RESEARCH ARTICLE SUMMARY
◥
IMMUNOGENOMICS
Single-cell RNA-seq reveals new types
of human blood dendritic cells,
monocytes, and progenitors
Alexandra-Chloé Villani,*† Rahul Satija,* Gary Reynolds, Siranush Sarkizova,
Karthik Shekhar, James Fletcher, Morgane Griesbeck, Andrew Butler, Shiwei Zheng,
Suzan Lazo, Laura Jardine, David Dixon, Emily Stephenson, Emil Nilsson,
Ida Grundberg, David McDonald, Andrew Filby, Weibo Li, Philip L. De Jager,
Orit Rozenblatt-Rosen, Andrew A. Lane, Muzlifah Haniffa,† Aviv Regev,† Nir Hacohen†
INTRODUCTION: Dendritic cells (DCs) and
monocytes consist of multiple specialized subtypes that play a central role in pathogen
sensing, phagocytosis, and antigen presentation.
However, their identities and interrelationships
are not fully understood, as these populations
have historically been defined by a combination
of morphology, physical properties, localization, functions, developmental origins, and
expression of a restricted set of surface markers.
RATIONALE: To overcome this inherently
biased strategy for cell identification, we per-
formed single-cell RNA sequencing of ~2400 cells
isolated from healthy blood donors and en-
riched for HLA-DR+ lineage− cells. This single-
cell profiling strategy and unbiased genomic
classification, together with follow-up profil-
ing and functional and phenotypic charac-
terization of prospectively isolated subsets,
led us to identify and validate six DC subtypes
and four monocyte subtypes, and thus revise
the taxonomy of these cells.
RESULTS: Our study reveals:
1) A new DC subset, representing 2 to 3% of
the DC populations across all 10 donors tested,
characterized by the expression of AXL, SIGLEC1,
and SIGLEC6 antigens, named AS DCs. The AS
DC population further divides into two populations
captured in the traditionally defined plasmacytoid
DC (pDC) and CD1C+
conventional DC (cDC) gates.
This split is further reflected through AS DC gene expression signatures
spanning a spectrum between cDC-like and pDC-like gene sets. Although AS DCs share properties with pDCs, they more potently activate
T cells. This discovery led us to reclassify pDCs
as the originally described “natural interferon-producing cells (IPCs)” with weaker T cell proliferation induction ability.
2) A new subdivision within the CD1C+ DC
subset: one defined by a major histocompatibility
complex class II–like gene set and one by a CD14+
monocyte–like prominent gene set. These CD1C+
DC subsets, which can be enriched by combining
CD1C with CD32B, CD36, and CD163 antigens,
can both potently induce T cell proliferation.
3) The existence of a circulating and dividing
cDC progenitor giving rise to CD1C+ and CLEC9A+
DCs through in vitro differentiation assays. This
blood precursor is defined by the expression of
CD100+CD34int and observed at a frequency of
~0.02% of the LIN–HLA-DR+ fraction.
4) Two additional monocyte populations: one
expressing classical monocyte genes and cytotoxic
genes, and the other with unknown functions.
5) Evidence for a relationship between blastic
plasmacytoid DC neoplasia (BPDCN) cells and
healthy DCs.
CONCLUSION: Our revised taxonomy will enable more accurate functional and developmental analyses as well as immune monitoring in
health and disease. The discovery of AS DCs
within the traditionally defined pDC population
explains many of the cDC properties previously
assigned to pDCs, highlighting the need to revisit the definition of pDCs. Furthermore, the
discovery of blood cDC progenitors represents a
new therapeutic target readily accessible in the
bloodstream for manipulation, as well as a new
source for better in vitro DC generation. Although
the current results focus on DCs and monocytes,
a similar strategy can be applied to build a comprehensive human immune cell atlas. ▪
The list of author affiliations is available in the full article online.
*These authors contributed equally to this work.
†Corresponding author. Email: cvillani@broadinstitute.org
(A.-C.V.); m.a.haniffa@newcastle.ac.uk (M.H.); aregev@
broadinstitute.org (A.R.); nhacohen@mgh.harvard.edu (N.H.)
Cite this article as A.-C. Villani et al., Science 356, eaah4573
(2017). DOI: 10.1126/science.aah4573
PBMCs
Deep scRNA-seq
(1–2 M reads/cell; ~5, 326 genes/cell)
Single cell RNA-seq
Cellular enrichment
Atlas of human blood dendritic cells and monocytes
CD1C+
(cDC2,
BDCA-1)
CD14+
monos
CD16+
monos
Mono3
Mono4
DC2
CD1C+_A
DC1
CLEC9A+
DC3
CD1C+_B
DC4
CD1C–
CD141–
CD11C+
DC5
AXL+ SIGLEC6+
(AS DCs)
DC6
pDC
Experimental
strategy
Original cell
classifcation
Cell type reclassifcation based on
scRNA-seq and functional studies
Mono1
CD14+
Mono2
CD16+
PCR
mRNA
Reverse
transcription
Single cell
cDNA
CD141+
(cDC1,
BDCA-3)
CD1C–
CD141–
CD11C+
pDC
(BDCA-2,
BDCA-4)
CD100+
CD34int
cDC progenitor
Establishing a human blood monocyte and dendritic cell atlas. We isolated ~2400 cells enriched from the healthy human blood lineage− HLA-DR+ compartment and subjected them to
single-cell RNA sequencing. This strategy, together with follow-up profiling and functional and
phenotypic characterization, led us to update the original cell classification to include six DCs, four
monocyte subtypes, and one conventional DC progenitor.
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Read the full article
at http://dx.doi.
org/10.1126/
science.aah4573
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