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Single-cell technologies for monitoring immune systems

Nature Immunology volume 15, pages 128–135 (2014)Cite this article

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Abstract

The complex heterogeneity of cells, and their interconnectedness with each other, are major challenges to identifying clinically relevant measurements that reflect the state and capability of the immune system. Highly multiplexed, single-cell technologies may be critical for identifying correlates of disease or immunological interventions as well as for elucidating the underlying mechanisms of immunity. Here we review limitations of bulk measurements and explore advances in single-cell technologies that overcome these problems by expanding the depth and breadth of functional and phenotypic analysis in space and time. The geometric increases in complexity of data make formidable hurdles for exploring, analyzing and presenting results. We summarize recent approaches to making such computations tractable and discuss challenges for integrating heterogeneous data obtained using these single-cell technologies.

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Figure 1: Evolving landscape of cellular traits.
Figure 2: Antibody staining in mass cytometry.
Figure 3: Classes of microtools for single-cell analysis.
Figure 4: Relative structure of data from single-cell analyses.
Figure 5

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Acknowledgements

This work was supported by the W.M. Keck Foundation and the US National Institute of Allergy And Infectious Diseases (1U19AI089992, 1R56AI104274 and 5R21AI106025). The content is solely the responsibility of the authors and does not necessarily represent the official views of the US National Institute of Allergy And Infectious Diseases or the US National Institutes of Health. We thank A. Shalek for helpful comments on scRNA-seq and N. Aghaeepour for discussions about data-analysis tools. J.C.L. is a Camille Dreyfus Teacher-Scholar. We acknowledge the service to the MIT community of the late Sean Collier.

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Authors and Affiliations

  1. ImmunoTechnology Section, Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, Maryland, USA

    Pratip K Chattopadhyay & Mario Roederer

  2. Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

    Todd M Gierahn & J Christopher Love

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Correspondence to J Christopher Love.

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Chattopadhyay, P., Gierahn, T., Roederer, M. et al. Single-cell technologies for monitoring immune systems. Nat Immunol 15, 128–135 (2014). https://doi.org/10.1038/ni.2796

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