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A guide to systems-level immunomics

Nature Immunology volume 23, pages 1412–1423 (2022)Cite this article

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Abstract

The immune system is highly complex and distributed throughout an organism, with hundreds to thousands of cell states existing in parallel with diverse molecular pathways interacting in a highly dynamic and coordinated fashion. Although the characterization of individual genes and molecules is of the utmost importance for understanding immune-system function, high-throughput, high-resolution omics technologies combined with sophisticated computational modeling and machine-learning approaches are creating opportunities to complement standard immunological methods with new insights into immune-system dynamics. Like systems immunology itself, immunology researchers must take advantage of these technologies and form their own diverse networks, connecting with researchers from other disciplines. This Review is an introduction and ‘how-to guide’ for immunologists with no particular experience in the field of omics but with the intention to learn about and apply these systems-level approaches, and for immunologists who want to make the most of interdisciplinary networks.

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Fig. 1: Milestone methods in immunology.
Fig. 2: ‘How to’ in immunomics.
Fig. 3: Experimental and analytical plan.

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Acknowledgements

J.L.S. is supported by the German Research Foundation (DFG) under Germany’s Excellence Strategy (EXC2151-390873048), as well as under SCHU 950/8-1; GRK 2168, TP11; SFB704, the BMBF-funded excellence project Diet–Body–Brain (DietBB); and the EU project SYSCID under grant number 733100. A.C.A. is supported by DFG under AS 637/1-1; AS 637/2-1; AS 637/3-1 and SFB1454/P02 (project no. 432325352). M.B. is supported by DFG (IRTG2168-272482170, SFB1454-432325352).

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Author notes

  1. These authors contributed equally: Lorenzo Bonaguro, Jonas Schulte-Schrepping, Thomas Ulas.

Authors and Affiliations

  1. Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany

    Lorenzo Bonaguro, Jonas Schulte-Schrepping, Thomas Ulas, Anna C. Aschenbrenner, Marc Beyer & Joachim L. Schultze

  2. PRECISE Platform for Single Cell Genomics and Epigenomics, DZNE and University of Bonn, Bonn, Germany

    Lorenzo Bonaguro, Jonas Schulte-Schrepping, Thomas Ulas, Anna C. Aschenbrenner, Marc Beyer & Joachim L. Schultze

  3. Genomics & Immunoregulation, LIMES Institute, University of Bonn, Bonn, Germany

    Lorenzo Bonaguro, Jonas Schulte-Schrepping, Thomas Ulas & Joachim L. Schultze

  4. Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands

    Anna C. Aschenbrenner

  5. Immunogenomics & Neurodegeneration, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany

    Marc Beyer

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  1. Lorenzo Bonaguro
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Contributions

L.B., J.S.-S. and J.L.S. developed the concept. L.B., J.S.-S., T.U., M.B., A.C.A. and J.L.S. discussed the concept. L.B. and J.L.S. designed the figures. L.B., J.S.-S., T.U., M.B. and J.L.S. wrote the original draft. L.B., J.S.-S., T.U., M.B., A.C.A. and J.L.S. reviewed and edited the manuscript.

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Correspondence to Joachim L. Schultze.

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Nature Immunology thanks Uri Hershberg and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. N. Bernard was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

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Bonaguro, L., Schulte-Schrepping, J., Ulas, T. et al. A guide to systems-level immunomics. Nat Immunol 23, 1412–1423 (2022). https://doi.org/10.1038/s41590-022-01309-9

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