Resource | Published:

Defining antigen-specific plasmablast and memory B cell subsets in human blood after viral infection or vaccination

Nature Immunology volume 17, pages 12261234 (2016) | Download Citation

Abstract

Antigen-specific B cells bifurcate into antibody-secreting cells (ASCs) and memory B cells (MBCs) after infection or vaccination. ASCs (plasmablasts) have been extensively studied in humans, but less is known about B cells that become activated but do not differentiate into plasmablasts. Here we have defined the phenotype and transcriptional program of a subset of antigen-specific B cells, which we have called 'activated B cells' (ABCs), that were distinct from ASCs and were committed to the MBC lineage. We detected ABCs in humans after infection with Ebola virus or influenza virus and also after vaccination. By simultaneously analyzing antigen-specific ASCs and ABCs in human blood after vaccination against influenza virus, we investigated the clonal overlap and extent of somatic hypermutation (SHM) in the ASC (effector) and ABC (memory) lineages. Longitudinal tracking of vaccination-induced hemagglutinin (HA)-specific clones revealed no overall increase in SHM over time, which suggested that repeated annual immunization might have limitations in enhancing the quality of influenza-virus-specific antibody.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Accessions

Primary accessions

Gene Expression Omnibus

Sequence Read Archive

References

  1. 1.

    & Memory B cells: effectors of long-lived immune responses. Eur. J. Immunol. 39, 2065–2075 (2009).

  2. 2.

    , , & Molecular programming of B cell memory. Nat. Rev. Immunol. 12, 24–34 (2011).

  3. 3.

    , & Gene regulatory networks in the immune system. Trends Immunol. 35, 211–218 (2014).

  4. 4.

    et al. Broadly cross-reactive antibodies dominate the human B cell response against 2009 pandemic H1N1 influenza virus infection. J. Exp. Med. 208, 181–193 (2011).

  5. 5.

    et al. Rapid and massive virus-specific plasmablast responses during acute dengue virus infection in humans. J. Virol. 86, 2911–2918 (2012).

  6. 6.

    et al. Rapid cloning of high-affinity human monoclonal antibodies against influenza virus. Nature 453, 667–671 (2008).

  7. 7.

    et al. A neutralizing antibody selected from plasma cells that binds to group 1 and group 2 influenza A hemagglutinins. Science 333, 850–856 (2011).

  8. 8.

    et al. Pandemic H1N1 influenza infection and vaccination in humans induces cross-protective antibodies that target the hemagglutinin stem. Front. Immunol. 3, 87 (2012).

  9. 9.

    & Tools to therapeutically harness the human antibody response. Nat. Rev. Immunol. 12, 709–719 (2012).

  10. 10.

    , , , & Clonal dissection of the human memory B-cell repertoire following infection and vaccination. Eur. J. Immunol. 39, 1260–1270 (2009).

  11. 11.

    et al. Secondary immunization generates clonally related antigen-specific plasma cells and memory B cells. J. Immunol. 185, 3103–3110 (2010).

  12. 12.

    & Genetic networks that regulate B lymphopoiesis. Curr. Opin. Hematol. 12, 203–209 (2005).

  13. 13.

    , , & Commitment to the B-lymphoid lineage depends on the transcription factor Pax5. Nature 401, 556–562 (1999).

  14. 14.

    & The transcriptional regulation of B cell lineage commitment. Immunity 26, 715–725 (2007).

  15. 15.

    et al. Regulation of bifurcating B cell trajectories by mutual antagonism between transcription factors IRF4 and IRF8. Nat. Immunol. 16, 1274–1281 (2015).

  16. 16.

    et al. Mucosal immune responses predict clinical outcomes during influenza infection independently of age and viral load. Am. J. Respir. Crit. Care Med. 189, 449–462 (2014).

  17. 17.

    et al. Pandemic H1N1 influenza vaccine induces a recall response in humans that favors broadly cross-reactive memory B cells. Proc. Natl. Acad. Sci. USA 109, 9047–9052 (2012).

  18. 18.

    et al. Clinical care of two patients with Ebola virus disease in the United States. N. Engl. J. Med. 371, 2402–2409 (2014).

  19. 19.

    et al. Human Ebola virus infection results in substantial immune activation. Proc. Natl. Acad. Sci. USA 112, 4719–4724 (2015).

  20. 20.

    et al. Molecular signatures of antibody responses derived from a systems biology study of five human vaccines. Nat. Immunol. 15, 195–204 (2014).

  21. 21.

    et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102, 15545–15550 (2005).

  22. 22.

    , & Duration of humoral immunity to common viral and vaccine antigens. N. Engl. J. Med. 357, 1903–1915 (2007).

  23. 23.

    et al. Cutting edge: long-term B cell memory in humans after smallpox vaccination. J. Immunol. 171, 4969–4973 (2003).

  24. 24.

    , , , & Memory B cells, but not long-lived plasma cells, possess antigen specificities for viral escape mutants. J. Exp. Med. 208, 2599–2606 (2011).

  25. 25.

    , , , & Generation of memory B cells inside and outside germinal centers. Eur. J. Immunol. 44, 1258–1264 (2014).

  26. 26.

    et al. Generation of migratory antigen-specific plasma blasts and mobilization of resident plasma cells in a secondary immune response. Blood 105, 1614–1621 (2005).

  27. 27.

    & Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics 22, 1540–1542 (2006).

  28. 28.

    et al. Systems biology of vaccination for seasonal influenza in humans. Nat. Immunol. 12, 786–795 (2011).

  29. 29.

    et al. A travel guide to Cytoscape plugins. Nat. Methods 9, 1069–1076 (2012).

  30. 30.

    & FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957–2963 (2011).

  31. 31.

    , , & IgBLAST: an immunoglobulin variable domain sequence analysis tool. Nucleic Acids Res. 41, W34–W40 (2013).

  32. 32.

    et al. Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639–1645 (2009).

Download references

Acknowledgements

We thank R. Karaffa and S. Durham for technical assistance. Supported by the National Institute of Allergy and Infectious Diseases of the US National Institutes of Health (HHSN266200700006C, 1P01AI097092 and U19AI117891 to R.A.; T32AI074492 to A.E.; and U19AI09525801, UM1AI100663 and U01AI104342 to S.D.B.), Advanced Immunization Technologies (280873), the European Union (R.A.), the National Center for Advancing Translational Sciences (UL1TR000454 to A.K.M.) and The National Council for Scientific and Technological Development of Brazil (H.I.N.). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institute of Allergy and Infectious Diseases or the National Institutes of Health or that of the Centers for Disease Control and Prevention.

Author information

Author notes

    • Ali H Ellebedy
    • , Katherine J L Jackson
    • , Scott D Boyd
    •  & Rafi Ahmed

    These authors contributed equally to this work.

Affiliations

  1. Emory Vaccine Center, School of Medicine, Emory University, Atlanta, Georgia, USA.

    • Ali H Ellebedy
    • , Carl W Davis
    •  & Rafi Ahmed
  2. Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, Georgia, USA.

    • Ali H Ellebedy
    • , Haydn T Kissick
    • , Carl W Davis
    •  & Rafi Ahmed
  3. Department of Pathology, Stanford University, Stanford, California, USA.

    • Katherine J L Jackson
    • , Krishna M Roskin
    •  & Scott D Boyd
  4. Department of Urology, School of Medicine, Emory University, Atlanta, Georgia, USA.

    • Haydn T Kissick
  5. Department of Pathology, School of Medicine, Emory University, Atlanta, Georgia, USA.

    • Helder I Nakaya
  6. Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo, Brazil.

    • Helder I Nakaya
  7. Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA.

    • Anita K McElroy
  8. Viral Special Pathogens Branch, US Centers for Disease Control and Prevention, Atlanta, Georgia, USA.

    • Anita K McElroy
    •  & Christina F Spiropoulou
  9. Department of Immunology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.

    • Christine M Oshansky
    •  & Paul G Thomas
  10. Division of Infectious Diseases, School of Medicine, Emory University, Atlanta, Georgia, USA.

    • Rivka Elbein
    • , Shine Thomas
    • , George M Lyon
    •  & Aneesh K Mehta

Authors

  1. Search for Ali H Ellebedy in:

  2. Search for Katherine J L Jackson in:

  3. Search for Haydn T Kissick in:

  4. Search for Helder I Nakaya in:

  5. Search for Carl W Davis in:

  6. Search for Krishna M Roskin in:

  7. Search for Anita K McElroy in:

  8. Search for Christine M Oshansky in:

  9. Search for Rivka Elbein in:

  10. Search for Shine Thomas in:

  11. Search for George M Lyon in:

  12. Search for Christina F Spiropoulou in:

  13. Search for Aneesh K Mehta in:

  14. Search for Paul G Thomas in:

  15. Search for Scott D Boyd in:

  16. Search for Rafi Ahmed in:

Contributions

A.H.E., K.J.L.J., S.D.B. and R.A. designed the study, interpreted data and wrote the paper; A.H.E. performed most of the experiments; K.J.L.J. performed next-generation sequencing of the IGH repertoire and devised, undertook and interpreted repertoire-data analysis; H.T.K. and H.I.N. analyzed the microarray data; C.W.D. and A.K.M. helped in data analysis and interpretation; K.M.R. processed repertoire-sequence data; and C.M.O., R.E., S.T., G.M.L., C.F.S., A.K.M. and P.G.T. helped in collecting and processing the clinical samples.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Scott D Boyd or Rafi Ahmed.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–7 and Supplementary Table 2

Excel files

  1. 1.

    Supplementary Table 1

    192 genes that were differentially upregulated in the ABC subset

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/ni.3533

Further reading