Cancer Genome Atlas ( 62) (http://cancergenome.
nih.gov/), they reveal dependencies between
different cell types and the molecules that may
mediate them: for example, the correlation between high levels of CD8+ T cells in a tumor and
the expression of complement proteins by its
CAFs ( 42).
Another study analyzed splenic CD4+ T cells,
monocytes, and DCs in the mouse response to
malaria ( 53), comparing uninfected mice to mice
at day 3 postinfection. Integrated analyses of the
changes in expression of chemokine ligands and
receptors across these populations predicted that
monocytes would support the differentiation of
activated CD4+ T cells toward a TH1 fate rather
than the alternative TFH fate. This was confirmed
in an experiment in which monocytes were depleted during T cell activation and before fate
Both studies inferred processes of intercellular
communication from the expression of cognate
receptors, co-receptors, and/or ligands in scRNA-seq data. Systematic and generalizable approaches
for such connections, and relating them to co-variation in cell proportions and states, will be
of great value. Furthermore, it is clear that methods that analyze single-cell gene expression in a
spatially resolved context will be very important
to understanding the interactions between cells
of the immune system. Indeed, imaging mass
cytometry has identified the presence of immune
cells within the spatial context of breast cancer
Future applications in immunity
The immune system is composed of numerous
cell types that work in concert to sense and appropriately respond to foreign challenges and
physiological changes in order to monitor and
maintain health. If the carefully orchestrated
functioning of the immune system is perturbed,
diseases such as infectious disease, autoimmune
disease, and cancer can arise.
The rich taxonomies and cell fate maps generated in immunology over the past several
decades relate cells by cellular function, differentiation potential, and expression of marker proteins. However, to date there is still no complete
reference map of immune cells. The additional
comprehensive profiles produced by single-cell
genomic approaches provide an important new
tool in this endeavor by helping to address some
of the fundamental questions in immunology—
from the taxonomy of cells, histological structure
in tissues, recruitment to tissues, developmental
biology, and cell fate and lineage to physiology
and homeostasis and their underlying molecular
Moreover, to deeply understand the full scope
and function of immune cells, it is most informative to study them in a challenged state—that is,
as manifested during disease, infection, development, aging, and environmental changes.
Studying immune cells in humans often requires
handling minute samples, and single-cell genomic approaches are highly compatible with such
limitations in input material.
Finally, genetic perturbations (natural or engineered) can also elicit changes in gene expression that may differ in response to environmental
cues or changes such as aging ( 18, 19, 64). As the
cost of single-cell experiments goes down, profiling more immune cells across conditions will be
possible via pooled genetic screens and by economically multiplexing a large number of individuals, using their sequence variations as a
natural genetic barcode ( 65).
Combining single-cell genomics, emerging
spatial approaches, immune repertoire analysis,
and multiplex immunophenotyping, together
with established approaches for functional
analysis, could also affect the next generation
of diagnostics and therapies. For diagnostics,
the white blood cell count might be reimagined
from a tally of major cell populations to an
assay that identifies cell signatures (defined
by single-cell genomics) of cell types and states
and their proportions. For therapy, comparing
the role and mechanisms of immune cells in
cellular ecosystems between healthy and diseased tissues can help to identify new therapeutic targets, as well as to better assess the
effect of current therapies in the context of
To help usher in this future, an effort to generate an Immune Cell Atlas (ICA) is emerging as
part of the international Human Cell Atlas initiative ( www.humancellatlas.org). The ICA will
assess the immune system at different stages of
differentiation, across different tissues, and in
the context of a wide range of diseases. To properly survey the spectrum of immune cells, even
the initial pilot effort will include samples from
small numbers of patients with a diversity of
diseases. Such a systematic characterization of
immunity requires an international collaboration among clinicians, immunologists, genomics experts, and computational biologists.
Overall, these types of approaches and projects
stand to radically transform our knowledge of
immune function and dysfunction in infection,
autoimmunity, allergy, inflammatory disorders,
and cancer, as well as to affect therapeutic
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We thank J. E. Rood, R. Majovski, V. Svensson, L. Gaffney, and
K. Meyer for help with preparation of this manuscript. A.R. was
supported by funds from the Howard Hughes Medicine Institute,
National Institute of Allergy and Infectious Diseases grants
U24AI118672 and R24AI072073, the Manton Foundation,
and the Klarman Cell Observatory. M.J. T.S. and S.A. T. were
supported by the Wellcome Trust grant 206194. A.R. is a
scientific advisory board member for ThermoFisher Scientific
and Syros Pharmaceuticals and a consultant for Driver Group;
the other authors have no conflicts of interest.