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The cellular composition of the human immune system is shaped by age and cohabitation

Nature Immunology volume 17, pages 461468 (2016) | Download Citation

Abstract

Detailed population-level description of the human immune system has recently become achievable. We used a 'systems-level' approach to establish a resource of cellular immune profiles of 670 healthy individuals. We report a high level of interindividual variation, with low longitudinal variation, at the level of cellular subset composition of the immune system. Despite the profound effects of antigen exposure on individual antigen-specific clones, the cellular subset structure proved highly elastic, with transient vaccination-induced changes followed by a return to the individual's unique baseline. Notably, the largest influence on immunological variation identified was cohabitation, with 50% less immunological variation between individuals who share an environment (as parents) than between people in the wider population. These results identify local environmental conditions as a key factor in shaping the human immune system.

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Acknowledgements

We thank all volunteers for their participation; the Cambridge BioResource staff for help with volunteer recruitment; members of the Cambridge BioResource SAB and Management Committee for support of this study; and A. Nuygen, D. Franckaert, D. Danso-Abeam and L. Van Eyck (KUL-VIB) for technical assistance. Supported by the National Institute for Health Research Cambridge Biomedical Research Centre; the European Research Council (Start Grant IMMUNO to A.L. and Start Grant TWILIGHT to M.A.L.). the NIHR (E.J.C.), the Biotechnology and Biological Sciences Research Council (M.A.L.), Research Fund KU Leuven (OT/11/087 to A.G.), Research Foundation Flanders (G073415N to A.G.) and the Wellcome Trust (105920/Z/14/Z to J.C.L.).

Author information

Author notes

    • Edward J Carr
    •  & James Dooley

    These authors contributed equally to this work.

    • Michelle A Linterman
    •  & Adrian Liston

    These authors jointly directed this work.

Affiliations

  1. Lymphocyte Signaling and Development ISP, Babraham Institute, Cambridge, UK.

    • Edward J Carr
    •  & Michelle A Linterman
  2. Translational Immunology Laboratory, VIB, Leuven, Belgium.

    • James Dooley
    • , Josselyn E Garcia-Perez
    • , Vasiliki Lagou
    •  & Adrian Liston
  3. Department of Microbiology and Immunology, University of Leuven, Leuven, Belgium.

    • James Dooley
    • , Josselyn E Garcia-Perez
    • , Vasiliki Lagou
    • , Carine Wouters
    • , Isabelle Meyts
    •  & Adrian Liston
  4. Department of Neurosciences, University of Leuven, Leuven, Belgium.

    • Vasiliki Lagou
    •  & An Goris
  5. Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.

    • James C Lee
  6. Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK.

    • James C Lee
  7. Department of Experimental Medicine, University of Leuven, Leuven, Belgium.

    • Guy Boeckxstaens

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Contributions

E.J.C. analyzed the data and drafted the manuscript. J.D. and J.E.G.-P. performed the experiments. V.L. analysed the vaccination cohort. J.C.L., C.W., I.M., A.N. and G.B. designed and recruited subcohorts. M.A.L. designed and supervised the vaccination study, contributed to the data analysis and the manuscript. A.L. designed and supervised the study and drafted the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Adrian Liston.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Tables and Figures

    Supplementary Figures 1–8 and Supplementary Tables 1 and 3

  2. 2.

    Supplementary Code 1: Code for resource data set

    R-compatible code for analysis of Belgian cohort (PDF format).

  3. 3.

    Supplementary Code 2: Code for vaccination data set

    R-compatible code for analysis of UK vaccination subcohort (PDF format)

Excel files

  1. 1.

    Supplementary Table 2: Immune parameter definitions and summary statistics.

    Definitions and characterization for each immune parameter. Summary statistics for each immune parameter (R2 values, P values, 95% confidence intervals).

  2. 2.

    Supplementary Data Set 1: Resource data set

    Raw data for Belgian cohort (Excel format).

  3. 3.

    Supplementary Data Set 2: Vaccination data set

    Raw data for UK vaccination subcohort (Excel format).

Zip files

  1. 1.

    Supplementary Data Set 3: Resource data set

    Raw data for Belgian cohort (RData format).

  2. 2.

    Supplementary Data Set 4: Vaccination data set

    Raw data for UK vaccination subcohort (RData format).

  3. 3.

    Supplementary Code 3: Code for resource data set

    R-compatible code for analysis of Belgian cohort (Rmd format).

  4. 4.

    Supplementary Code 4: Code for vaccination data set

    R-compatible code for analysis of UK vaccination subcohort (Rmd format).

About this article

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DOI

https://doi.org/10.1038/ni.3371

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