Distinct mechanisms define murine B cell lineage immunoglobulin heavy chain (IgH) repertoires

  1. Yang Yang  Is a corresponding author
  2. Chunlin Wang
  3. Qunying Yang
  4. Aaron B Kantor
  5. Hiutung Chu
  6. Eliver EB Ghosn
  7. Guang Qin
  8. Sarkis K Mazmanian
  9. Jian Han
  10. Leonore A Herzenberg
  1. Stanford University, United States
  2. HudsonAlpha Institute for Biotechnology, United States
  3. California Institute of Technology, United States

Abstract

Processes that define immunoglobulin repertoires are commonly presumed to be the same for all murine B cells. However, studies here that couple high-dimensional FACS sorting with large-scale quantitative IgH deep-sequencing demonstrate that B-1a IgH repertoire differs dramatically from the follicular and marginal zone B cells repertoires and is defined by distinct mechanisms. We track B-1a cells from their early appearance in neonatal spleen to their long-term residence in adult peritoneum and spleen. We show that de novo B-1a IgH rearrangement mainly occurs during the first few weeks of life, after which their repertoire continues to evolve profoundly, including convergent selection of certain V(D)J rearrangements encoding specific CDR3 peptides in all adults and progressive introduction of hypermutation and class-switching as animals age. This V(D)J selection and AID-mediated diversification operate comparably in germ-free and conventional mice, indicating these unique B-1a repertoire-defining mechanisms are driven by antigens that are not derived from microbiota.

Article and author information

Author details

  1. Yang Yang

    Genetics Department, Stanford University, Stanford, United States
    For correspondence
    yang71@stanford.edu
    Competing interests
    No competing interests declared.
  2. Chunlin Wang

    HudsonAlpha Institute for Biotechnology, Huntsville, United States
    Competing interests
    Chunlin Wang, founder of iRepertoire.
  3. Qunying Yang

    HudsonAlpha Institute for Biotechnology, Huntsville, United States
    Competing interests
    No competing interests declared.
  4. Aaron B Kantor

    Genetics Department, Stanford University, Stanford, United States
    Competing interests
    No competing interests declared.
  5. Hiutung Chu

    Biology and Biological Engineering Department, California Institute of Technology, Pasadena, United States
    Competing interests
    No competing interests declared.
  6. Eliver EB Ghosn

    Genetics Department, Stanford University, Stanford, United States
    Competing interests
    No competing interests declared.
  7. Guang Qin

    Genetics Department, Stanford University, Stanford, United States
    Competing interests
    No competing interests declared.
  8. Sarkis K Mazmanian

    Biology and Biological Engineering Department, California Institute of Technology, Pasadena, United States
    Competing interests
    No competing interests declared.
  9. Jian Han

    HudsonAlpha Institute for Biotechnology, Huntsville, United States
    Competing interests
    Jian Han, founder of iRepertoire.
  10. Leonore A Herzenberg

    Genetics Department, Stanford University, Stanford, United States
    Competing interests
    No competing interests declared.

Copyright

© 2015, Yang et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 4,214
    views
  • 1,197
    downloads
  • 112
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Yang Yang
  2. Chunlin Wang
  3. Qunying Yang
  4. Aaron B Kantor
  5. Hiutung Chu
  6. Eliver EB Ghosn
  7. Guang Qin
  8. Sarkis K Mazmanian
  9. Jian Han
  10. Leonore A Herzenberg
(2015)
Distinct mechanisms define murine B cell lineage immunoglobulin heavy chain (IgH) repertoires
eLife 4:e09083.
https://doi.org/10.7554/eLife.09083

Share this article

https://doi.org/10.7554/eLife.09083

Further reading

    1. Cell Biology
    2. Immunology and Inflammation
    Richard A Kahn, Harvinder Virk ... Skye Longworth
    Feature Article

    Antibodies are used in many areas of biomedical and clinical research, but many of these antibodies have not been adequately characterized, which casts doubt on the results reported in many scientific papers. This problem is compounded by a lack of suitable control experiments in many studies. In this article we review the history of the ‘antibody characterization crisis’, and we document efforts and initiatives to address the problem, notably for antibodies that target human proteins. We also present recommendations for a range of stakeholders – researchers, universities, journals, antibody vendors and repositories, scientific societies and funders – to increase the reproducibility of studies that rely on antibodies.

    1. Cancer Biology
    2. Cell Biology
    Francesca Butera, Julia E Sero ... Chris Bakal
    Research Article

    The canonical NF-κB transcription factor RELA is a master regulator of immune and stress responses and is upregulated in PDAC tumours. In this study, we characterised previously unexplored endogenous RELA-GFP dynamics in PDAC cell lines through live single cell imaging. Our observations revealed that TNFα stimulation induces rapid, sustained, and non-oscillatory nuclear translocation of RELA. Through Bayesian analysis of single cell datasets with variation in nuclear RELA, we predicted that RELA heterogeneity in PDAC cell lines is dependent on F-actin dynamics. RNA-seq analysis identified distinct clusters of RELA-regulated gene expression in PDAC cells, including TNFα-induced RELA upregulation of the actin regulators NUAK2 and ARHGAP31. Further, siRNA-mediated depletion of ARHGAP31 and NUAK2 altered TNFα-stimulated nuclear RELA dynamics in PDAC cells, establishing a novel negative feedback loop that regulates RELA activation by TNFα. Additionally, we characterised the NF-κB pathway in PDAC cells, identifying how NF-κB/IκB proteins genetically and physically interact with RELA in the absence or presence of TNFα. Taken together, we provide computational and experimental support for interdependence between the F-actin network and the NF-κB pathway with RELA translocation dynamics in PDAC.