPs), that the proliferative potential of these CS memory B cells is limited and they fail to re-enter germinal centres (GCs). However, VLP-specific memory B cells quickly differentiated into secondary plasma cells (PCs) with the virtue of elevated antibody production compared with primary PCs. Whereas the induction of VLP+ memory B cells was strongly dependent on T helper cells, we were wondering whether re-stimulation of VLP+ memory B cells and their differentiation into secondary PCs would also require T helper cells. Global absence of T helper cells led to strongly impaired memory B cell proliferation and PC differentiation. In contrast, lack of interleukin-21 receptor-dependent follicular T helper cells or CD40 ligand signalling strongly affected proliferation of memory B cells, but differentiation into mature secondary PCs exhibiting increased antibody production was essentially normal. This contrasts with primary B-cell responses, where a strong dependence on CD40 ligand but limited importance of interleukin-21 receptor was seen. Hence, T helper cell dependence differs between primary and secondary B-cell responses as well as between memory B-cell proliferation and PC differentiation.
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Affiliation(s)
- Franziska Zabel
- Department of Dermatology, Zurich University Hospital, Schlieren/Zurich, Switzerland
| | - Antonia Fettelschoss
- Department of Dermatology, Zurich University Hospital, Schlieren/Zurich, Switzerland
| | - Monique Vogel
- Inselspital, Department of Immunology, University of Bern, Bern, Switzerland
| | - Pål Johansen
- Department of Dermatology, Zurich University Hospital, Zurich, Switzerland
| | - Thomas M Kündig
- Department of Dermatology, Zurich University Hospital, Zurich, Switzerland
| | - Martin F Bachmann
- Department of Dermatology, Zurich University Hospital, Schlieren/Zurich, Switzerland.,Inselspital, Department of Immunology, University of Bern, Bern, Switzerland
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32
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Wang P, Shih CM, Qi H, Lan YH. A Stochastic Model of the Germinal Center Integrating Local Antigen Competition, Individualistic T-B Interactions, and B Cell Receptor Signaling. THE JOURNAL OF IMMUNOLOGY 2016; 197:1169-82. [PMID: 27421481 DOI: 10.4049/jimmunol.1600411] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 06/10/2016] [Indexed: 11/19/2022]
Abstract
The germinal center (GC) reaction underlies productive humoral immunity by orchestrating competition-based affinity maturation to produce plasma cells and memory B cells. T cells are limiting in this process. How B cells integrate signals from T cells and BCRs to make fate decisions while subjected to a cyclic selection process is not clear. In this article, we present a spatiotemporally resolved stochastic model that describes cell behaviors as rate-limited stochastic reactions. We hypothesize a signal integrator protein integrates follicular helper T (Tfh)- and Ag-derived signals to drive different B cell fates in a probabilistic manner and a dedicated module of Tfh interaction promoting factors control the efficiency of contact-dependent Tfh help delivery to B cells. Without assuming deterministic affinity-based decisions or temporal event sequence, this model recapitulates GC characteristics, highlights the importance of efficient T cell help delivery during individual contacts with B cells and intercellular positive feedback for affinity maturation, reveals the possibility that antagonism between BCR signaling and T cell help accelerates affinity maturation, and suggests that the dichotomy between affinity and magnitude of GC reaction can be avoided by tuning the efficiency of contact-dependent help delivery during reiterative T-B interactions.
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Affiliation(s)
- Peng Wang
- Department of Physics, Tsinghua University, Beijing 100084, China; Collaborative Innovation Center of Quantum Matter, Beijing 100084, China
| | - Chang-Ming Shih
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China; Institute for Immunology, Tsinghua University, Beijing 100084, China; and Department of Basic Biomedical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Hai Qi
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China; Institute for Immunology, Tsinghua University, Beijing 100084, China; and Department of Basic Biomedical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yue-Heng Lan
- Department of Physics, Tsinghua University, Beijing 100084, China; Collaborative Innovation Center of Quantum Matter, Beijing 100084, China;
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33
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Hershberg U, Luning Prak ET. The analysis of clonal expansions in normal and autoimmune B cell repertoires. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0239. [PMID: 26194753 PMCID: PMC4528416 DOI: 10.1098/rstb.2014.0239] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Clones are the fundamental building blocks of immune repertoires. The number of different clones relates to the diversity of the repertoire, whereas their size and sequence diversity are linked to selective pressures. Selective pressures act both between clones and within different sequence variants of a clone. Understanding how clonal selection shapes the immune repertoire is one of the most basic questions in all of immunology. But how are individual clones defined? Here we discuss different approaches for defining clones, starting with how antibodies are diversified during different stages of B cell development. Next, we discuss how clones are defined using different experimental methods. We focus on high-throughput sequencing datasets, and the computational challenges and opportunities that these data have for mining the antibody repertoire landscape. We discuss methods that visualize sequence variants within the same clone and allow us to consider collections of shared mutations to determine which sequences share a common ancestry. Finally, we comment on features of frequently encountered expanded B cell clones that may be of particular interest in the setting of autoimmunity and other chronic conditions.
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Affiliation(s)
- Uri Hershberg
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Bossone 7-711, 3141 Chestnut Street, Philadelphia, PA 19104, USA Department of Immunology and Microbiology, College of Medicine, Drexel University, Bossone 7-711, 3141 Chestnut Street, Philadelphia, PA 19104, USA
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, 405B Stellar Chance Labs, 422 Curie Boulevard, Philadelphia, PA 19104, USA
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34
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Yaari G, Benichou JIC, Vander Heiden JA, Kleinstein SH, Louzoun Y. The mutation patterns in B-cell immunoglobulin receptors reflect the influence of selection acting at multiple time-scales. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0242. [PMID: 26194756 DOI: 10.1098/rstb.2014.0242] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
During the several-week course of an immune response, B cells undergo a process of clonal expansion, somatic hypermutation of the immunoglobulin (Ig) genes and affinity-dependent selection. Over a lifetime, each B cell may participate in multiple rounds of affinity maturation as part of different immune responses. These two time-scales for selection are apparent in the structure of B-cell lineage trees, which often contain a 'trunk' consisting of mutations that are shared across all members of a clone, and several branches that form a 'canopy' consisting of mutations that are shared by a subset of clone members. The influence of affinity maturation on the B-cell population can be inferred by analysing the pattern of somatic mutations in the Ig. While global analysis of mutation patterns has shown evidence of strong selection pressures shaping the B-cell population, the effect of different time-scales of selection and diversification has not yet been studied. Analysis of B cells from blood samples of three healthy individuals identifies a range of clone sizes with lineage trees that can contain long trunks and canopies indicating the significant diversity introduced by the affinity maturation process. We here show that observed mutation patterns in the framework regions (FWRs) are determined by an almost purely purifying selection on both short and long time-scales. By contrast, complementarity determining regions (CDRs) are affected by a combination of purifying and antigen-driven positive selection on the short term, which leads to a net positive selection in the long term. In both the FWRs and CDRs, long-term selection is strongly dependent on the heavy chain variable gene family.
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Affiliation(s)
- Gur Yaari
- Bioengineering Program, Faculty of Engineering, Bar-Ilan University, Ramat Gan 5290002, Israel
| | | | - Jason A Vander Heiden
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA
| | - Steven H Kleinstein
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA Departments of Pathology and Immunobiology, Yale School of Medicine, New Haven, CT 06511, USA
| | - Yoram Louzoun
- Department of Mathematics, Bar-Ilan University, Ramat Gan 5290002, Israel Gonda Brain Research Center, Bar-Ilan University, Ramat Gan 5290002, Israel
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35
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Liberman G, Benichou JIC, Maman Y, Glanville J, Alter I, Louzoun Y. Estimate of within population incremental selection through branch imbalance in lineage trees. Nucleic Acids Res 2015; 44:e46. [PMID: 26586802 PMCID: PMC4797263 DOI: 10.1093/nar/gkv1198] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 10/18/2015] [Indexed: 01/09/2023] Open
Abstract
Incremental selection within a population, defined as limited fitness changes following mutation, is an important aspect of many evolutionary processes. Strongly advantageous or deleterious mutations are detected using the synonymous to non-synonymous mutations ratio. However, there are currently no precise methods to estimate incremental selection. We here provide for the first time such a detailed method and show its precision in multiple cases of micro-evolution. The proposed method is a novel mixed lineage tree/sequence based method to detect within population selection as defined by the effect of mutations on the average number of offspring. Specifically, we propose to measure the log of the ratio between the number of leaves in lineage trees branches following synonymous and non-synonymous mutations. The method requires a high enough number of sequences, and a large enough number of independent mutations. It assumes that all mutations are independent events. It does not require of a baseline model and is practically not affected by sampling biases. We show the method's wide applicability by testing it on multiple cases of micro-evolution. We show that it can detect genes and inter-genic regions using the selection rate and detect selection pressures in viral proteins and in the immune response to pathogens.
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Affiliation(s)
- Gilad Liberman
- Gonda Multidisciplinary Brain Research Center, Bar Ilan University, Ramat-Gan 5290002, Israel
| | | | - Yaakov Maman
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520-8011, USA Howard Hughes Medical Institute, New Haven, CT 06519, USA
| | - Jacob Glanville
- Program in Computational and Systems Immunology, Stanford University, Stanford, CA 94305, USA Department of Pathology, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA Program in Immunology, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA Distributed Bio, San Francisco, CA 94080, USA
| | - Idan Alter
- Department of Mathematics, Bar Ilan University, Ramat-Gan 5290002, Israel
| | - Yoram Louzoun
- Gonda Multidisciplinary Brain Research Center, Bar Ilan University, Ramat-Gan 5290002, Israel Department of Mathematics, Bar Ilan University, Ramat-Gan 5290002, Israel
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36
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Hara Y, Tashiro Y, Murakami A, Nishimura M, Shimizu T, Kubo M, Burrows PD, Azuma T. High affinity IgM(+) memory B cells are generated through a germinal center-dependent pathway. Mol Immunol 2015; 68:617-27. [PMID: 26514429 DOI: 10.1016/j.molimm.2015.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 09/30/2015] [Accepted: 10/08/2015] [Indexed: 12/19/2022]
Abstract
During a T cell-dependent immune response, B cells undergo clonal expansion and selection and the induction of isotype switching and somatic hypermutation (SHM). Although somatically mutated IgM(+) memory B cells have been reported, it has not been established whether they are really high affinity B cells. We tracked (4-hydroxy-3-nitrophenyl) acetyl hapten-specific GC B cells from normal immunized mice based on affinity of their B cell receptor (BCR) and performed BCR sequence analysis. SHM was evident by day 7 postimmunization and increased with time, such that high affinity IgM(+) as well as IgG(+) memory B cells continued to be generated up to day 42. In contrast, class-switch recombination (CSR) was almost completed by day 7 and then the ratio of IgG1(+)/IgM(+) GC B cells remained unchanged. Together these findings suggest that IgM(+) B cells undergo SHM in the GC to generate high affinity IgM(+) memory cells and that this process continues even after CSR is accomplished.
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Affiliation(s)
- Yasushi Hara
- Laboratory for Structural Immunology, Research Institute for Biomedical Sciences, Tokyo University of Science, 2669 Yamazaki, Noda, Chiba 278-0022, Japan
| | - Yasuyuki Tashiro
- Laboratory for Structural Immunology, Research Institute for Biomedical Sciences, Tokyo University of Science, 2669 Yamazaki, Noda, Chiba 278-0022, Japan; Division of Development and Aging, Research Institute for Biomedical Sciences, Tokyo University of Science, 2669 Yamazaki, Noda, Chiba 278-0022, Japan
| | - Akikazu Murakami
- Laboratory for Structural Immunology, Research Institute for Biomedical Sciences, Tokyo University of Science, 2669 Yamazaki, Noda, Chiba 278-0022, Japan
| | - Miyuki Nishimura
- Laboratory for Structural Immunology, Research Institute for Biomedical Sciences, Tokyo University of Science, 2669 Yamazaki, Noda, Chiba 278-0022, Japan
| | - Takeyuki Shimizu
- Department of Immunology, Kochi Medical School, Kochi University, Oko-cho Kohasu, Nankoku, Kochi 783-8505, Japan
| | - Masato Kubo
- Division of Molecular Pathology, Research Institute for Biomedical Sciences, Tokyo University of Science, 2669 Yamazaki, Noda, Chiba 278-0022, Japan; Laboratory for Cytokine Regulation, Riken Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Peter D Burrows
- Department of Microbiology, University of Alabama at Birmingham, UAB 406 SHEL, 1530 Third Avenue South, Birmingham, AL 35294, USA; Department of Genetics, University of Alabama at Birmingham, UAB 406 SHEL, 1530 Third Avenue South, Birmingham, AL 35294, USA
| | - Takachika Azuma
- Laboratory for Structural Immunology, Research Institute for Biomedical Sciences, Tokyo University of Science, 2669 Yamazaki, Noda, Chiba 278-0022, Japan; Antibody Technology Research Center, Co., Ltd., 2361-1-S401 Yamazaki, Noda, Chiba 278-0022, Japan.
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37
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Le D, Miller JD, Ganusov VV. Mathematical modeling provides kinetic details of the human immune response to vaccination. Front Cell Infect Microbiol 2015; 4:177. [PMID: 25621280 PMCID: PMC4288384 DOI: 10.3389/fcimb.2014.00177] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 12/04/2014] [Indexed: 02/01/2023] Open
Abstract
With major advances in experimental techniques to track antigen-specific immune responses many basic questions on the kinetics of virus-specific immunity in humans remain unanswered. To gain insights into kinetics of T and B cell responses in human volunteers we combined mathematical models and experimental data from recent studies employing vaccines against yellow fever and smallpox. Yellow fever virus-specific CD8 T cell population expanded slowly with the average doubling time of 2 days peaking 2.5 weeks post immunization. Interestingly, we found that the peak of the yellow fever-specific CD8 T cell response was determined by the rate of T cell proliferation and not by the precursor frequency of antigen-specific cells as has been suggested in several studies in mice. We also found that while the frequency of virus-specific T cells increased slowly, the slow increase could still accurately explain clearance of yellow fever virus in the blood. Our additional mathematical model described well the kinetics of virus-specific antibody-secreting cell and antibody response to vaccinia virus in vaccinated individuals suggesting that most of antibodies in 3 months post immunization were derived from the population of circulating antibody-secreting cells. Taken together, our analysis provided novel insights into mechanisms by which live vaccines induce immunity to viral infections and highlighted challenges of applying methods of mathematical modeling to the current, state-of-the-art yet limited immunological data.
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Affiliation(s)
- Dustin Le
- Department of Microbiology, University of TennesseeKnoxville, TN, USA
| | - Joseph D. Miller
- Hope Clinic of the Emory Vaccine Center, Emory University School of MedicineAtlanta, GA, USA
| | - Vitaly V. Ganusov
- Department of Microbiology, University of TennesseeKnoxville, TN, USA
- Department of Mathematics, University of TennesseeKnoxville, TN, USA
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38
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Calis JJA, Rosenberg BR. Characterizing immune repertoires by high throughput sequencing: strategies and applications. Trends Immunol 2014; 35:581-590. [PMID: 25306219 PMCID: PMC4390416 DOI: 10.1016/j.it.2014.09.004] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 09/05/2014] [Accepted: 09/09/2014] [Indexed: 01/09/2023]
Abstract
As the key cellular effectors of adaptive immunity, T and B lymphocytes utilize specialized receptors to recognize, respond to, and neutralize a diverse array of extrinsic threats. These receptors (immunoglobulins in B lymphocytes, T cell receptors in T lymphocytes) are incredibly variable, the products of specialized genetic diversification mechanisms that generate complex lymphocyte repertoires with extensive collections of antigen specificities. Recent advances in high throughput sequencing (HTS) technologies have transformed our ability to examine antigen receptor repertoires at single nucleotide, and more recently, single cell, resolution. Here we review current approaches to examining antigen receptor repertoires by HTS, and discuss inherent biological and technical challenges. We further describe emerging applications of this powerful methodology for exploring the adaptive immune system.
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Affiliation(s)
| | - Brad R Rosenberg
- The Rockefeller University, New York, NY, USA; John C. Whitehead Presidential Fellows Program, The Rockefeller University, New York, NY, USA.
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39
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Chernova I, Jones DD, Wilmore JR, Bortnick A, Yucel M, Hershberg U, Allman D. Lasting antibody responses are mediated by a combination of newly formed and established bone marrow plasma cells drawn from clonally distinct precursors. THE JOURNAL OF IMMUNOLOGY 2014; 193:4971-9. [PMID: 25326027 DOI: 10.4049/jimmunol.1401264] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Current models hold that serum Ab titers are maintained chiefly by long-lived bone marrow (BM) plasma cells (PCs). In this study, we characterize the role of subpopulations of BM PCs in long-term humoral responses to T cell-dependent Ag. Surprisingly, our results indicate that 40-50% of BM PCs are recently formed cells, defined, in part, by rapid steady-state turnover kinetics and secretion of low-affinity IgM Abs. Further, for months after immunization with a hapten-protein conjugate, newly formed Ag-induced, IgM-secreting BM PCs were detected in parallel with longer-lived IgG-secreting cells, suggesting ongoing and parallel input to the BM PC pool from two distinct pools of activated B cells. Consistent with this interpretation, IgM and IgG Abs secreted by cells within distinct PC subsets exhibited distinct L chain usage. We conclude that long-term Ab responses are maintained by a dynamic BM PC pool composed of both recently formed and long-lived PCs drawn from clonally disparate precursors.
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Affiliation(s)
- Irene Chernova
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
| | - Derek D Jones
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
| | - Joel R Wilmore
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
| | - Alexandra Bortnick
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104
| | - Mesut Yucel
- Department of Bioengineering, Ege University, 35100, Izmir, Turkey; and
| | - Uri Hershberg
- School of Biomedical Engineering Science and Health Systems, Drexel University, Philadelphia, PA 19104
| | - David Allman
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104;
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40
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Conter LJ, Song E, Shlomchik MJ, Tomayko MM. CD73 expression is dynamically regulated in the germinal center and bone marrow plasma cells are diminished in its absence. PLoS One 2014; 9:e92009. [PMID: 24664100 PMCID: PMC3963874 DOI: 10.1371/journal.pone.0092009] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Accepted: 02/19/2014] [Indexed: 12/20/2022] Open
Abstract
CD73 catalyzes the conversion of extracellular nucleosides to adenosine, modulating inflammatory and T cell responses. Elevated expression of CD73 marks subpopulations of murine memory B cells (MBC), but its role in memory development or function is unknown. Here, we demonstrate that CD73 is progressively upregulated on germinal center (GC) B cells following immunization, is expressed at even higher levels among T follicular helper cells, but is absent among plasma cells (PC) and plasmablasts (PB). We analyzed the T-dependent B cell response in CD73 knockout mice (CD73KO). During the early response, CD73KO and wild type (WT) mice formed GCs, MBCs and splenic PBs and PCs similarly, and MBCs functioned similarly in the early secondary response. Late in the primary response, however, bone marrow (BM) PCs were markedly decreased in CD73KO animals. Tracking this phenotype, we found that CD73 expression was required on BM-derived cells for optimal BM PC responses. However, deletion of CD73 from either B or T lymphocytes alone did not recapitulate the phenotype. This suggests that CD73 expression is sufficient on either cell type, consistent with its function as an ectoenzyme. Together, these findings suggest that CD73-dependent adenosine signaling is prominent in the mature GC and required for establishment of the long-lived PC compartment, thus identifying a novel role for CD73 in humoral immunity.
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Affiliation(s)
- Laura J. Conter
- Department of Dermatology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Eunice Song
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Mark J. Shlomchik
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Mary M. Tomayko
- Department of Dermatology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- * E-mail:
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41
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Randall KL. Generating humoral immune memory following infection or vaccination. Expert Rev Vaccines 2014; 9:1083-93. [DOI: 10.1586/erv.10.103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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42
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Uduman M, Shlomchik MJ, Vigneault F, Church GM, Kleinstein SH. Integrating B cell lineage information into statistical tests for detecting selection in Ig sequences. THE JOURNAL OF IMMUNOLOGY 2013; 192:867-74. [PMID: 24376267 DOI: 10.4049/jimmunol.1301551] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Detecting selection in B cell Ig sequences is critical to understanding affinity maturation and can provide insights into Ag-driven selection in normal and pathologic immune responses. The most common sequence-based methods for detecting selection analyze the ratio of replacement and silent mutations using a binomial statistical analysis. However, these approaches have been criticized for low sensitivity. An alternative method is based on the analysis of lineage trees constructed from sets of clonally related Ig sequences. Several tree shape measures have been proposed as indicators of selection that can be statistically compared across cohorts. However, we show that tree shape analysis is confounded by underlying experimental factors that are difficult to control for in practice, including the sequencing depth and number of generations in each clone. Thus, although lineage tree shapes may reflect selection, their analysis alone is an unreliable measure of in vivo selection. To usefully capture the information provided by lineage trees, we propose a new method that applies the binomial statistical framework to mutations identified based on lineage tree structure. This hybrid method is able to detect selection with increased sensitivity in both simulated and experimental data sets. We anticipate that this approach will be especially useful in the analysis of large-scale Ig sequencing data sets generated by high-throughput sequencing technologies.
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Affiliation(s)
- Mohamed Uduman
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520
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43
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Six A, Mariotti-Ferrandiz ME, Chaara W, Magadan S, Pham HP, Lefranc MP, Mora T, Thomas-Vaslin V, Walczak AM, Boudinot P. The past, present, and future of immune repertoire biology - the rise of next-generation repertoire analysis. Front Immunol 2013; 4:413. [PMID: 24348479 PMCID: PMC3841818 DOI: 10.3389/fimmu.2013.00413] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 11/12/2013] [Indexed: 01/09/2023] Open
Abstract
T and B cell repertoires are collections of lymphocytes, each characterized by its antigen-specific receptor. We review here classical technologies and analysis strategies developed to assess immunoglobulin (IG) and T cell receptor (TR) repertoire diversity, and describe recent advances in the field. First, we describe the broad range of available methodological tools developed in the past decades, each of which answering different questions and showing complementarity for progressive identification of the level of repertoire alterations: global overview of the diversity by flow cytometry, IG repertoire descriptions at the protein level for the identification of IG reactivities, IG/TR CDR3 spectratyping strategies, and related molecular quantification or dynamics of T/B cell differentiation. Additionally, we introduce the recent technological advances in molecular biology tools allowing deeper analysis of IG/TR diversity by next-generation sequencing (NGS), offering systematic and comprehensive sequencing of IG/TR transcripts in a short amount of time. NGS provides several angles of analysis such as clonotype frequency, CDR3 diversity, CDR3 sequence analysis, V allele identification with a quantitative dimension, therefore requiring high-throughput analysis tools development. In this line, we discuss the recent efforts made for nomenclature standardization and ontology development. We then present the variety of available statistical analysis and modeling approaches developed with regards to the various levels of diversity analysis, and reveal the increasing sophistication of those modeling approaches. To conclude, we provide some examples of recent mathematical modeling strategies and perspectives that illustrate the active rise of a "next-generation" of repertoire analysis.
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Affiliation(s)
- Adrien Six
- UPMC University Paris 06, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; CNRS, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; AP-HP, Hôpital Pitié-Salpêtrière, CIC-BTi Biotherapy , Paris , France ; AP-HP, Hôpital Pitié-Salpêtrière, Département Hospitalo-Universitaire (DHU), Inflammation-Immunopathology-Biotherapy (i2B) , Paris , France
| | - Maria Encarnita Mariotti-Ferrandiz
- UPMC University Paris 06, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; CNRS, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; AP-HP, Hôpital Pitié-Salpêtrière, Département Hospitalo-Universitaire (DHU), Inflammation-Immunopathology-Biotherapy (i2B) , Paris , France
| | - Wahiba Chaara
- UPMC University Paris 06, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; CNRS, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; AP-HP, Hôpital Pitié-Salpêtrière, CIC-BTi Biotherapy , Paris , France ; AP-HP, Hôpital Pitié-Salpêtrière, Département Hospitalo-Universitaire (DHU), Inflammation-Immunopathology-Biotherapy (i2B) , Paris , France
| | - Susana Magadan
- Institut National de la Recherche Agronomique, Unité de Virologie et Immunologie Moléculaires , Jouy-en-Josas , France
| | - Hang-Phuong Pham
- UPMC University Paris 06, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; CNRS, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France
| | - Marie-Paule Lefranc
- IMGT®, The International ImMunoGeneTics Information System®, Institut de Génétique Humaine, UPR CNRS 1142, Université Montpellier 2 , Montpellier , France
| | - Thierry Mora
- Laboratoire de Physique Statistique, UMR8550, CNRS and Ecole Normale Supérieure , Paris , France
| | - Véronique Thomas-Vaslin
- UPMC University Paris 06, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; CNRS, UMR 7211, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (I3) , Paris , France ; AP-HP, Hôpital Pitié-Salpêtrière, Département Hospitalo-Universitaire (DHU), Inflammation-Immunopathology-Biotherapy (i2B) , Paris , France
| | - Aleksandra M Walczak
- Laboratoire de Physique Théorique, UMR8549, CNRS and Ecole Normale Supérieure , Paris , France
| | - Pierre Boudinot
- Institut National de la Recherche Agronomique, Unité de Virologie et Immunologie Moléculaires , Jouy-en-Josas , France
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44
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Schwartz GW, Hershberg U. Germline Amino Acid Diversity in B Cell Receptors is a Good Predictor of Somatic Selection Pressures. Front Immunol 2013; 4:357. [PMID: 24265630 PMCID: PMC3820969 DOI: 10.3389/fimmu.2013.00357] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Accepted: 10/21/2013] [Indexed: 11/13/2022] Open
Abstract
The diversity of the immune repertoire is important for the adaptive immune system’s ability to detect pathogens. Much of this diversity is generated in two steps, first through the recombination of germline gene segments and second through hypermutation during an immune response. While both steps are to some extent based on the germline level repertoire of genes, the final structure and selection of specific receptors is at the somatic level. How germline diversity and selection relate to somatic diversity and selection has not been clear. To investigate how germline diversity relates to somatic diversity and selection, we considered the published repertoire of Ig heavy chain V genes taken from the blood of 12 individuals, post-vaccination against influenza, sequenced by 454 high-throughput sequencing. We here show that when we consider individual amino acid positions in the heavy chain V gene sequence, there exists a strong correlation between the diversity of the germline repertoire at a position and the number of B cell clones that change amino acids at that position. At the same time, we find that the diversity of amino acids used in the mutated positions is greater than in the germline, albeit still correlated to germline diversity. From these findings, we propose that while germline diversity and germline amino acid usage at a given position do not fully specify the amino acid mutant needed to promote survival of specific clones, germline diversity at a given position is a good indicator for the potential to survive after somatic mutation at that position. We would therefore suggest that germline diversity at each specific position is the better a priori model for the effects of somatic mutation and selection, than simply the division into complementarity determining and framework regions.
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Affiliation(s)
- Gregory W Schwartz
- Systems Immunology Laboratory, School of Biomedical Engineering, Science, and Health Systems, Drexel University , Philadelphia, PA , USA
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45
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Liberman G, Benichou J, Tsaban L, Glanville J, Louzoun Y. Multi Step Selection in Ig H Chains is Initially Focused on CDR3 and Then on Other CDR Regions. Front Immunol 2013; 4:274. [PMID: 24062742 PMCID: PMC3775539 DOI: 10.3389/fimmu.2013.00274] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 08/28/2013] [Indexed: 11/13/2022] Open
Abstract
AFFINITY MATURATION OCCURS THROUGH TWO SELECTION PROCESSES the choice of appropriate clones (clonal selection), and the internal evolution within clones, induced by somatic hyper-mutations, where high affinity mutants are selected for. When a final population of immunoglobulin sequences is observed, the genetic composition of this population is affected by a combination of these two processes. Different immune induced diseases can result from the failure of regulation of clonal selection or of the regulation of the within clone affinity maturation. In order to understand each of these processes separately, we propose a mixed lineage tree/sequence based method to detect within clone selection as defined by the effect of mutations on the average number of offspring. Specifically, we measure the imbalance in the number of leaves in lineage trees branches following synonymous and non-synonymous (NS) mutations. If a mutation is positively selected, we expect the number of leaves in the sub-tree below this mutation to be larger than in the parallel sub-tree without the mutation. The ratio between the number of leaves in such branches following NS mutations can be used to measure selection within a clone. We apply this method to the sampled Ig repertoire from multiple healthy volunteers and show that within clone selection is positive in the CDR2 region and either positive or negative in the CDR3 and FWR3 regions. Selection occurs already at the IgM isotype level mainly in the DH gene region, with a strong negative selection in the join region. This is followed in the later memory stages in the CDR2 region. We have not studied here the FWR1 and CDR1 regions. An important advantage of this method is that it is very weakly affected by the baseline mutation model or by sampling biases, as are most synonymous to NS mutations ratio based methods.
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Affiliation(s)
- Gilad Liberman
- Gonda Multidisciplinary Brain Research Center, Bar-Ilan University , Ramat Gan , Israel
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46
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Strino F, Parisi F, Micsinai M, Kluger Y. TrAp: a tree approach for fingerprinting subclonal tumor composition. Nucleic Acids Res 2013; 41:e165. [PMID: 23892400 PMCID: PMC3783191 DOI: 10.1093/nar/gkt641] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Revealing the clonal composition of a single tumor is essential for identifying cell subpopulations with metastatic potential in primary tumors or with resistance to therapies in metastatic tumors. Sequencing technologies provide only an overview of the aggregate of numerous cells. Computational approaches to de-mix a collective signal composed of the aberrations of a mixed cell population of a tumor sample into its individual components are not available. We propose an evolutionary framework for deconvolving data from a single genome-wide experiment to infer the composition, abundance and evolutionary paths of the underlying cell subpopulations of a tumor. We have developed an algorithm (TrAp) for solving this mixture problem. In silico analyses show that TrAp correctly deconvolves mixed subpopulations when the number of subpopulations and the measurement errors are moderate. We demonstrate the applicability of the method using tumor karyotypes and somatic hypermutation data sets. We applied TrAp to Exome-Seq experiment of a renal cell carcinoma tumor sample and compared the mutational profile of the inferred subpopulations to the mutational profiles of single cells of the same tumor. Finally, we deconvolve sequencing data from eight acute myeloid leukemia patients and three distinct metastases of one melanoma patient to exhibit the evolutionary relationships of their subpopulations.
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Affiliation(s)
- Francesco Strino
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA, NYU Center for Health Informatics and Bioinformatics, New York University Langone Medical Center, 227 East 30th Street, New York, NY 10016, USA and Yale Cancer Center, New Haven, CT 06520, USA
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47
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Duke JL, Liu M, Yaari G, Khalil AM, Tomayko MM, Shlomchik MJ, Schatz DG, Kleinstein SH. Multiple transcription factor binding sites predict AID targeting in non-Ig genes. THE JOURNAL OF IMMUNOLOGY 2013; 190:3878-88. [PMID: 23514741 DOI: 10.4049/jimmunol.1202547] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Aberrant targeting of the enzyme activation-induced cytidine deaminase (AID) results in the accumulation of somatic mutations in ≈ 25% of expressed genes in germinal center B cells. Observations in Ung(-/-) Msh2(-/-) mice suggest that many other genes efficiently repair AID-induced lesions, so that up to 45% of genes may actually be targeted by AID. It is important to understand the mechanisms that recruit AID to certain genes, because this mistargeting represents an important risk for genome instability. We hypothesize that several mechanisms combine to target AID to each locus. To resolve which mechanisms affect AID targeting, we analyzed 7.3 Mb of sequence data, along with the regulatory context, from 83 genes in Ung(-/-) Msh2(-/-) mice to identify common properties of AID targets. This analysis identifies three transcription factor binding sites (E-box motifs, along with YY1 and C/EBP-β binding sites) that may work together to recruit AID. Based on previous knowledge and these newly discovered features, a classification tree model was built to predict genome-wide AID targeting. Using this predictive model, we were able to identify a set of 101 high-interest genes that are likely targets of AID.
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Affiliation(s)
- Jamie L Duke
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA
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48
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Wensveen FM, van Gisbergen KPJM, Eldering E. The fourth dimension in immunological space: how the struggle for nutrients selects high-affinity lymphocytes. Immunol Rev 2013; 249:84-103. [PMID: 22889217 DOI: 10.1111/j.1600-065x.2012.01156.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Lymphocyte activation via the antigen receptor is associated with radical shifts in metabolism and changes in requirements for nutrients and cytokines. Concomitantly, drastic changes occur in the expression of pro-and anti-apoptotic proteins that alter the sensitivity of lymphocytes to limiting concentrations of key survival factors. Antigen affinity is a primary determinant for the capacity of activated lymphocytes to access these vital resources. The shift in metabolic needs and the variable access to key survival factors is used by the immune system to eliminate activated low-affinity cells and to generate an optimal high-affinity response. In this review, we focus on the control of apoptosis regulators in activated lymphocytes by nutrients, cytokines, and costimulation. We propose that the struggle among individual clones that leads to the formation of high-affinity effector cell populations is in effect an 'invisible' fourth signal required for effective immune responses.
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Affiliation(s)
- Felix M Wensveen
- Department of Experimental Immunology, Academic Medical Center, Amsterdam, The Netherlands
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49
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Shlomchik MJ, Weisel F. Germinal center selection and the development of memory B and plasma cells. Immunol Rev 2012; 247:52-63. [PMID: 22500831 DOI: 10.1111/j.1600-065x.2012.01124.x] [Citation(s) in RCA: 308] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A hallmark of adaptive immune responses is the generation of long-lived protection after primary exposure to a pathogen. In humoral responses, this protection stems from a combination of sustained antibody titers and long-lived memory B cells (MBCs), with the former deriving from long-lived plasma cells (PCs). Both types of cell are thought to primarily derive from the germinal center (GC), a unique structure that forms during the immune response to many types of antigenic stimuli. GCs are seeded by antigen-specific B and T cells that were previously activated in the early stages of the response. The GC does not directly or immediately generate effector function; rather, it is a site of intense B-cell proliferation and cell death. GC B cells undergo both somatic hypermutation and isotype switch, and a Darwinian process very efficiently selects B cells with higher fitness for survival and expansion. GC B cells adopt a unique activation and transcriptional state, and the cells become poised to differentiate to either MBCs or PCs. Despite this general understanding of the events in the GC, the mechanisms that control both affinity selection as well as differentiation have not been well worked out. In this review, we address what is known about what determines whether GC B cells become MBCs or PCs. This is discussed in the broader context of the origins of both cell types, whether from the GC or potentially other sources. We present a model encompassing recent data from several laboratories including our own that suggests that the GC undergoes a temporal switch that alters the nature of its output from MBCs to PCs as the response progresses. We will discuss B-cell receptor signaling in the GC as it relates to potential mechanisms for affinity-based selection during the reaction.
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Affiliation(s)
- Mark J Shlomchik
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT 06520-8035, USA.
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Khalil AM, Cambier JC, Shlomchik MJ. B cell receptor signal transduction in the GC is short-circuited by high phosphatase activity. Science 2012; 336:1178-81. [PMID: 22555432 PMCID: PMC3777391 DOI: 10.1126/science.1213368] [Citation(s) in RCA: 208] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Germinal centers (GCs) generate memory B and plasma cells, which are essential for long-lived humoral immunity. GC B cells with high-affinity B cell receptors (BCRs) are selectively expanded. To enable this selection, BCRs of such cells are thought to signal differently from those with lower affinity. We show that, surprisingly, most proliferating GC B cells did not demonstrate active BCR signaling. Rather, spontaneous and induced signaling was limited by increased phosphatase activity. Accordingly, both SH2 domain-containing phosphatase-1 (SHP-1) and SH2 domain-containing inositol 5 phosphatase were hyperphosphorylated in GC cells and remained colocalized with BCRs after ligation. Furthermore, SHP-1 was required for GC maintenance. Intriguingly, GC B cells in the cell-cycle G(2) period regained responsiveness to BCR stimulation. These data have implications for how higher-affinity B cells are selected in the GC.
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Affiliation(s)
- Ashraf M Khalil
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
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