Abstract

B-cell responses result in clonal expansion, and can occur in a variety of tissues. To define how B-cell clones are distributed in the body, we sequenced 933,427 B-cell clonal lineages and mapped them to eight different anatomic compartments in six human organ donors. We show that large B-cell clones partition into two broad networks—one spans the blood, bone marrow, spleen and lung, while the other is restricted to tissues within the gastrointestinal (GI) tract (jejunum, ileum and colon). Notably, GI tract clones display extensive sharing of sequence variants among different portions of the tract and have higher frequencies of somatic hypermutation, suggesting extensive and serial rounds of clonal expansion and selection. Our findings provide an anatomic atlas of B-cell clonal lineages, their properties and tissue connections. This resource serves as a foundation for studies of tissue-based immunity, including vaccine responses, infections, autoimmunity and cancer.

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

Sequence Read Archive

References

  1. 1.

    et al. Generation of antibody diversity in the immune response of BALB/c mice to influenza virus hemagglutinin. Proc. Natl. Acad. Sci. USA 81, 3180–3184 (1984).

  2. 2.

    , & Maturation of the immune response in germinal centers. Cell 67, 1121–1129 (1991).

  3. 3.

    , , & Variability in the lambda light chain sequences of mouse antibody. Nature 228, 1045–1047 (1970).

  4. 4.

    , , & Intraclonal generation of antibody mutants in germinal centres. Nature 354, 389–392 (1991).

  5. 5.

    & Antibody production by single cells. Nature 181, 1419–1420 (1958).

  6. 6.

    & Structure and function of immunoglobulins. J. Allergy Clin. Immunol. 125 (Suppl. 2), S41–S52 (2010).

  7. 7.

    , & B-1 cells and their reactivity with the murine intestinal microflora. Semin. Immunol. 8, 11–18 (1996).

  8. 8.

    et al. Diversification of memory B cells drives the continuous adaptation of secretory antibodies to gut microbiota. Nat. Immunol. 16, 880–888 (2015).

  9. 9.

    , , , & Role of commensal bacteria in development of gut-associated lymphoid tissues and preimmune antibody repertoire. J. Immunol. 172, 1118–1124 (2004).

  10. 10.

    et al. Differences in mouse and human nonmemory B cell pools. J. Immunol. 192, 4610–4619 (2014).

  11. 11.

    Human spleen microanatomy: why mice do not suffice. Immunology 145, 334–346 (2015).

  12. 12.

    et al. Spatial map of human T cell compartmentalization and maintenance over decades of life. Cell 159, 814–828 (2014).

  13. 13.

    et al. Distribution and compartmentalization of human circulating and tissue-resident memory T cell subsets. Immunity 38, 187–197 (2013).

  14. 14.

    et al. Early-life compartmentalization of human T cell differentiation and regulatory function in mucosal and lymphoid tissues. Nat. Med. 22, 72–77 (2016).

  15. 15.

    , , & Improved detection of diffuse large B-cell lymphoma by flow cytometric immunophenotyping-Effect of tissue disaggregation method. Cytometry B Clin. Cytom. 90, 455–461 (2016).

  16. 16.

    , , & Identification and nucleotide sequence of a diversity DNA segment (D) of immunoglobulin heavy-chain genes. Nature 290, 562–565 (1981).

  17. 17.

    et al. Precise determination of the diversity of a combinatorial antibody library gives insight into the human immunoglobulin repertoire. Proc. Natl. Acad. Sci. USA 106, 20216–20221 (2009).

  18. 18.

    , , & Discrimination of germline V genes at different sequencing lengths and mutational burdens: A new tool for identifying and evaluating the reliability of V gene assignment. J. Immunol. Methods 427, 105–116 (2015).

  19. 19.

    & The analysis of clonal expansions in normal and autoimmune B cell repertoires. Phil. Trans. R. Soc. Lond. B 370, 20140239 (2015).

  20. 20.

    & Practical guidelines for B-cell receptor repertoire sequencing analysis. Genome Med. 7, 121 (2015).

  21. 21.

    et al. Models and estimators linking individual-based and sample based rarefaction, extrapolation and comparison of assemblages. J. Plant Ecol. 5, 3–21 (2012).

  22. 22.

    , & Precursors to lymphoproliferative malignancies. Cancer Epidemiol. Biomarkers Prev. 22, 533–539 (2013).

  23. 23.

    , , & ImmuneDB: a system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data. Bioinformatics 33, 292–293 (2017).

  24. 24.

    , & Clearcut: a fast implementation of relaxed neighbor joining. Bioinformatics 22, 2823–2824 (2006).

  25. 25.

    , , & Using a novel clumpiness measure to unite data with metadata: Finding common sequence patterns in immune receptor germline V genes. Pattern Recognit. Lett. 74, 24–29 (2016).

  26. 26.

    et al. Evidence for local expansion of IgA plasma cell precursors in human ileum. J. Immunol. 183, 4871–4878 (2009).

  27. 27.

    & The route of re-circulation of lymphocytes in the rat. Proc. R. Soc. Lond. B Biol. Sci. 159, 257–282 (1964).

  28. 28.

    & Evidence for a common mucosal immunologic system. I. Migration of B immunoblasts into intestinal, respiratory, and genital tissues. J. Immunol. 122, 1892–1898 (1979).

  29. 29.

    , , & Somatic diversification of immunoglobulins. Proc. Natl. Acad. Sci. USA 81, 2162–2166 (1984).

  30. 30.

    , & Somatic mutation and clonal expansion of B cells in an antigen-driven immune response. EMBO J. 4, 345–350 (1985).

  31. 31.

    , , , & Tissue-specific expressed antibody variable gene repertoires. PLoS One 9, e100839 (2014).

  32. 32.

    , & Generation of immunoglobulin diversity in human gut-associated lymphoid tissue. Semin. Immunol. 21, 139–146 (2009).

  33. 33.

    , & Sequence analysis of human IgVH genes indicates that ileal lamina propria plasma cells are derived from Peyer's patches. Eur. J. Immunol. 27, 463–467 (1997).

  34. 34.

    et al. Detecting selection in immunoglobulin sequences. Nucleic Acids Res. 39, W499–W504 (2011).

  35. 35.

    , , & Improved methods for detecting selection by mutation analysis of Ig V region sequences. Int. Immunol. 20, 683–694 (2008).

  36. 36.

    , & IgA and IgM V(H) repertoires in human colon: evidence for clonally expanded B cells that are widely disseminated. Gastroenterology 119, 1253–1266 (2000).

  37. 37.

    et al. Generation of colonic IgA-secreting cells in the caecal patch. Nat. Commun. 5, 3704 (2014).

  38. 38.

    et al. Circulating human CD27-IgA+ memory B cells recognize bacteria with polyreactive Igs. J. Immunol. 195, 1417–1426 (2015).

  39. 39.

    et al. Accurate and predictive antibody repertoire profiling by molecular amplification fingerprinting. Sci. Adv. 2, e1501371 (2016).

  40. 40.

    et al. Hierarchical clustering can identify B cell clones with high confidence in ig repertoire sequencing data. J. Immunol. 198, 2489–2499 (2017).

  41. 41.

    & Likelihood-based inference of B cell clonal families. PLoS Comput. Biol. 12, e1005086 (2016).

  42. 42.

    et al. Design and standardization of PCR primers and protocols for detection of clonal immunoglobulin and T-cell receptor gene recombinations in suspect lymphoproliferations: report of the BIOMED-2 Concerted Action BMH4-CT98-3936. Leukemia 17, 2257–2317 (2003).

  43. 43.

    et al. Trials and tribulations with VH replacement. Front. Immunol. 5, 10 (2014).

  44. 44.

    et al. pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires. Bioinformatics 30, 1930–1932 (2014).

  45. 45.

    et al. Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform. Nucleic Acids Res. 43, e37 (2015).

  46. 46.

    & Germline amino acid diversity in B cell receptors is a good predictor of somatic selection pressures. Front. Immunol. 4, 357 (2013).

  47. 47.

    & Conserved variation: identifying patterns of stability and variability in BCR and TCR V genes with different diversity and richness metrics. Phys. Biol. 10, 035005 (2013).

  48. 48.

    et al. MiXCR: software for comprehensive adaptive immunity profiling. Nat. Methods 12, 380–381 (2015).

  49. 49.

    et al. VDJtools: unifying post-analysis of T cell receptor repertoires. PLoS Comput. Biol. 11, e1004503 (2015).

Download references

Acknowledgements

We thank the Human Immunology Core facility at the University of Pennsylvania for assistance with cell preparations and sequencing support. We thank Y. Louzoun, M. Cancro and R. Thomas Jr. for discussions. We thank the organ donor families and the LiveOnNY transplant staff and coordinators. This work was supported by NIH P01 AI106697 (D.L.F., U.H., M.J.S., W.M., B.Z., A.M.R., D.R., D.J.C., N.M., T.G. and E.T.L.P.), P30-CA016520 (E.T.L.P.) and F31AG047003 (J.J.C.T.). G.W.S. was funded by the US Department of Education Graduate Assistance in Areas of National Need (GAANN) program, CFDA Number: 84.200.

Author information

Author notes

    • Wenzhao Meng
    •  & Bochao Zhang

    These authors have contributed equally to this work.

Affiliations

  1. Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

    • Wenzhao Meng
    • , Daqiu Ren
    •  & Eline T Luning Prak
  2. School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, Pennsylvania, USA.

    • Bochao Zhang
    • , Gregory W Schwartz
    • , Aaron M Rosenfeld
    •  & Uri Hershberg
  3. Columbia Center for Translational Immunology, Columbia University Medical Center, New York, New York, USA.

    • Joseph J C Thome
    • , Dustin J Carpenter
    • , Nobuhide Matsuoka
    • , Tomer Granot
    •  & Donna L Farber
  4. LiveOnNY, New York, New York, USA.

    • Harvey Lerner
    •  & Amy L Friedman
  5. Department of Surgery and Department of Microbiology and Immunology, Columbia University School of Medicine, New York, New York, USA.

    • Donna L Farber
  6. Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.

    • Mark J Shlomchik
  7. Department of Microbiology and Immunology, Drexel College of Medicine, Drexel University, Philadelphia, Pennsylvania, USA.

    • Uri Hershberg

Authors

  1. Search for Wenzhao Meng in:

  2. Search for Bochao Zhang in:

  3. Search for Gregory W Schwartz in:

  4. Search for Aaron M Rosenfeld in:

  5. Search for Daqiu Ren in:

  6. Search for Joseph J C Thome in:

  7. Search for Dustin J Carpenter in:

  8. Search for Nobuhide Matsuoka in:

  9. Search for Harvey Lerner in:

  10. Search for Amy L Friedman in:

  11. Search for Tomer Granot in:

  12. Search for Donna L Farber in:

  13. Search for Mark J Shlomchik in:

  14. Search for Uri Hershberg in:

  15. Search for Eline T Luning Prak in:

Contributions

W.M. designed and performed experiments, developed methods, analyzed data, prepared figures and helped write the manuscript. B.Z., G.W.S. and A.M.R. developed methods for data analysis and visualization, analyzed data, prepared figures and helped revise the manuscript. D.R. performed experiments and helped revise the manuscript. J.J.C.T., D.J.C., N.M., H.L., A.L.F. and T.G. were involved in donor recruitment, organ recovery and helped revise the manuscript. D.L.F. directs the organ donor tissue resource for acquisition of tissues and helped write the manuscript. M.J.S. designed experiments, contributed ideas and helped write the manuscript. E.T.L.P. and U.H. planned the study. U.H. developed methods for data analysis and visualization, designed the data analysis and helped write the manuscript. E.T.L.P. designed experiments, contributed ideas to the data analysis, oversaw the overall study and wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Uri Hershberg or Eline T Luning Prak.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–11 and Supplementary Tables 1 and 2

  2. 2.

    Life Sciences Reporting Summary

Text files

  1. 1.

    Supplementary Table 3

  2. 2.

    Supplementary Table 4

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/nbt.3942

Further reading