MiRNAs and Immune System

REVIEWS
MicroRNAs as regulatory elements

inimmune system logic
Arnav Mehta1,2 and David Baltimore1
Abstract | MicroRNAs (miRNAs) are crucial post-transcriptional regulators of haematopoietic cell

fate decisions. They act by negatively regulating the expression of key immune development
genes, thus contributing important logic elements to the regulatory circuitry. Deletion studies
have made it increasingly apparent that they confer robustness to immune cell development,
especially under conditions of environmental stress such as infectious challenge and ageing.
Aberrant expression of certain miRNAs can lead to pathological consequences, such as
autoimmunity and haematological cancers. In this Review, we discuss the mechanisms by which
several miRNAs influence immune development and buffer normal haematopoietic output, first
at the level of haematopoietic stem cells, then in innate and adaptive immune cells. We then
discuss the pathological consequences of dysregulation of these miRNAs.
Haematopoiesis
The physiological process of
creating immune cells in our
body.
Long-term haematopoietic
stem cell
(LTHSC). A cell from which all
other immune cells originate
and that has the unique ability
to self-renew.
Multipotent progenitors
(MPPs). Early haematopoietic
progenitors that can
differentiate into all mature
immune cell types but do not
have the ability to self-renew.
Division of Biology and

Biological Engineering,
California Institute of
Technology, Pasadena,
California 90025, USA.
2
David Geffen School of
Medicine, University of
California, Los Angeles,
Los Angeles, California 90095,
USA.
Correspondence to
A.M.andD.B.
amehta@mednet.ucla.edu
baltimo@caltech.edu
1
doi:10.1038/nri.2016.40
Published online 28 Apr 2016
Mammalian haematopoiesis has conventionally been

thought of as a hierarchical process of cell state tran
sitions involving a complex interplay of genetic and
epigenetic regulation18. Whereas the structure of the
haematopoietic tree (FIG.1a) has been debated exten
sively 918, it is generally agreed that almost every cell
originates from the long-term haematopoietic stem
cell(LTHSC). At steady state, to maintain a balanced,
non-aberrant haematopoietic output, LTHSCs main
tain a balance between self-renewal and differentiation
into committed progenitors36,1921. These cells give rise
to short-term haematopoietic stem cells (STHSCs) and,
in turn, to multipotent progenitors (MPPs), which form
a continuum of progenitor subsets with limited self-
renewal capacity while maintaining the ability to pro
duce all mature immune cell types2225. MPPs give rise to
lineage-restricted progenitors such as common myeloid
progenitors (CMPs) and common lymphoid progenitors
(CLPs), which lead to production of the mature cells that
constitute the immune system3,5.
Under conditions of environmental stress, the
haematopoietic system must respond to ensure appropri
ate output of immune cells26,27. These stresses may include
acute processes, such as pathogenic challenge28,29, or
chronic processes, such as replicative stress from ageing
or inflammation3033. To this end, LTHSCs are equipped
with a complex array of cellular and molecular adapta
tions to withstand environmental perturbations. These
adaptations include epigenomic and transcriptomic
changes38, including the expression of key genes as well
as non-coding RNAs such as microRNAs (miRNAs)3437,
which help to modulate the balance between self-renewal
and differentiation (FIG.1b). Appropriate and balanced

haematopoietic output is further achieved by regulating
LTHSC mobilization29, cell cycle and proliferation6,38,
survival and autophagy30,39, as well as the direct secretion
and sensing of signals such as cytokines26,32,40,41.
miRNAs are a class of small non-coding RNAs that
negatively regulate gene expression by directly binding
to the 3 untranslated region (3 UTR) of their mRNA
targets42,43 (BOX1). Inflammatory responses modify the
biogenesis of miRNAs, regulating expression by altering
the transcription, processing or stabilization of mature or
precursor miRNA transcripts4447. Importantly, several key
roles for miRNAs are evident during periods of cellular
stress48,49. However, the dysregulated expression of many
miRNAs can lead to aberrant immune function, including
the development of leukaemia and autoimmunity 5052.
Several reports have suggested a regulatory logic of
haematopoietic fate, considering only transcription fac
tors5,5355. However, cell fate decisions seem to require
more complex input than this. By working to fine-tune
protein expression levels, miRNAs can contribute to regu
latory circuits by providing quantitative control of gene
output. In particular, they often exert their influence by
regulating dosage-sensitive genes for which small fluctu
ations in protein expression may contribute to a substan
tial functional output. Several models have been proposed
in which miRNAs may contribute to the robustness and
precision of cell fate decisions and functional responses
in the haematopoietic system56,57. miRNAs are elements of
regulatory networks, providing positive or negative feed
back of gene expression. They may function in coherent or
incoherent feed-forward loops, which can alter the timing
NATURE REVIEWS | IMMUNOLOGY
VOLUME 16 | MAY 2016 | 279

.
d
e
v
r
e
s
e
r
s
t
h
g
i
r
l
l
A
.
d
e
t
i
m
i
L
s
r
e
h
s
i
l
b
u
P
n
a
l
l
i
m
c
a
M
6
1
0
2
REVIEWS
a
Self-renewal
LT-HSC
Dierentiation
ST-HSC
MPP
LMPP
CMP
MEP
Erythroid
GMP
Megakaryocyte
CLP
Granulocyte Macrophage
DC
B cell
T cell
NK cell
b Bone marrow niche signals

SCF
KIT
ANG1
Chromosome silencing
CXCL12
DNA methylation
lincRNA
Transcription
CXCR4
Splicing
microRNA
P P
P P P
Post-translational
modication
Translation
HSC
Figure 1 | Overview of immune system development and the regulatory

Nature Reviews | Immunology
elements governing HSC function. a | A diagram of our
current model of
haematopoiesis, which begins with haematopoietic stem cells (HSCs) that are able to
self-renew and sequentially differentiate into more committed, lineage-restricted
progenitors. b | An illustration of the regulatory processes that contribute to
altering HSC function. Several regulatory elements form an elaborate network of
genes that influence these processes, including extracellular signalling proteins,
epigenetic modifiers such as chromatin remodellers and DNA methyltransferases,
splicing factors, transcription factors, long non-coding RNAs (lincRNAs),
microRNAs and translational and post-translational protein modifiers. ANG1,
angiopoietin 1; CLP, common lymphoid progenitor; CMP, common myeloid
progenitor; CXCL12, CXC-chemokine ligand 12; CXCR4, CXC-chemokine
receptor 4; DC, dendritic cell; GMP, granulocytemonocyte progenitor;
LMPP, lymphoid-primed multipotent progenitor; LTHSC, long-term haematopoietic
stem cell; MEP, megakaryocyteerythrocyte progenitor; MPP, multipotent progenitor;
NK, natural killer; SCF, stem cell factor; STHSC, short-term hematopoietic stem cell.
and outcome of cell fate in a context-dependent man

ner 48,49,58. In the haematopoietic system, these network
motifs also serve to buffer protein expression noise5962, both
at a steady state and under conditions of environmental
stress, and to set thresholds for gene expression that are
necessary for fate commitment63 (FIG.2). Importantly, we
find that multiple miRNAs can act either in a cooperative
or antagonistic fashion, and single miRNAs may regulate
several targets in a gene network64.
In recent years, the number of miRNAs implicated
in immune system development and function has
increased dramatically, and there has been widespread
discussion of their potential use as therapeutics for
immune-related disease. In this Review, we discuss the
mechanisms by which miRNAs can confer robustness
to immune cell function, with a particular emphasis
on haematopoietic stem cells. We then discuss recent
advances in miRNA regulation of innate and adaptive
immunity, focusing on the network motifs and key
mechanisms underlying this regulation. In the final sec
tions, we explore the connection between dysregulated
miRNA expression and human disease. With our current
understanding of the mechanisms of miRNA biogenesis
and function, we find that there is tremendous promise
in the field for using miRNAs both to understand the
basic mechanisms of haematopoietic cell fate decisions
and to develop diagnostic and therapeutic strategies for
aberrant haematopoiesis.
Mechanisms of miRNA regulation of cell fate

Several mechanisms have been uncovered whereby
miRNAs may confer robustness to haematopoietic cell
fate decisions and immune function49,56. Many of these
mechanisms can be simplified to one of a handful of
network motifs that provides a theoretical framework
for understanding the important components of a cell
fate decision5,7,8,65,66. In thinking of these simplified motif
structures, however, it is important to consider that
many miRNAs may be involved in regulating a single
mRNA target and that a single miRNA may be involved
in regulating many mRNA targets.
Positive feedback loops involve induction of a
miRNA, usually by a transcription factor (X) that has
a crucial role in driving primary transcript expression,
coupled with the miRNA-targeted repression of a second
factor (Y) that is involved in repressing the induction of
X (FIG.2a). Thus, induction of X leads to repression ofY,
which in turn leads to further induction of X. In this
way, positive feedback can drive lineage commitment
by reinforcing the expression of a gene that leads to a
particular cell fate. Negative feedback loops involve the
induction of a miRNA (X), which in turn represses a
gene (Y) that has a crucial role in the pathway respon
sible for its induction (FIG.2b). Thus, X repressesY,
which in turn further represses the expression of X.
Anetwork motif involving the mutual repression of two
genes (X andY) results in a bistable switch. This motif
creates binary output in response to an external signal.
Induction of X leads to the repression of Y, which in turn
further reinforces the expression of X by removing the
repressive signal contributed by Y (FIG.2c).
280 | MAY 2016 | VOLUME 16
www.nature.com/nri
.
d
e
v
r
e
s
e
r
s
t
h
g
i
r
l
l
A
.
d
e
t
i
m
i
L
s
r
e
h
s
i
l
b
u
P
n
a
l
l
i
m
c
a
M
6
1
0
2
REVIEWS
Box 1 | Biogenesis of miRNAs and mechanisms of action
MicroRNAs (miRNAs) are a class of ~1823bp non-coding
RNAs that fine-tune gene expression through translational
inhibition and mRNA degradation of their targets235,236.
Whendysregulated, they can drastically alter the balance
ofdynamic biological processes, such as immune system
development37,100,109.
Most miRNAs are transcribed as a primary transcript
(pri-miRNA) by RNA polymerase II (Pol II) and sequentially
cleaved by the enzymes Drosha and the microprocessor
complex subunit DiGeorge syndrome critical region 8
(DGCR8), collectively referred to as the microprocessor
complex237. The resultant precursor miRNA (pre-miRNA) is
exported by exportin 5 into the cytoplasm, where it is cleaved
into a double-stranded RNA duplex by the enzyme Dicer237.
Asingle strand of this duplex is subsequently incorporated
into the RNA-induced silencing complex (RISC)238, at which
point it serves as a template for binding to mRNA targets.
EachmiRNA pairs with the 3 untranslated region of many
mRNA targets in an interaction primarily mediated by a
68-nucleotide seed sequence at the 5 end of the miRNA235,239.
The biogenesis of miRNAs in the immune system is
regulated at the level of transcription94,103,240,241,
microprocessor and Dicer cleavage44,45,71,242,243, RNA
editing244, loading onto the RISC complex and localization
ofaction46,49,245 (see the figure). These mechanisms are
discussed in detail elsewhere47,237.
Although the primary mode of action of most miRNAs
involves translational inhibition and mRNA degradation,
several instances have been reported of miRNAs that induce
mRNA or protein expression246248. Importantly, the action of
amiRNA may also be influenced by binding to RNA-binding
proteins249252 and by sequestration by endogenous sponges,
such as competing endogenous RNAs (ceRNAs)253255.
TF,transcription factor.
Signal: developmental
programme, growth factors,
cytokines, antigens and
Toll-like receptors
Mature miRNA
sequence
mRNA
Processes regulated
by the immune
system
TF
TF
RNA editing
Pol II
Pri-miRNA
transcript
Microprocessor
(Drosha, DGCR8)
Pre-miRNA
transcript
Nucleus
Exportin 5
Cytoplasm
Dicer
Double-stranded
miRNA duplex
Loading onto
the RISC
Localization
of action
Reduced protein
expression
Stress granule
Autophagy
A normal physiological process
through which the cell
degrades unnecessary cellular
components.
3 untranslated region
(3 UTR). The sequence of an
mRNA that is downstream of
the stop codon.
Robustness
The resilience of different
cellular functions to
perturbations from
extracellular insults.
Protein expression noise

The intrinsic variation in
translation that results
indifferent protein
expressionlevels with the
samemRNA input.
Bistable switch
A network motif in which there
is a binary outcome of either
expression of one gene or
another.
The coherent and incoherent feed-forward motifs

involve three components: a regulator, X, which regu
lates Y and Z, with the latter also being regulated by Y
(FIG.2d,e). The three regulatory interactions can either
be activating or repressing; thus, there are eight pos
sible motif structures. A detailed discussion of these
can be found elsewhere65; in this Review, we focus on
certain motifs that are relevant to specific miRNAs in
haematopoiesis. Of note, feed-forward loops can be
instrumental in immune development and function by
imposing temporal delays in the induction or repression
of responsegenes.
Two major manifestations of these network motifs
in providing robustness to immune cell function arein
buffering protein expression noise and in establishing
thresholds for mRNA expression that are necessary
for commitment. Through negative feedback, many
miRNAs buffer the expression of regulatory proteins to
within narrow concentration ranges5962 (FIG.2f). For this
to happen, however, both the miRNA and its mRNA
target must be expressed at an adequate concentration
for the regulatory interaction to occur. It is now clear
that miRNAs are effective in establishing a threshold
level of target mRNA: below this level, the mRNA is
effectively repressed but, above this level, the miRNA
is saturated and little repression of the mRNA target
occurs (FIG.2g). In the haematopoietic system, these

thresholds can often establish checkpoints, whereby
the expression of a master regulator must exceed a cer
tain level for the development of a cell type to occur. Of
note, these thresholds may be altered by the expression
of target mimics, such as competing endogenous RNAs
(ceRNAs).
63
Regulation of HSC function by miRNAs

HSCs predominantly reside in the bone marrow and
are charged with the difficult task of maintaining pro
duction of the entire gamut of immune cells in our
body throughout our lifetime, even under conditions
of marked environmental stress3,67,68. To do this, they
must balance between self-renewal and differentiation
into committed progenitors1921. Over the past 10years,
substantial progress has been made in profiling miRNA
expression in HSCs34,37,69,70 and in understanding the
various roles they may have in altering function either
in unperturbed conditions or following stimuli such as
stress (FIG.3a), acute infection orageing.
Homeostatic conditions. There is abundant evidence
from recent years suggesting that miRNAs have an
important physiological role in the function of HSCs
in normal, non-perturbed conditions. LTHSCs from
VOLUME 16 | MAY 2016 | 281

.
d
e
v
r
e
s
e
r
s
t
h
g
i
r
l
l
A
.
d
e
t
i
m
i
L
s
r
e
h
s
i
l
b
u
P
n
a
l
l
i
m
c
a
M
6
1
0
2
REVIEWS
Microprocessor complex
The complex of two enzymes,

Drosha and DGCR8, that
cleave pri-miRNAs to
pre-mRNAs.
Buffering protein expression
Maintaining the expression of a

protein to within a narrowly
defined range.
b
miRNA
Y
X (miRNA)
d
X (miRNA)
Competing endogenous
RNAs
Y
Z
f
1. More consistent protein
output with miRNAs
(ceRNA). RNAs that bind

microRNAs and prevent them
from interacting with
functionally relevant mRNA
targets.
Polycistron
Master regulator
A regulatory element that is
essential for the regulation of a
developmental process.
Translation
Noisy protein expression from

translation without miRNAs
Transcription
2. Negative feedback can provide

a break to protein expression
A collection of microRNAs that

are expressed in a single
transcriptional unit.
Signal
Protein
miRNA
3. Buering protein concentration to within a narrow range

mRNA
miRNA
miRNA
Protein
Protein
Buered protein range
Threshold
mRNA
miRNA
Protein
Figure 2 | The different roles of miRNAs in network motifs

Nature MicroRNAs
Reviews | Immunology
and in regulating gene expression.
(miRNAs)
can regulate gene expression through: a positive feedback
loop (part a), a negative feedback loop (part b), the mutual
repression of two genes to create a bistable switch (part c),
acoherent feed-forward loop (part d) or an incoherent
feed-forward loop (part e). Mechanisms by which miRNAs
buffer protein expression noise include (part f): first, a
combination of more consistent translational output in
response to transcriptional bursts; second, negative
feedback regulation to block aberrant protein expression;
and third, helping to define a narrow protein concentration
range for normal cellular response. miRNAs can establish
thresholds (part g) for the level of target mRNA expression
required to achieve a substantial protein output.
mice deficient in the essential miRNA-processing pro

tein Dicer undergo apoptosis and have an impaired abil
ity to undergo long-term reconstitution in competitive
transplantation assays35. Loss of arsenite-resistance pro
tein 2 (ARS2; also known as SRRT), which is a compo
nent of the nuclear RNA cap-binding complex that is
important in miRNA biogenesis, results in bone marrow
failure71. This is possibly due to an altered proliferation

of LTHSCs and impaired processing of several known
haematopoietic miRNAs, including miR155, let7 and
miR21 (REF.71).
The recent discovery of several miRNAs that are
enriched in unperturbed HSCs has started to reveal
the extent to which they can affect HSC function37. The
miR125 family, which is composed of two members that
share a seed sequence, miR125a and miR125b, has a
vital role in maintaining normal haematopoietic out
put35,37. Both of these miRNAs exert their influence by tar
geting several mRNAs that are important in development
and apoptosis, thereby altering HSC biology in complex
ways. miR125a is expressed in a cluster with miR99b
and let7e, all of which are enriched in LT-HSCs35,72.
The enrichment of miR125a is significantly higher
than other members of the cluster 35,37; this phenomenon
has been observed for other clusters that are expressed
in the haematopoietic system36,73,74, and the mechanism
for this remains unclear. One hypothesis is that it may
be due to the selective blockade of other m
iRNAs in the
cluster by RNA-binding proteins75. Enforced expression
of miR125a alone leads to decreased apoptosis and an
eightfold increase in the total number of bone marrow
LT-HSCs35. This effect is mediated in part by the direct
repression of the pro-apoptotic BCL2 homologous
antagonist/killer 1 (BAK1) protein by miR125a35.
Enforced expression of miR125b leads to an
improvement in the function of LTHSCs in competi
tive transplantation assays37,76, with no change in the
number of these cells in the bone marrow compartment
compared with control mice73. Constitutive expression
of miR125b, however, leads to myeloid or lymphoid
leukaemia in a miRNA concentration-dependent man
ner 73,76. One hypothesis is that low levels of enforced
miR125b expression lead to expansion of lymphoid-
biased LTHSC subsets through direct targeting of the
pro-apoptotic genes Kruppel-like factor 13 (Klf13)
and BCL2modifying factor (Bmf)76. Beyond a given
threshold of miR125b expression, direct repression
of the genes Lin28 and interferon regulatory factor 4
(Irf4), in addition to other targets, leads to uncontrolled
myeloid proliferation73,77.
miR125b is expressed in a cluster with let7c,
miR99a and miR-100 at two different genomic loci78.
This polycistron is activated by homeobox protein
HOXA10 in LTHSCs, and all the miRNAs converge
to target SMAD2 and SMAD4, which are two crucial
transducers in transforming growth factor- (TGF)
signalling, as well as anaphase-promoting complex
subunit 2 (APC2; also known as ANAPC2), which
stabilizes catenin to enhance WNT signalling 78. This
cluster therefore has a role in balancing the competing
actions of TGF signalling (which maintains LTHSC
quiescence)6,79 and WNT signalling (which promotes
LTHSC self-renewal and proliferation)6,80. Importantly,
the effect of WNT signalling is dose dependent 80, and
we may thus hypothesize that this cluster has a role in
setting a threshold for switching between quiescence and
proliferation of LTHSCs in a manner that is dependent
on the concentrations of miRNA targets (FIG.3b).
282 | MAY 2016 | VOLUME 16
www.nature.com/nri
.
d
e
v
r
e
s
e
r
s
t
h
g
i
r
l
l
A
.
d
e
t
i
m
i
L
s
r
e
h
s
i
l
b
u
P
n
a
l
l
i
m
c
a
M
6
1
0
2
REVIEWS
a
LT-HSC
WNT1 and TGF signalling

miR-125blet-7cmiR-99a
Cytokine response
miR-146a
miR-193b
miR-221
miR-222
DNA methylation
miR-29a
miR-124
Engraftment
miR-125b
Cell cycling and self-renewal

miR-29a
miR-33
miR-126
miR-146a
miR-212 and miR-132
LIN28Blet-7
Survival and autophagy
miR-29a
miR-124
miR-125a
miR-125b
miR-212 and miR132
miR-125blet-7cmiR-99a
miR-126
PI3KAKT
GSK3
SMAD2 and SMAD4

TGF signalling
APC2
WNT1 signalling
Quiescence
Small PI3K signal

needed for HSC
activation
Self-renewal
LIN28B
Large PI3K signal

needed for HSC
activation
TLR
TRAF6, IRAK1
Let-7
Fetal HSC: high LIN28B
Adult HSC: low LIN28B
IL-6
NF-B
miR-146a
HMGA2
Proliferation and myeloipoiesis
HSC self-renewal
miR-132
FOXO3
p53
miR-33
Buered FOXO3 range

Apoptosis
Altered self-renewal
and dierentiation
Proliferation
Exhaustion
Poor function
miRNA sponge
(microRNA sponge).
Atranscript with several
miRNA-binding sites that
isused to downregulate
thefunctional response of
amiRNA.
Exhaustion
A state of cellular dysfunction
or loss that occurs after
aberrant activation and
proliferation of a cell.
miR29a is also enriched in LT-HSCs 81, but its

function remains ambiguous. Enforced expression
of miR29a in haematopoietic progenitors leads to
increased cell cycling and may have a role in biasing
LTHSCs towards myeloid differentiation81. Several
targets contribute to this phenotype, including the cell
cycle genes schlafen4 (SLFN4), DNA (cytosine5)-
methyltransferase 3like (DNMT3L), CDC42 effector
protein2 (CDC42EP2) and HMG box-containing fac
tor1 (HBP1), which is a known negative regulator of
the G1 to S/G2 transition81. However, genetic deletion
ofthe miR29amiRNA29b1 bicistron also increases
cell cycling of LTHSCs and induces apoptosis, partially
by targeting DNMT3A82.
A similar mechanism has been proposed for the
increased self-renewal and defective differentiation of
LTHSCs with conditional expression of miR22 (REF.83).
This miRNA targets the methylcytosine dioxygenase
Figure 3 | Overview of miRNAs that alter HSC

function. a | Several microRNAs (miRNAs) are
enriched in haematopoietic stem cells (HSCs) and
contribute to the regulatory logic of HSC cell fate by
regulating diverse processes, including self-renewal,
differentiation, survival and DNA methylation. They
also regulate signal transduction, including signalling
through WNT1, transforming growth factor- (TGF)
and other cytokines. Specific examples contributing
to HSC function are illustrated. b | The miR125b
let7cmiR99amiR100 cluster buffers against
aberrant self-renewal and differentiation. It does this
by targeting SMAD2 and SMAD4, and anaphasepromoting complex subunit 2 (APC2) to inhibit
overactivation of TGF and WNT1 signalling,
respectively. TGF and WNT1 signalling have opposing
actions on HSC function by modulating quiescence
and self-renewal. c | miR126 targets several proteins
in the phosphoinositide 3kinase (PI3K)AKTglycogen
synthase kinase 3 (GSK3) pathway, thus setting a
threshold for signalling that is necessary to achieve
HSC activation. The graded expression of miR126
may further contribute to the strength of extrinsic
signals that are needed for this activation to occur.
Forexample, higher miR126 expression represses this
signalling pathway such that smaller signals are
needed for activation to occur. d|The LIN28Blet7
high mobility group protein A2 (HMGA2) axis
contributes to a coherent feed-forward loop that
drives fetal HSC self-renewal. e | miR146a is induced
by Toll-like receptor (TLR) signalling and negatively
regulates the nuclear factor- B (NFB) response by
targeting TNF receptor-associated factor 6 (TRAF6)
and interleukin1 receptor-associated kinase 1
(IRAK1), thus serving as a brake to prevent aberrant
immune activation. f | The mutual repression of p53
and miR33 creates a bistable switch, which results in
a binary functional response. g | miR132 buffers the
expression of forkhead box protein O3 (FOXO3) to
within a narrow range in HSCs. Too much FOXO3
leadsto apoptosis and altered self-renewal and
differentiation, whereas too little FOXO3 leads
toproliferation and exhaustion of these cells.
IL6,interleukin6.
TET2, which catalyses the oxidation of 5methylcyto

sine to 5hydroxymethylcytosine and is likely to regulate
gene expression through its effect on DNA methylation83.
miR124 also regulates LTHSC cycling and self-renewal
by targeting cyclin D3 and polycomb complex protein
BMI1, respectively, and is silenced by DNA methyla
tion at its promoter by ecotropic virus integration site 1
protein homolog (EVI1)84. In LTHSCs, the expression
of miR126 also impairs cell cycle entry and inhibits
normal haematopoiesis, whereas antagonizing its func
tion using a miRNA sponge leads to proliferation with
out exhaustion85,86. By targeting several components of
the p
hosphoinositide3kinase (PI3K)AKTglycogen
synthase kinase 3 (GSK3) pathway, miR126 governs
LTHSC pool size by setting a threshold for activation that
is necessary for cell expansion86 (FIG.3c). In leukaemic stem
cells (LSCs), miR126 inhibits the cell cycle and differenti
ation, and promotes self-renewal, thus having the opposite
VOLUME 16 | MAY 2016 | 283

.
d
e
v
r
e
s
e
r
s
t
h
g
i
r
l
l
A
.
d
e
t
i
m
i
L
s
r
e
h
s
i
l
b
u
P
n
a
l
l
i
m
c
a
M
6
1
0
2
REVIEWS
effects to those observed in healthy HSCs87. miR126 also
exerts its effect by targeting HOXA9, a member of the
HOX family of genes that are crucial for haematopoiesis88.
Recent work has also revealed a crucial role
for m
iRNAs in the normal transition from fetal to
adult haematop oiesis89,90. LIN28B, which is a post-
transcriptional regulator of the let7 family of miRNAs,
signals a coherent feed-forward loop (FIG.3d) that directly
drives self-renewal and lymphoid programming in
fetal LTHSCs. By downregulating the expression of
let7 family proteins, which are negative regulators
ofhigh mobility group protein HMGA2 (also known as
HMGIC), LIN28B expression also accentuates HMGA2
expression89. HMGA2 independently reinforces the
action of LIN28B on fetal LTHSC self-renewal. Thus,
the LIN28Blet7HMGA2 axis drives fetal haemato
poiesis, and suppression of this axis is crucial in the
developmentally timed change of key functions of adult
LTHSCs, which do not express LIN28B89. Interestingly,
enforced expression of LIN28B and HMGA2 in adult
LTHSCs leads to increased self-renewal and, in the case
of LIN28B, activation of a fetal lymphoid programme89,90.
miR193b and miR132 are both induced in LTHSCs

in response to thrombopoietin signalling, in a signal
transducer and activator of transcription 5 (STAT5)dependent manner 97. Enforced expression of miR193b
restricts LTHSC repopulating ability 97. Genetic deletion
of miR193b leads to a gradual enrichment in LTHSCs
owing to defective differentiation of these cells, with no
changes in cell cycling and survival97. miR193b itself
negatively regulates cytokine signalling by targeting
KIT; as such, miR193b-deficient LTHSCs demonstrate
increased basal STAT5 and AKT signalling 97. Thus,
similarly to miR146a, this miRNA may serve to buffer
cytokine signalling to prevent defective haematopoiesis.
miR221 and miR222 have also been shown to target
KIT, and their dysregulation leads to defective LTHSC
proliferation and repopulation capacity 98.
Aged LTHSCs develop a requirement for basal
autophagy to survive as a result of replication stress
and the accumulation of reactive oxygen species, which
have a deleterious effect on self-renewal and differenti
ation19,30,33,39. The miR212 and miR132 cluster is upregu
lated with age and buffers the expression of forkhead box
protein O3 (FOXO3) to maintain an appropriate bal
Non-homeostatic conditions. Several roles for miRNAs ance between pro-survival signals through autophagy,
have been discovered to provide robustness to LTHSC and cell cycling and differentiation36. Enforced expres
function during times of environmental stress. Such sion of miR132 results in dramatic downregulation of
stresses may include acute inflammatory responses to FOXO3, leading to LTHSC proliferation and exhaus
pathogen invasion2729,31,32 or DNA damage from toxic tion36. Genetic deletion of the miR212 and miR132
insults or replicative stress30,33, such as fromageing.
cluster leads to elevated FOXO3 expression, which causes
Haematopoietic progenitors are potent, direct defective haematopoiesis with age owing to dysregulated
responders to Toll-like receptor (TLR) ligands. TLR2 differentiation and increased autophagy 36. Thus, miR212
and TLR4 stimulation in LTHSCs results in the pro and miR132 must reliably buffer FOXO3 protein levels
liferation of these cells and the initiation of emergency to within a narrow range in order to maintain a normal
granulopoiesis91. Importantly, these progenitors also haematopoietic output (FIG.3g).
secrete cytokines41 that may amplify their own inflam
These models of the regulation of LTHSC function
matory response in an uncontrolled manner. miR146a reveal that miRNAs have important physiological roles
is induced by nuclear factorB (NFB) in response in maintaining steady-state haematopoiesis and in allow
to TLR stimulation and serves as a negative feedback ing for the robustness of haematopoietic output to acute
regulator of TLR signalling by targeting TNFreceptor- and chronic environmental perturbations. Future work
associated factor 6 (TRAF6) and interleukin1 will reveal the mechanisms that alter miRNA expres
receptor-associated kinase 1 (IRAK1)92,93. Deletion of sion in LTHSCs and how the evolutionary pressure
miR146a leads to dysregulated myelopoiesis94, and from subtle alterations in protein expression can lead to
proliferation and exhaustion of LT-HSCs95; both of dysregulated haematopoiesis.
these processes are partially dependent on secretion
ofinterleukin6 (IL6)95. Loss of miR146a also results Regulation of innate immune cells by miRNAs
in increased secretion of cytokines, such as IL6, from Myeloid cell development and function provide the
haematopoietic progenitors41. miR146a thus partici best-characterized processes for miRNA regulation
pates in a negative feedback loop that tempers cytokine (FIG.4a). In this section, we touch on key examples of net
secretion from, and proliferation of, haematopoietic work motifs and unique mechanisms involving miRNAs
progenitors (FIG.3e). This network motif allows for the in myeloid cell development and function. We direct the
induction of emergency myelopoiesis and LTHSC reader elsewhere for a more comprehensive discussion
proliferation with dampening of NFB signalling to of miRNAs in myeloid biology 99,100.
prevent an uncontrolled response.
Activation of the DNA damage response in LTHSCs Macrophages. Two major players in the regulation of
as a result of acute injury leads to the induction of p53, macrophage development and immunity are miR155
which has an important role in cell cycling 96. p53 represses and miR146a101106. miR155 is strongly induced in
the expression of miR33, and miR33, in turn, directly macrophages and dendritic cells by NFB and activator
represses p53 by directly binding to two sites in its protein 1 (AP1) in response to a broad range of TLRs
3UTR96. This mutual repression therefore forms a bistable and cytokine signals103. LPS stimulation also activates
switch (FIG.3f) that can influence the commitment between AKT1, causing repression of miR155 and miR125b,
quiescence and cell cycling in conditions ofstress.
and induction of let7e, which negatively regulates TLR4
284 | MAY 2016 | VOLUME 16
www.nature.com/nri
.
d
e
v
r
e
s
e
r
s
t
h
g
i
r
l
l
A
.
d
e
t
i
m
i
L
s
r
e
h
s
i
l
b
u
P
n
a
l
l
i
m
c
a
M
6
1
0
2
REVIEWS
a
CMP
miR-29a
MEP
miR-144
and
miR-451
miR-150
and
miR-10a
Erythrocyte
Megakaryocyte
GMP
miR-155,
miR-223,
miR-196b
and
miR-21
miR-155, miR-146a,
miR-125b, miR-124,
miR-21, miR-9 and
let-7e
Granulocyte
TLR4
Macrophage
C/EBP
E2F1
TRAF6, IRAK1
AP-1
AKT1
SHIP1,
SOCS1
miR-223
MEF2C
NFI-A
Granulocyte
dierentiation
NF-B
miR-146a
miR-155
Figure 4 | miRNAs that regulate innate immune cell development and function.
Nature in
Reviews
Immunology
a|Aschematic describing some key microRNAs (miRNAs) involved
innate |immune
cell
development and the developmental processes that they influence. b | miR155 and
miR146a participate in an intricate network architecture that regulates the inflammatory
response. miR155 participates in an incoherent feed-forward loop that is initiated by
Toll-like receptor (TLR) signalling. Upon TLR activation, it is induced by nuclear factor- B
(NFB); however, TLRs also activate AKT1, which in turn represses miR155 expression.
This miRNA also positively feeds back to the NFB response by inhibiting the
phosophatases SH2 domain-containing inositol 5-phosphatase 1 (SHIP1) and suppressor
of cytokine signalling 1 (SOCS1). As described in haematopoietic stem cells (HSCs),
miR146a dampens NFB signalling by repressing TNF receptor-associated factor 6
(TRAF6) and interleukin1 receptor-associated kinase 1 (IRAK1). c | Two network motifs
contribute to granulocyte cell fate commitment. CCAAT/enhancer-binding protein-
(C/EBP) initiates a coherent feed-forward loop by increasing the expression of miR223
and inhibiting the transcription factor E2F1, which is a repressor of miR223 expression. In
addition, miR223 and nuclear factor 1 A type (NFI-A) are mutual repressors of each other,
thus forming a bistable switch. Activation of miR223 in turn leads to targeted inhibition
ofmyocyte-specific enhancer factor 2C (MEF2C), which is an inhibitor of granulocyte
differentiation. AP1, activator protein 1; CMP, common myeloid progenitor; GMP,
granulocytemonocyte progenitor; MEP, megakaryocyteerythrocyte progenitor.
(REF.107). Thus, TLR4 activation initiates an incoherent
Rheostat
A gene that allows, through its
cellular function, for graded,
quantitative control of a
biological process, such as
cellsignalling.
feed-forward loop that drives macrophage activation

(FIG.4b). Incoherent feed-forward loops induce rapid
acceleration of the initial response, such as miR155
production, followed by temporal dampening of the
response, creating a pulse-like dynamic. Interestingly,
miR155 is also repressed by IL10 signalling through
STAT3 (REF.108). miR155 expression in turn ampli
fies inflammatory signalling by downregulating SH2
domain-containing inositol 5-phosphatase 1 (SHIP1)
and suppressor of cytokine signalling 1 (SOCS1)102.
miR146a is also induced by NFB and negatively regu
lates TLR signalling by targeting TRAF6 and IRAK1
(REF.93). A working hypothesis is that these miRNAs may
act antagonistically to produce a robust and coordinated
inflammatory response. In addition to its function in

immunity, miR155 drives myeloid cell differentiation,
presumably by downregulating PU.1, BRCA1interacting
protein C-terminal helicase1 (BACH1; also known as
FANCJ), colony stimulating factor 1 receptor (CSF1R),
CCAAT/enhancer-binding protein- (C/EBP) and
other regulators of myeloid cell differentiation109.
Granulocytes. miR223 is upregulated throughout
granulocyte differentiation and is the first miRNA
that was discovered to dramatically alter granulocyte
fate100,110. The transcription factors nuclear factor 1
Atype (NFIA) and C/EBP compete for binding to
the miR223 promoter 110. C/EBP drives the expres
sion of miR223 (REF.110) and reinforces this expression
through a coherent feed-forward loop by inhibiting
E2F1, which itself inhibits miR223 expression111. NFIA,
however, maintains sub-threshold levels of miR223 and
is directly repressed by miR223 itself, thus creating a
bistable switch110. Genetic deletion of miR223 results
in increased expression of its target myocyte-specific
enhancer factor 2C (MEF2C), which drives myeloid pro
genitor proliferation and expansion of the granulocyte
lineage112. Concomitant deletion of MEF2C rescues this
defect in miR223deficient mice112. Thus, miR223 has
a crucial role in commitment to granuclocyte cell fate
(FIG.4c). PU.1 and C/EBP may also have a role in the
regulation of miR223 expression113,114.
Several other miRNAs also influence granulocyte fate.
The zinc finger protein GFI1 is a transcriptional repressor
that is crucial for granulocyte differentiation and directly
binds to the miR21 and miR196b promoters115,116.
Enforced expression of these two miRNAs results in a
block in granulocyte differentiation that phenocopies
mice deficient in GFI1 (REF.116). Interestingly, miR130a
is also implicated in granulocyte differentiation by serv
ing as a rheostat for TGF1 s ignalling as a result of direct
modulation of SMAD4 (REF.117).
NK and NKT cells. Substantial progress has been made
over the past 5 years in identifying specific miRNAs
that regulate natural killer (NK) cell fate118121. miR181
has been shown to drive early NK cell development by
potentiating Notch signalling 119. Enforced expression of
miR181a or miR181b results in repression of its target
Nemo-like kinase (NLK), which inhibits Notch119. The
expression of miR150 has been shown to regulate the
commitment between NK and invariant NK T (iNKT)
cells. Mice lacking miR150 upregulate MYB expression
and are defective in their ability to produce NK cells120.
Conversely, constitutive expression of miR150 leads
to increased output of NK cells and a reduction in the
production of iNKT cells120. The let7 miRNA family
has also been implicated in the regulation of iNKT cells
through direct repression of the transcription factor
promyelocytic leukaemia zinc finger protein (PLZF;
also known as ZBTB16)118. Let7 is induced in NKT cells
by IL15 signalling 118. Higher levels of let7 expression
lead to the production of interferon (IFN)-producing
NKT cells, whereas low levels of let7 expression lead to
IL4- or IL17producing iNKT cells118.
VOLUME 16 | MAY 2016 | 285

.
d
e
v
r
e
s
e
r
s
t
h
g
i
r
l
l
A
.
d
e
t
i
m
i
L
s
r
e
h
s
i
l
b
u
P
n
a
l
l
i
m
c
a
M
6
1
0
2
REVIEWS
Megakaryocytes, erythrocytes and other immune cells.
Profiling studies have revealed enrichment of several
miRNAs in cells of the megakaryocyte and erythroid
lineage, although little is known about the miRNA
networks that regulate cell fate in these cell types122124.
Commitment to the megakaryocyte fate may involve
downregulation of several miRNAs and upregulation of
miR10a, which targets HOXA1 (REF.124). Expression
ofmiR150 drives megakaryocyteerythrocyte progeni
tor (MEP) differentiation to the megakaryocyte lineage
through downregulation of MYB123. Commitment to
the erythroid fate involves the expression of miR144
and miR451, which together regulate several genes,
CLP
Pre-pro-B cell
miR-21,
miR-148,
Activated
miR-155
B cell
and miR-125b
Plasma cell
Pro-B cell
miR-155, miR-142,
miR-46a, miR-181b,
miR-210 and
miR-217
miR-150
CLP
miR-150,
miR-34a and
miR-17~92
miR-212
and
miR-132
miR-181a
LMPP
including RAS-related C3 botulinum substrate 1

(RAC1), which drives MEP proliferation, and ETS pro
to-oncogene 2 (ETS2), which drives megakaryocyte
differentiation125.
Less is known about miRNAs that influence the
development of eosinophils, basophils and mast cells.
A recent study demonstrated that loss of miR223
leads to the proliferation of eosinophilic progenitors
by upregulating insulin-like growth factor 1 receptor
(IGF1R)126. The expression of miR221 and miR222
is upregulated in mast cells, and enforced expression
of these miRNAs leads to the alteration of mast cell
proliferation, presumably through p27 (also known as
Pre-B cell
Mature
B cell
Immature
B cell
miR-181a
DN
SP
DP
miR-155, miR-17~92,
miR-182, miR-31, let-7,
miR-98 and miR-146a
miR-155, miR-20b,
miR-212 and miR-132,
miR-21, miR-301
and miR-326
CD4+ Treg cell
miR-17~92,
miR-155 and let-7c
TH1 cell
TH17 cell
CD4+ T cell
CD8+ T cell
miR-126,
miR-24 and
miR-27
TH2 cell
Threshold
miR-150
IL-21
SOX4 mRNA
STAT3
MYB
miR-21
miR-132
Buered MYB range

B cell expansion
Cancer
BLIMP1
SOX4
protein
Loss of B cells
Plasma cells
miR-181a
PTNP22, SHP2,
DUSP6
Selection in thymus
Low-anity antigens
Immunity in periphery
High-anity antigens
Proliferation
and cancer
h
miR-181a
CD69
TCR
signalling
miR-17,
miR-20a
Activation and
proliferation
IL-2R
STAT5
miR-182
Activation and
proliferation
FOXO1

286 | MAY 2016 | VOLUME 16
www.nature.com/nri
.
d
e
v
r
e
s
e
r
s
t
h
g
i
r
l
l
A
.
d
e
t
i
m
i
L
s
r
e
h
s
i
l
b
u
P
n
a
l
l
i
m
c
a
M
6
1
0
2
REVIEWS
(also known as TCF3), early B cell factor 1 (EBF1), paired
box 5 (PAX5) and SRY-box4 (SOX4) (REFS138142). The
rearrangement of immunoglobulin- locus (IGL) is initi
ated in preBcells, which leads to expression of the Bcell
receptor (BCR) in immature Bcells.
Regulation of adaptive immune cells by miRNAs
It was initially shown that the expression of miR181
The adaptive immune system mostly comprises Bcells could drive the differentiation of Bcells without altering
and Tcells, which together provide a targeted second line myeloid cells or Tcells143. Since then, several profiling
of immune defence against foreign pathogens after prim studies have revealed that miRNAs are differentially
ing from the innate immune system. Comprehensive expressed in various Bcell subsets144146. Genetic deletion
reviews of all the miRNAs implicated in adaptive immu of Dicer results in a block in the proB cell to preBcell
nity can be found elsewhere128134. Here, we hone in on transition147, thus demonstrating an essential role for
the most recent discoveries and emphasize key examples miRNA processing in normal Bcell development. The
that highlight either unique facets of miRNA biology or combinatorial effect of many specific miRNAs acting on
network motifs by which miRNAs can influence adaptive diverse cellular processes has been found to mediate this
immune development and function (FIG.5a,b).
transition.
Enforced expression of miR150 inhibits the pro
Bcell development. The development of Bcells begins gression of proBcells to preBcells, in part by inducing
with lymphoid-primed multipotent progenitors (LMPPs), proBcell apoptosis148,149. This is mediated by a dose-
which differentiate into CLPs in a process driven by dependent repression of the miR150 target MYB149.
PU.1 and Ikaros135,136. CLPs express recombination- Consistent with this, partial loss of MYB leads to a dra
activating protein 1 (RAG1) and RAG2, which initi matic loss in Bcells149. Genetic deletion of miR150 leads
ate the rearrangement of immunoglobulin heavy locus to increased expression of its target MYB upon BCR
(IGH)137. Lineage specification to precursor-progenitor activation in Bcells, causing an expansion of B1 Bcells149.
B cells (pre-proB cells), progenitor B cells (proB cells) Uncontrolled expression of MYB, however, leads to the
and eventually precursor B cells (preB cells) involves the development of lymphoid cancers150,151. Thus, as was
coordinated expression of several genes, including E2A observed with miR132 and FOXO3 in HSCs, miR150
has a critical role in buffering MYB expression to within
an appropriate range to prevent aberrant B lymphopoiesis
(FIG.5c).
Figure 5 | miRNAs that regulate adaptive immune cell development and function.
a | The schematic describes the microRNAs (miRNAs) that have key roles in Bcell immune
As well as being induced by p53 in the stress response,
function and development. b | The schematic describes miRNAs that have key roles in
miR34a inhibits the proB cell to preBcell transition
Tcell immune function and development. c | miR150 buffers the expression of the
by targeting FOXP1, which is a known oncogene152. The
oncogene MYB to within a narrow concentration range. Too little MYB results in a Bcell
miR212 and miR132 cluster has recently also been
developmental block, whereas too much MYB leads to dysregulated expansion of
shown to inhibit the pre-proB cell to proB cell transi
Bcellpopulations and can cause leukaemia. d | The miR212 and miR132 cluster
tion by targeting SOX4 (REF.74), which is a crucial medi
establishes a Bcell developmental checkpoint by setting a threshold for SRY-box 4 (SOX4)
ator of proBcell development. Both miR34a and the
mRNA expression that is necessary for Bcell development to continue. SOX4 protein is
miR212 and miR132 cluster establish a checkpoint for
expressed once SOX4 mRNA expression increases enough to negate the repression by
Bcell development by setting a threshold for the expres
miR132. e|miR21 participates in an incoherent feed-forward loop. Signaltransducer
sion of their targets FOXP1 and SOX4, respectively
and activator of transcription 3 (STAT3) induces both miR21 and Blymphocyte-induced
maturation protein 1 (BLIMP1), the latter of which subsequently represses miR21
(FIG.5d). That is, for Bcell development to continue, the
expression. Together, this initiates Bcell proliferation with a temporally delayed inhibition
expression of each target must exceed a certain concen
of this signal to prevent cancerous transformation. f | miR181a serves as a rheostat for
tration to circumvent miRNA-mediated negative feed
Tcell receptor (TCR) signalling. Increased expression of miR181a in the periphery leads to back. By contrast, the miR17~92 cluster acts to preserve
targeted repression of several phosphatases, including tyrosine-protein phosphatase
the proBcell to preBcell transition by negatively regu
non-receptor type 22 (PTPN22), SH2 domain-containing protein tyrosine phosphatase 2
lating the pro-apoptotic protein BIM (also known as
(SHP2) and dual specificity protein phosphatase 6 (DUSP6), which in turn can potentiate
BCL2L11)153.
the signalling response. Decreased levels of miR181a in thethymus have the opposite
The latter stages of Bcell development involve the
effect and thus require stronger TCR signals for signal transduction to occur. g | miR181a
activation of naive Bcells and the formation of plasma
also participates in an incoherent feed-forward loopthat drives Tcell activation but
cells154. Several specific miRNAs act in a concerted fash
imparts a temporally delayed mitigation of this response to prevent aberrant immunity.
Increased expression of miR181a leads to the potentiation of Tcell signalling and
ion to influence commitment to the plasma cell fate by
increased Tcell activation; however, this miRNA also downregulates CD69 expression,
converging to upregulate B lymphocyte-induced matur
which is important for this response. Interestingly, asecond miRNA-mediated incoherent
ation protein 1 (BLIMP1; also known as PRDM1) and
feed-forward loop also has a role in Tcell activation. TCR activation induces CD69
IRF4, and to repress BACH2 and PAX5 (REFS155,156).
expression, in addition to miR17a and miR20, which together directly inhibit CD69
IL21 signalling, an important step in initiating plasma
expression. h | The STAT5mediated activation of miR182 by the interleukin2 receptor
cell differentiation, activates STAT3, which leads to
(IL2R) initiates a positive feedback response. miR182 directly inhibits forkhead box
the induction of both BLIMP1 and miR21 (REF.157).
protein O1 (FOXO1), which is an inhibitor of Tcell activation and proliferation. CLP,
BLIMP1 initiates the plasma cell differentiation pro
common lymphoid progenitor; DN, double negative; DP, double positive; LMPP,
gramme but also overrides STAT3 to repress the expres
lymphoid-primed multipotent progenitor; pre-B cell, precursor B cell; pre-pro-B cell,
sion of miR21, a known oncogenic miRNA157. Thus,
precursor-progenitor B cell; pro-B cell, progenitor-B cell; SP, single positive; TH, T
helper; Treg cell, regulatory T cell.
this miRNA participates in an incoherent feed-forward
B1 Bcells
A subset of Bcells expressing

high levels of IgM that secrete
low-affinity, broad specificity
antibodies.
KIP1)127. A deeper understanding of miRNA-mediated

fate commitment in these cell types may provide new
avenues for using miRNAs to alter the differentiation
and function of specific myeloid cell subsets.
VOLUME 16 | MAY 2016 | 287

.
d
e
v
r
e
s
e
r
s
t
h
g
i
r
l
l
A
.
d
e
t
i
m
i
L
s
r
e
h
s
i
l
b
u
P
n
a
l
l
i
m
c
a
M
6
1
0
2
REVIEWS
Germinal centre
Sites within lymph nodes, the
spleen and other secondary
lymphoid organs where mature
Bcells proliferate and undergo
class-switch recombination and
somatic hypermutation.
Class-switch recombination
(CSR). The somatic
recombination process by
which the class of an
immunoglobulin is switched
from IgM to IgA, IgE or IgG.
B2 Bcells
Conventional Bcells that
secrete highly specific
high-affinity antibodies.
Activation-induced
deaminase
(AID). An RNA-editing enzyme
that is essential for class-switch
recombination and somatic
hypermutation.
Somatic hypermutation
(SHM). The somatic process by
which the antibody repertoire
of an activated Bcell is
mutated to achieve much
higher specificity, which is
thenrequired for Bcell
proliferation and survival in
thegerminal centre.
Double negative 1
(DN1). An early developmental
stage of Tcell progenitors in
the thymus that do not express
either CD4 or CD8.
Double positive
(DP). A late developmental
stage of Tcell progenitors in
the thymus that express both
CD4 and CD8 on their surface.
loop that allows for early expansion of cells that are

committed to the plasma cell fate, with a temporally
delayed repression of this effect to avoid dysregulated
proliferation (FIG.5e).
Both miR155 and miR148a are instrumental in
fate commitment to plasma cells by downregulating
genes that maintain the germinal centre response158,159.
miR155 is induced in response to BCR activation160
and directly inhibits PU.1 (REF.161). This in turn leads
to PAX5 downregulation, which enables plasma cell
commitment 158. Mutation of the miR155 binding site
on PU.1 mRNA invivo leads to increased PU.1 expres
sion during Bcell activation with defective class-switch
recombination (CSR) and plasma cell differentiation158.
miR148a is also upregulated in activated Bcells and
enables plasma cell commitment and survival by down
regulating BACH2 and the pro-apoptotic genes PTEN
(phosphatase and tensin homolog) and BIM159. This ele
vated expression of miR148 also impairs Bcell tolerance
by targeting GADD45, an autoimmunity suppressor 162.
Moreover, miR125b represses both BLIMP1 and IRF4
to inhibit plasma cell differentiation, thus highlighting
the intricate interplay of several miRNAs in maintaining
appropriate Bcell memory 163.
Bcell development in the fetus is heavily biased to the
B1 Bcell lineage164. A role for the LIN28Blet7 axis has
recently been uncovered in the switch from fetal to adult
Bcell lymphopoiesis165. Enforced expression of LIN28B
drives BCR signalling-dependent B1a Bcell develop
ment 165. Conversely, enforced expression of let7 drives
the transition of fetal Bcells to adult B2 Bcells by down
regulating the transcription factor ARID3A (AT-rich
interactive domain-containing protein 3A)165.
cancers173, which may be why negative feedback regu

lation of this enzyme is reinforced by other miRNAs,
such as miR181b174. Enforced expression of miR210,
an octamer-binding protein 2 (OCT2; also known as
POU2F2)induced miRNA in activated Bcells, also
results in defective antibody production and prolifer
ation, although the mechanism that is responsible for
this effect remains unknown175. Interestingly, miR217
was recently found to downregulate the DNA damage
response and stabilize B cell lymphoma 6 (BCL6), thus
driving CSR and SHM in germinal centre Bcells176.
Tcell development. The bulk of Tcell development

begins after the migration of a lymphoid-primed progeni
tor tothe thymus. Notch signalling in the thymus is essen
tial for the survival of early Tcell progenitors, and cells
sequentially transit through several stages described as
double negative 1 (DN1), DN2a, DN2b, DN3a, DN3b, DN4
and double positive (DP) to produce adult Tcells177,178.
Two key checkpoints define this process: first, the transi
tion from DN2a to DN2b represents an irreversible com
mitment to the Tcell lineage; and second, only cells with
a functional preTcell receptor (pre-TCR) can undergo
the DN3a to DN3b transition178.
As has been observed in Bcells, profiling studies on
Tcell subsets have revealed diverse and cell-specific
expression patterns of miRNAs179,180. The conditional
deletion of Dicer in early Tcell progenitors leads to
a decreased output of the number of mature adult
Tcells181,182. miR150 has a role in inhibiting early Tcell
development by downregulating Notch183. Notably,
miR181a also has a unique role in early Tcell develop
ment 184. miR181a expression is higher in the thymus,
particularly in immature DP Tcells that are exposed to
Bcell immune function. An important role has been low-affinity antigens, and lower in the periphery where
described for miRNAs in the antigen-mediated humoral mature cells are responsive to high-affinity antigens184.
immune response. Activation of immature Bcells leads Antagonizing miR181a activity impairs positive and
to a potent proliferative response in germinal centres. negative selection in DP cells184. This is mediated by
Deletion of miR142 leads to an expansion of marginal the direct targeting of miR181a to several negative
zone Bcells, and a loss of peripheral B1 Bcells166. This is signalling regulators, including tyrosine-protein phos
in part due to elevated expression of the miR142 target phatase non-receptor type 22 (PTPN22), SH2 domain-
Bcell-activating factor receptor (BAFFR; also known as containing protein tyrosine phosphatase 2 (SHP2; also
TNFRSF13C), which leads to a sensitization to BAFF known as PTPN11) and dual specificity protein phos
signalling. Interestingly, this was associated with a pro phatase 6 (DUSP6)184. Thus, miR181a is described as a
found decrease in antibody production. Thus, miR142 rheostat for tuning TCR signalling (FIG.5f).
sets a signalling threshold to inhibit uncontrolled acti
An instructive example of how the coordinated regu
vation through BAFF. miR146a similarly sets a thresh lation of multiple targets by many miRNAs can alter a
old for NFB signalling in Bcells; genetic deletion of single developmental pathway occurs during Thelper17
miR146a results in the production of autoantibodies (TH17) cell differentiation. TH17 cell differentiation
from Bcells, which leads to autoimmune disease167.
occurs in response to TGF and IL23 signalling in
Possibly the first miRNA implicated in Bcell immu naive Tcells, which then induces the expression of the
nity, miR155 is a crucial player in the germinal centre master regulator RORt (retinoic acid receptor-related
response168170. Both miR155 and activation-induced orphan receptor-t) in a STAT3dependent manner 185.
deaminase (AID) an essential catalyst of CSR and
The pro-inflammatory miR155 drives TH17 cell out
somatic hypermutation (SHM) that is necessary for anti
put by targeting ETS1 (REF.186), a negative regulator of
body maturation are upregulated in response to BCR TH17 cell differentiation, and the phosphatase SOCS1
signalling 160,171. miR155, in turn, directly represses (REF.187). miR21 drives TH17 cell differentiation by
AID 172, thus participating in an incoherent feed- targeting SMAD7, a negative regulator of TGF sig
forward loop that represses uncontrolled AID expres nalling 188. Analogously, miR301 potentiates STAT3
sion with a temporal delay after a rapid initial induction. signalling through IL23 by targeting the negative sig
Dysregulated AID expression can lead to haematopoietic nalling regulator PIAS3 (REF.189). miR326 ensures
288 | MAY 2016 | VOLUME 16
www.nature.com/nri
.
d
e
v
r
e
s
e
r
s
t
h
g
i
r
l
l
A
.
d
e
t
i
m
i
L
s
r
e
h
s
i
l
b
u
P
n
a
l
l
i
m
c
a
M
6
1
0
2
REVIEWS
Oncomirs
MicroRNAs that lead to
cancerous transformation
when overexpressed.
TH17 lineage commitment by targeting ETS1 (REF.190).

The action of these three miRNAs is counteracted by
miR20b, enforced expression of which inhibits TH17cell
differentiation by direct targeting of both STAT3 and
RORt 191. A minor role for miR212 and miR132 has
also been reported in TH17 cell differentiation through
induction of the aryl hydrocarbon receptor 192.
a dominant role200. Of note, miR146a has an additional

role in the suppressor function of regulatory T (Treg) cells
by directly targeting STAT1 (REF.202). Interestingly, the
miR17~92 cluster also has a role in TFH cell function
by regulating PI3K signalling through suppression of
the PH domain leucine-rich r epeat-containing protein
phosphatase 2 (PHLPP2)203.
Tcell immune function. The regulated activation of

mature Tcells involves a complex interplay of several
miRNAs, which has been reviewed in some recent
publications129,133,134. The activation of mature Tcells is
coordinated by miRNAs that alter TCR signalling and
proliferation. As discussed earlier, miR181a reduces the
TCR signalling threshold in adult Tcells by negatively
regulating several phosphatases184. It also downregulates
CD69, which promotes Tcell proliferation61. Thus, this
miRNA contributes to an incoherent feed-forward loop
that initially enhances Tcell activation, and later represses
this activation after a temporal delay (FIG.5g). Through a
similar mechanism, two miRNAs in the miR17~92 clus
ter, miR17 and miR20a, also participate in an incoher
ent feed-forward loop to regulate Tcell activation61. Both
of these miRNAs are induced with CD69 in response to
TCR signalling but, in turn, directly repress CD69 expres
sion61. Through this network motif, it is hypothesized that
these miRNAs are able to reduce celltocell variability in
response to TCR signalling.
Interestingly, it has been reported that members of
the miR17~92 cluster work in a coordinated fashion on
different pathways that converge to alter a single biologi
cal function193. In Tcells, this is evidenced by the coordi
nated regulation of PTEN by miR19b and of TGF
receptor II and CREBI by miR17, which together pro
mote TH1 cell responses194. In Thelper cells, IL2 recep
tor activation also leads to the induction of miR182
through STAT5 (REF. 195). miR182 in turn directly
represses FOXO1, a negative regulator of cell cycling,
thus contributing to a positive feedback loop that drives
the proliferation of activated Tcells195 (FIG.5h). miR214,
which is induced during Tcell activation, also drives
proliferation by targeting PTEN196. Recent work has
also revealed an important role for miR24 and miR27
in inhibiting TH2 cell function in a coordinated fashion
through inhibition of IL4 production197,198.
An interesting role for the counteracting actions of
two inflammatory miRNAs, miR146a and miR155,
has recently been elucidated in Tcell immunity 199,200.
Activation of NFB through the TCR leads to induction
of miR146a201. This miRNA, as in HSCs and myeloid
cells, forms a negative feedback loop by downregulat
ing the NFB signal transducers TRAF6 and IRAK1
(REF.201). In mice lacking miR146a, elevated NFB
expression leads to a miR155-dependent increase
in T follicular helper (TFH) cells199. Deletion of both
miRNAs diminishes this effect, suggesting that the loss
of miR146a enables a miR155mediated increase in
TFHcell numbers199. An epistatic interaction between
these two miRNAs also occurs during antitumour immu
nity, whereby miR155 enhances and miR146a inhibits
the IFN response, and it was found that miR155 has
Pathological outcomes of miRNA dysregulation

Numerous profiling studies have revealed enrichment of
miRNAs in various haematological cancers52,204209 and
autoimmune diseases210,211, including multiple sclero
sis, rheumatoid arthritis, systemic lupus erythemato
sus, inflammatory bowel disease, Sjgren syndrome
and autoimmune gastritis. Here, we focus on specific
miRNAs that illustrate the general mechanisms that lead
to dysregulated, pathological haematopoietic function.
Haematological cancers. Several specific miR NAs
behave as either oncomirs or tumour suppressors by
regulating many targets that together co-ordinately drive
haematological cancers (FIG.6a). An illustrative example
is the oncomir miR125b, which causes a variety of mye
loid and lymphoid malignancies73,77,212,213 by regulating
several targets that are involved in differentiation, such
as LIN28A73 and IRF4 (REF.77), and in survival, suchas
transformation-related protein 53 inducible nuclear
protein 1 (TRP53INP1)213, BMF and KLF13 (REF.76)
(FIG.6b). Another miRNA, miR28, acts as a tumour
suppressor and is downregulated in Burkitt lymphoma
and B cell non-Hodgkin lymphoma214. Suppression of
miR28 by the oncogene MYC leads to derepression
of several targets, including MAD2L1 (also known as
MAD2A), a component of the spindle checkpoint, and
BAG1, an activator of the extracellular signal-regulated
kinase (ERK) pathway 214. Together, this leads to the
uncontrolled proliferation of certain Bcell subsets.
An interesting example of miRNA addiction during
tumour formation was uncovered with miR21 (REF.51).
Enforced expression of this miRNA results in a preBcell
lymphoma, and the abrupt cessation of its expression
results in tumour apoptosis and regression51. The exact
mechanism of this miRNA addiction remains unknown.
In many cases, the expression of a miRNA leads to
the direct repression of a tumour suppressor gene or the
indirect derepression of an oncogene. The miR17~92
cluster has been implicated in the evolution of myeloid
and lymphoid leukaemia193,215217, and may drive leukae
mic stem cell formation by repressing the tumour sup
pressor p21 (REF.216). Contributing to this phenotype,
this cluster has also been implicated in downregulating
the pro-apoptotic BIM153,218 and PTEN218 genes. Enforced
expression of another oncomir, miR223, is regulated
by the T cell acute lymphocytic leukaemia protein 1
(TAL1) complex and initiates a Tcell acute lympho
blastic leukaemia in mice by downregulating several
tumour suppressors and differentiation genes, includ
ing HEB (also known as TCF12), E2A, LIM domain
only protein1 (LMO1; also known as rhombotin 1)
and/or LMO2, GATA-binding protein 3 (GATA3) and
RUNT-related transcription factor 1 (RUNX1)219.
VOLUME 16 | MAY 2016 | 289

.
d
e
v
r
e
s
e
r
s
t
h
g
i
r
l
l
A
.
d
e
t
i
m
i
L
s
r
e
h
s
i
l
b
u
P
n
a
l
l
i
m
c
a
M
6
1
0
2
REVIEWS
a
Oncomir drives cancer by

repressing many targets
miRNA
Tumour
suppressor
miRNA
Repressors
Normal
haematopoietic cells
Oncogene
miRNA
Oncogene
Leukaemia or lymphoma
Loss of tumour suppressor

miRNA
miR-125b
BMF
KLF13
TRP53INP1
Genes regulating
survival
NF-B
LIN28B
IL-6
let-7
LIN28A
IRF4
Genes regulating
dierentiation
miR-146b
STAT3
Figure 6 | miRNAs in aberrant haematopoiesis. a | Overview of the

mechanisms by which aberrant microRNA (miRNA) expression can lead to cancer.
b|Overexpression of miR125b leads to the developmentNature
of myeloid
or lymphoid
Reviews
| Immunology
leukaemia by the coordinated dysregulation of several targets involved in cell
proliferation, differentiation and survival. c|The nuclear factor- B (NFB)LIN28B
let7interleukin6 (IL6) axis creates a positive feedback loop that can drive cancerous
transformation. Nuclear localization of NFB leads to increased LIN28B expression,
which in turn inhibits let7 processing. Decreased let7 leads to upregulation of its
target IL6, which in turn leads to further activation of NFB and tumorigenesis.
Interestingly, activation of IL6 negatively regulates NFB activation. IL6 signalling
leads to signal transducer and activator of transcription 3 (STAT3)dependent
induction of miR146b, which downregulates several NFB signalling proteins.
BMF,BCL2 modifying factor; IRF4, interferon regulatory factor4; KLF13, Kruppel-like
factor 13; TRP53INP1, transformation-related protein53 inducible nuclear protein 1.
In recent years, miRNAs have also been implicated

in the regulatory networks that link chronic inflam
mation and tumour formation. The enforced expres
sion of miR155 has been implicated in myeloid and
lymphoid leukaemia, in part by downregulation of
the negative signalling regulators SHIP1 and SOCS1
(REFS102,103,109). The genetic deletion of miR146a
leads to uncontrolled NFB signalling, which also
potently induces chronic inflammation and tumour
formation in a manner dependent on NFB p50
expression9395,167. The aberrant activation of NFB
initiates a positive feedback loop that may be a crucial
driver of tumour formation (FIG.6c). Nuclear trans
location of NFB activates LIN28B transcription,
which inhibits processing of the let7 miRNA family 220.
Let7 family members directly target IL6, and thus this
pathway increases IL6 signalling, which potentiates
NFB activation and also drives induction of STAT3
(REF. 220) . Interestingly, STAT3 induces miR146b,
which shares a seed sequence with miR146a, and
this in turn negatively regulates NFBdependent
production of IL6 (REF.221) (FIG.5b).
Autoimmune disease. Many profiling studies have

revealed dysregulated expression of miRNAs in immune
cells during active autoimmune disease50,210,211,218; how
ever, the exact mechanisms by which these miRNAs act
largely remain unknown. Several miRNAs have been
implicated in the potentiation of pro-inflammatory
TH17 cell function, which accelerates disease in the
experimental autoimmune encephalitis mouse model
of multiple sclerosis. These miRNAs include miR155
(REFS186,187), miR20b191, miR21 (REF.188), miR212,
miR132 (REF.192), miR301 (REF.189) and miR326
(REF.190), and each one exercises its effect by repressing
a different target. The ectopic expression of miR17~92
also leads to lymphoproliferative disease and auto
immunity, which are most probably due to aberrant
survival of dysfunctional lymphocytes from BIM and
PTEN downregulation218. The pro-inflammatory dele
tion of miR146a potentiates NFB signalling and
causes a severe systemic autoimmune reaction167, which
is most probably due to a combination of autoantibody
production from Bcells167 and aberrant Tcell activa
tion 201. Inhibition of inflammatory signalling with
deletion of the pro-inflammatory miR155 leads to
resistance to collagen-induced arthritis, which is most
probably due to decreased autoantibody production and
suppression of antigen-specific TH17 cells58,222,223. These
results suggest that miRNAs may indeed be promising
therapeutic targets for autoimmune conditions.
Substantial progress has been made in elucidating the
mechanisms by which miRNAs contribute to pathological
immunity. Future work should hone in on comprehen
sively describing and modelling the gene regulatory net
works that drive aberrant immune responses, with the aim
of identifying key nodes for targeted therapeutic delivery.
Concluding remarks
Over the past decade, dramatic advances have been
made in understanding the network architecture by
which miRNAs regulate immune system development
and function. Exosome and serum profiling studies
have further sparked the possibility of using miRNA
signatures for cancer diagnoses224. Promising attempts to
deliver miRNA mimics and antagonists invivo through
viruses and nanoparticles have opened an exciting
array of new therapeutic possibilities for modulation of
pathological haematopoiesis225228. Several approaches
for genetic modification of miRNAs using transcription
activator-like effector nucleases (TALENs)229231 and
CRISPRCas9-mediated232,233 cleavage in mammalian
cells bring further promise to the field, both for under
standing basic mechanisms of miRNA function and for
the development of therapeutics.
To continue the exciting progress made in the
field, several areas warrant future investigation. New
approaches, such as high-throughput sequencing of
RNA isolated by crosslinking immunoprecipitation
(HITS-CLIP)234, need to be developed to effectively
identify miRNA targets within the immune system in
a cell- and context-dependent manner. In many cases,
miRNAs mediate their effects predominantly at the pro
tein level, making high-throughput target identification
290 | MAY 2016 | VOLUME 16
www.nature.com/nri
.
d
e
v
r
e
s
e
r
s
t
h
g
i
r
l
l
A
.
d
e
t
i
m
i
L
s
r
e
h
s
i
l
b
u
P
n
a
l
l
i
m
c
a
M
6
1
0
2
REVIEWS
using transcriptome data particularly difficult. We need
to develop a better understanding of the coordinated
function and selective processing of miRNA clusters in
the immune system. We need to continue building on
and identifying new network motifs that elucidate the
logic of haematopoietic cell fate decisions. To do this
effectively, we need better mathematical and experimen
tal models of how subtle repression of multiple targets
in a pathway by a single miRNA can lead to dramatic
Kondo,M., Weissman,I.L. & Akashi,K. Identification

of clonogenic common lymphoid progenitors in
mouse bone marrow. Cell 91, 661672 (1997).
2. Akashi,K., Traver,D., Miyamoto,T. & Weissman,I.L.
A clonogenic common myeloid progenitor that gives
rise to all myeloid lineages. Nature 404, 193197
(2000).
3. Orkin,S.H. & Zon,L.I. Hematopoiesis: an evolving
paradigm for stem cell biology. Cell 132, 631644
(2008).
4. Passegue,E., Wagers,A.J., Giuriato,S.,
Anderson,W.C. & Weissman,I.L. Global analysis of
proliferation and cell cycle gene expression in the
regulation of hematopoietic stem and progenitor cell
fates. J.Exp. Med. 202, 15991611 (2005).
5. Novershtern,N. etal. Densely interconnected
transcriptional circuits control cell states in human
hematopoiesis. Cell 144, 296309 (2011).
6. Rossi,L. etal. Less is more: unveiling the functional
core of hematopoietic stem cells through knockout
mice. Cell Stem Cell 11, 302317 (2012).
7. Laurenti,E. etal. The transcriptional architecture of
early human hematopoiesis identifies multilevel
control of lymphoid commitment. Nat. Immunol. 14,
756763 (2013).
8. Cabezas-Wallscheid,N. etal. Identification of
regulatory networks in HSCs and their immediate
progeny via integrated proteome, transcriptome,
and DNA Methylome analysis. Cell Stem Cell 15,
507522 (2014).
9. Martin,C.H. etal. Efficient thymic immigration of
B220+ lymphoid-restricted bone marrow cells with
Tprecursor potential. Nat. Immunol. 4, 866873
(2003).
10. Laiosa,C.V., Stadtfeld,M. & Graf,T. Determinants
oflymphoid-myeloid lineage diversification.
Annu.Rev.Immunol. 24, 705738 (2006).
11. Kondo,M. etal. Cell-fate conversion of lymphoidcommitted progenitors by instructive actions of
cytokines. Nature 407, 383386 (2000).
12. Adolfsson,J. etal. Identification of Flt3+ lymphomyeloid stem cells lacking erythro-megakaryocytic
potential a revised road map for adult blood lineage
commitment. Cell 121, 295306 (2005).
13. Yamamoto,R. etal. Clonal analysis unveils selfrenewing lineage-restricted progenitors generated
directly from hematopoietic stem cells. Cell 154,
11121126 (2013).
14. Schroeder,T. Hematopoietic stem cell heterogeneity:
subtypes, not unpredictable behavior. Cell Stem Cell
6, 203207 (2010).
15. Pronk,C.J. etal. Elucidation of the phenotypic,
functional, and molecular topography of a
myeloerythroid progenitor cell hierarchy. Cell Stem
Cell 1, 428442 (2007).
16. Murre,C. Defining the pathways of early adult
hematopoiesis. Cell Stem Cell 1, 357358 (2007).
17. Arinobu,Y. etal. Reciprocal activation of GATA1 and
PU.1 marks initial specification of hematopoietic
stem cells into myeloerythroid and myelolymphoid
lineages. Cell Stem Cell 1, 416427 (2007).
18. Naik,S.H. etal. Diverse and heritable lineage
imprinting of early haematopoietic progenitors.
Nature 496, 229232 (2013).
19. Wilson,A., Laurenti,E. & Trumpp,A. Balancing
dormant and self-renewing hematopoietic stem cells.
Curr. Opin. Genet. Dev. 19, 461468 (2009).
20. Wilson,A. etal. Hematopoietic stem cells reversibly
switch from dormancy to self-renewal during
homeostasis and repair. Cell 135, 11181129 (2008).
21. Morrison,S.J. & Weissman,I.L. The long-term
repopulating subset of hematopoietic stem cells is
deterministic and isolatable by phenotype. Immunity
1, 661673 (1994).
1.
changes in biological function. In addition, we need

models to better understand how several miRNAs work
synergistically on the 3 UTR of a single mRNA target.
An integrated and comprehensive network model of
how many miRNAs interact with many mRNAs in the
immune system will allow us to identify nodes that may
be viable therapeutic targets. Finally, we must continue
to build tools to enhance or inhibit miRNA function in
the immunesystem.
22. Pietras,E.M. etal. Functionally distinct subsets of

lineage-biased multipotent progenitors control blood
production in normal and regenerative conditions.
Cell Stem Cell 17, 3546 (2015).
23. Mansson,R. etal. Molecular evidence for hierarchical
transcriptional lineage priming in fetal and adult stem
cells and multipotent progenitors. Immunity 26,
407419 (2007).
24. Majeti,R., Park,C.Y. & Weissman,I.L. Identification
of a hierarchy of multipotent hematopoietic
progenitors in human cord blood. Cell Stem Cell 1,
635645 (2007).
25. Kiel,M.J. etal. SLAM family receptors distinguish
hematopoietic stem and progenitor cells and reveal
endothelial niches for stem cells. Cell 121,
11091121 (2005).
26. King,K.Y. & Goodell,M.A. Inflammatory modulation
of HSCs: viewing the HSC as a foundation for the
immune response. Nature reviews. Immunology 11,
685692 (2011).
27. Baldridge,M.T., King,K.Y. & Goodell,M.A.
Inflammatory signals regulate hematopoietic stem
cells. Trends Immunol. 32, 5765 (2011).
28. Scumpia,P.O. etal. Cutting edge: bacterial infection
induces hematopoietic stem and progenitor cell
expansion in the absence of TLR signaling.
J.Immunol. 184, 22472251 (2010).
29. Burberry,A. etal. Infection mobilizes hematopoietic
stem cells through cooperative NOD-like receptor and
Toll-like receptor signaling. Cell Host Microbe 15,
779791 (2014).
30. Tothova,Z. etal. FoxOs are critical mediators of
hematopoietic stem cell resistance to physiologic
oxidative stress. Cell 128, 325339 (2007).
31. Esplin,B.L. etal. Chronic exposure to a TLR ligand
injures hematopoietic stem cells. J.Immunol. 186,
53675375 (2011).
32. Baldridge,M.T., King,K.Y., Boles,N.C.,
Weksberg,D.C. & Goodell,M.A. Quiescent
haematopoietic stem cells are activated by IFN- in
response to chronic infection. Nature 465, 793797
(2010).
33. Flach,J. etal. Replication stress is a potent driver of
functional decline in ageing haematopoietic stem cells.
Nature 512, 198202 (2014).
34. Georgantas,R.W., 3rd etal. CD34+ hematopoietic
stem-progenitor cell microRNA expression and
function: a circuit diagram of differentiation control.
Proc. Natl Acad. Sci. USA 104, 27502755
(2007).
35. Guo,S. etal. MicroRNA miR125a controls
hematopoietic stem cell number. Proc. Natl Acad. Sci.
USA 107, 1422914234 (2010).
36. Mehta,A. etal. The microRNA132 and
microRNA212 cluster regulates hematopoietic stem
cell maintenance and survival with age by buffering
FOXO3 expression. Immunity 42, 10211032
(2015).
37. OConnell,R.M. etal. MicroRNAs enriched in
hematopoietic stem cells differentially regulate longterm hematopoietic output. Proc. Natl Acad. Sci. USA
107, 1423514240 (2010).
This study highlights the role of several miRNAs
inregulating HSC function as measured by bone
marrow engraftment.
38. Arai,F. etal. Tie2/angiopoietin1 signaling regulates
hematopoietic stem cell quiescence in the bone
marrow niche. Cell 118, 149161 (2004).
39. Warr,M.R. etal. FOXO3A directs a protective
autophagy program in haematopoietic stem cells.
Nature 494, 323327 (2013).
40. Nagai,Y. etal. Toll-like receptors on hematopoietic
progenitor cells stimulate innate immune system
replenishment. Immunity 24, 801812 (2006).
41. Zhao,J.L. etal. Conversion of danger signals

intocytokine signals by hematopoietic stem and
progenitor cells for regulation of stress-induced
hematopoiesis. Cell Stem Cell 14, 445459 (2014).
42. Krol,J., Loedige,I. & Filipowicz,W. The widespread
regulation of microRNA biogenesis, function and
decay. Nat. Rev. Genet. 11, 597610 (2010).
43. Bartel,D.P. MicroRNAs: genomics, biogenesis,
mechanism, and function. Cell 116, 281297
(2004).
44. Wiesen,J.L. & Tomasi,T.B. Dicer is regulated by
cellular stresses and interferons. Mol. Immunol. 46,
12221228 (2009).
45. Suzuki,H.I. etal. Modulation of microRNA processing
by p53. Nature 460, 529533 (2009).
This study describes a mechanism by which miRNA
processing is altered in response to environmental
stress.
46. Leung,A.K., Calabrese,J.M. & Sharp,P.A.
Quantitative analysis of Argonaute protein reveals
microRNA-dependent localization to stress granules.
(2006).
47. Bronevetsky,Y. & Ansel,K.M. Regulation of miRNA
biogenesis and turnover in the immune system.
Immunol. Rev. 253, 304316 (2013).
48. Mendell,J.T. & Olson,E.N. MicroRNAs in stress
signaling and human disease. Cell 148, 11721187
(2012).
49. Leung,A.K. & Sharp,P.A. MicroRNA functions in
stress responses. Mol. Cell 40, 205215 (2010).
50. Pauley,K.M., Cha,S. & Chan,E.K. MicroRNA in
autoimmunity and autoimmune diseases.
J.Autoimmun. 32, 189194 (2009).
51. Medina,P.P., Nolde,M. & Slack,F.J. OncomiR
addiction in an invivo model of microRNA21induced
preBcell lymphoma. Nature 467, 8690 (2010).
This is the first model for oncomir addiction in
haematopoietic malignancies.
52. Esquela-Kerscher,A. & Slack,F.J. Oncomirs
microRNAs with a role in cancer. Nat. Rev. Cancer 6,
259269 (2006).
53. Lin,Y.C. etal. A global network of transcription
factors, involving E2A, EBF1 and Foxo1, that
orchestrates Bcell fate. Nat. Immunol. 11, 635643
(2010).
54. Mansson,R. etal. Positive intergenic feedback
circuitry, involving EBF1 and FOXO1, orchestrates
Bcell fate. Proc. Natl Acad. Sci. USA 109,
2102821033 (2012).
55. Neph,S. etal. Circuitry and dynamics of human
transcription factor regulatory networks. Cell 150,
12741286 (2012).
56. Ebert,M.S. & Sharp,P.A. Roles for microRNAs in
conferring robustness to biological processes.
Cell 149, 515524 (2012).
57. Ivey,K.N. &Srivastava,D. MicroRNAs as regulators
of differentiation and cell fate decisions. Cell Stem Cell
7, 3641 (2010).
58. Lu,L.F. etal. A Single miRNA-mRNA interaction
affects the immune response in a context- and celltype-specific manner. Immunity 43, 5264 (2015).
59. Strovas,T.J., Rosenberg,A.B., Kuypers,B.E.,
Muscat,R.A. & Seelig,G. MicroRNA-based singlegene circuits buffer protein synthesis rates against
perturbations. ACS Synthet. Biol. 3, 324331
(2014).
60. Schmiedel,J.M. etal. Gene expression. MicroRNA
control of protein expression noise. Science 348,
128132 (2015).
61. Blevins,R. etal. microRNAs regulate celltocell
variability of endogenous target gene expression in
developing mouse thymocytes. PLoS Genet. 11,
e1005020 (2015).
VOLUME 16 | MAY 2016 | 291

.
d
e
v
r
e
s
e
r
s
t
h
g
i
r
l
l
A
.
d
e
t
i
m
i
L
s
r
e
h
s
i
l
b
u
P
n
a
l
l
i
m
c
a
M
6
1
0
2
REVIEWS
62. Kim,D., Grun,D. & van Oudenaarden,A. Dampening
of expression oscillations by synchronous regulation
ofa microRNA and its target. Nat. Genet. 45,
13371344 (2013).
This study quantitatively describes how miRNAs
can buffer oscillations in protein expression.
63. Mukherji,S. etal. MicroRNAs can generate
thresholds in target gene expression. Nat. Genet. 43,
854859 (2011).
This study quantitatively describes how miRNAs
can set thresholds for target gene expression.
64. Na,Y.J. & Kim,J.H. Understanding cooperativity
ofmicroRNAs via microRNA association networks.
BMC genomics 14 (Suppl. 5), S17 (2013).
65. Alon,U. Network motifs: theory and experimental
approaches. Nat. Rev. Genet. 8, 450461 (2007).
This is an overview of network motifs and their
biological implications.
66. Herranz,H. & Cohen,S.M. MicroRNAs and gene
regulatory networks: managing the impact of noise
in biological systems. Genes Dev. 24, 13391344
(2010).
67. Morrison,S.J. & Scadden,D.T. The bone marrow
niche for haematopoietic stem cells. Nature 505,
327334 (2014).
68. Acar,M. etal. Deep imaging of bone marrow shows
non-dividing stem cells are mainly perisinusoidal.
Nature 526, 126130 (2015).
69. Liao,R. etal. MicroRNAs play a role in the
development of human hematopoietic stem cells.
J.Cell. Biochem. 104, 805817 (2008).
70. Bissels,U. etal. Combined characterization of
microRNA and mRNA profiles delineates early
differentiation pathways of CD133+ and CD34+
hematopoietic stem and progenitor cells. Stem Cells
29, 847857 (2011).
71. Gruber,J.J. etal. Ars2 links the nuclear cap-binding
complex to RNA interference and cell proliferation.
Cell 138, 328339 (2009).
72. Gerrits,A. etal. Genetic screen identifies microRNA
cluster 99b/let7e/125a as a regulator of primitive
hematopoietic cells. Blood 119, 377387 (2012).
73. Chaudhuri,A.A. etal. Oncomir miR125b regulates
hematopoiesis by targeting the gene Lin28A.
Proc. Natl Acad. Sci. USA 109, 42334238 (2012).
74. Mehta,A. etal. The microRNA212/132 cluster
regulates Bcell development by targeting Sox4.
J.Exp. Med. 212, 16791692 (2015).
75. Heinrich,E.M. etal. Regulation of miR1792a cluster
processing by the microRNA binding protein SND1.
FEBS Lett. 587, 24052411 (2013).
76. Ooi,A.G. etal. MicroRNA125b expands
hematopoietic stem cells and enriches for the
lymphoid-balanced and lymphoid-biased subsets.
(2010).
77. So,A.Y. etal. Dual mechanisms by which miR125b
represses IRF4 to induce myeloid and Bcell
leukemias. Blood 124, 15021512 (2014).
78. Emmrich,S. etal. miR99a/100~125b tricistrons
regulate hematopoietic stem and progenitor cell
homeostasis by shifting the balance between TGF
and Wnt signaling. Genes Dev. 28, 858874
(2014).
79. Challen,G.A., Boles,N.C., Chambers,S.M. &
Goodell,M.A. Distinct hematopoietic stem cell
subtypes are differentially regulated by TGF1.
Cell Stem Cell 6, 265278 (2010).
80. Luis,T.C. etal. Canonical wnt signaling regulates
hematopoiesis in a dosage-dependent fashion.
Cell Stem Cell 9, 345356 (2011).
81. Han,Y.C. etal. microRNA29a induces aberrant selfrenewal capacity in hematopoietic progenitors, biased
myeloid development, and acute myeloid leukemia.
J.Exp. Med. 207, 475489 (2010).
82. Hu,W. etal. miR29a maintains mouse hematopoietic
stem cell self-renewal by regulating Dnmt3a. Blood
125, 22062216 (2015).
83. Song,S.J. etal. The oncogenic microRNA miR22
targets the TET2 tumor suppressor to promote
hematopoietic stem cell self-renewal and
transformation. Cell Stem Cell 13, 87101 (2013).
84. Dickstein,J. etal. Methylation and silencing of
miRNA124 by EVI1 and self-renewal exhaustion of
hematopoietic stem cells in murine myelodysplastic
syndrome. Proc. Natl Acad. Sci. USA 107,
97839788 (2010).
85. Gentner,B. etal. Identification of hematopoietic
stem cell-specific miRNAs enables gene therapy of
globoid cell leukodystrophy. Sci. Transl Med. 2,
58ra84 (2010).
86. Lechman,E.R. etal. Attenuation of miR126 activity

expands HSC invivo without exhaustion. Cell Stem
Cell 11, 799811 (2012).
87. Lechman,E.R. etal. miR126 regulates distinct
self-renewal outcomes in normal and malignant
hematopoietic stem cells. Cancer Cell 29, 214228
(2016).
88. Shen,W.F., Hu,Y.L., Uttarwar,L., Passegue,E. &
Largman,C. MicroRNA126 regulates HOXA9 by
binding to the homeobox. Mol. Cell. Biol. 28,
46094619 (2008).
89. Copley,M.R. etal. The Lin28blet7Hmga2 axis
determines the higher self-renewal potential of fetal
haematopoietic stem cells. Nature Cell Biol. 15,
916925 (2013).
90. Yuan,J., Nguyen,C.K., Liu,X., Kanellopoulou,C. &
Muljo,S.A. Lin28b reprograms adult bone marrow
hematopoietic progenitors to mediate fetal-like
lymphopoiesis. Science 335, 11951200 (2012).
This study demonstrates how altering the
post-transcriptional processing of a specific miRNA
can reprogramme adult haematopoietic cells to
fetal haematopoiesis.
91. Manz,M.G. & Boettcher,S. Emergency
granulopoiesis. Nat. Rev. Immunol. 14, 302314
(2014).
92. ONeill,L.A., Sheedy,F.J. & McCoy,C.E.
MicroRNAs: the fine-tuners of Toll-like receptor
signalling. Nat. Rev. Immunol. 11, 163175 (2011).
93. Taganov,K.D., Boldin,M.P., Chang,K.J. &
Baltimore,D. NFB-dependent induction of
microRNA miR146, an inhibitor targeted to signaling
proteins of innate immune responses. Proc. Natl Acad.
Sci. USA 103, 1248112486 (2006).
This is the first study to demonstrate induction of
miRNAs in response to inflammatory stimuli.
94. Zhao,J.L. etal. NFB dysregulation in
microRNA146adeficient mice drives the
development of myeloid malignancies. Proc. Natl
Acad. Sci. USA 108, 91849189 (2011).
95. Zhao,J.L., Rao,D.S., OConnell,R.M., GarciaFlores,Y. & Baltimore,D. MicroRNA146a acts as a
guardian of the quality and longevity of hematopoietic
stem cells in mice. eLife 2, e00537 (2013).
96. Herrera-Merchan,A. etal. miR33mediated
downregulation of p53 controls hematopoietic stem
cell self-renewal. Cell Cycle) 9, 32773285 (2010).
97. Haetscher,N. etal. STAT5regulated microRNA193b
controls haematopoietic stem and progenitor cell
expansion by modulating cytokine receptor signalling.
Nature Commun. 6, 8928 (2015).
98. Felli,N. etal. MicroRNAs 221 and 222 inhibit normal
erythropoiesis and erythroleukemic cell growth via kit
receptor down-modulation. Proc. Natl Acad. Sci. USA
102, 1808118086 (2005).
99. OConnell,R.M., Rao,D. S. & Baltimore,D.
microRNA regulation of inflammatory responses.
Annu. Rev. Immunol. 30, 295312 (2012).
100. OConnell,R.M., Zhao,J.L. & Rao,D.S. MicroRNA
function in myeloid biology. Blood 118, 29602969
(2011).
101. Curtis,A.M.etal. Circadian control of innate immunity
in macrophages by miR155 targeting Bmal1.
102. OConnell,R.M., Chaudhuri,A.A., Rao,D.S. &
Baltimore,D. Inositol phosphatase SHIP1 is a primary
target of miR155. Proc. Natl Acad. Sci. USA 106,
71137118 (2009).
103. OConnell,R.M., Taganov,K.D., Boldin,M.P.,
Cheng,G. & Baltimore,D. MicroRNA155 is induced
during the macrophage inflammatory response.
104. Wang,L. etal. Notch-dependent repression of
miR155 in the bone marrow niche regulates
hematopoiesis in an NFB-dependent manner.
Cell Stem Cell 15, 5165 (2014).
105. Turner,M.L., Schnorfeil,F.M. & Brocker,T.
MicroRNAs regulate dendritic cell differentiation and
function. J.Immunol. 187, 39113917 (2011).
106. Mann,M. Barad,O., Agami,R., Geiger,B. &
Hornstein,E. miRNA-based mechanism for the
commitment of multipotent progenitors to a single
cellular fate. Proc. Natl Acad. Sci. USA 107,
1580415809 (2010).
107. Androulidaki,A. etal. The kinase Akt1 controls
macrophage response to lipopolysaccharide by
regulating microRNAs. Immunity 31, 220231
(2009).
108. McCoy,C.E. etal. IL10 inhibits miR155 induction by
toll-like receptors. J.Biol. Chem. 285, 2049220498
(2010).
292 | MAY 2016 | VOLUME 16
109. OConnell,R.M. etal. Sustained expression of

microRNA155 in hematopoietic stem cells causes
amyeloproliferative disorder. J.Exp. Med. 205,
585594 (2008).
This is one of the first studies to demonstrate
thataberrant miRNA expression can lead to
myeloproliferative disorders.
110. Fazi,F. etal. A minicircuitry comprised of
microRNA223 and transcription factors NFIA and
C/EBP regulates human granulopoiesis. Cell 123,
819831 (2005).
111. Pulikkan,J.A. etal. Cell-cycle regulator E2F1 and
microRNA223 comprise an autoregulatory negative
feedback loop in acute myeloid leukemia. Blood 115,
17681778 (2010).
112. Johnnidis,J.B. etal. Regulation of progenitor cell
proliferation and granulocyte function by
microRNA223. Nature 451, 11251129 (2008).
This is the first demonstration of a miRNA that
cancontribute to granulocyte development.
113. Fukao,T. etal. An evolutionarily conserved
mechanism for microRNA223 expression revealed
by microRNA gene profiling. Cell 129, 617631
(2007).
114. Vian,L. etal. Transcriptional fine-tuning of
microRNA223 levels directs lineage choice of human
hematopoietic progenitors. Cell Death Differ. 21,
290301 (2014).
115. Hock,H. etal. Intrinsic requirement for zinc finger
transcription factor Gfi1 in neutrophil differentiation.
Immunity 18, 109120 (2003).
116. Velu,C.S., Baktula,A.M. & Grimes,H.L. Gfi1
regulates miR21 and miR196b to control
myelopoiesis. Blood 113, 47204728 (2009).
117. Hager,M. etal. MicroRNA130amediated downregulation of Smad4 contributes to reduced sensitivity
to TGF1 stimulation in granulocytic precursors.
Blood 118, 66496659 (2011).
118. Pobezinsky,L.A. etal. Let7 microRNAs target the
lineage-specific transcription factor PLZF to regulate
terminal NKT cell differentiation and effector function.
Blood 16, 517524 (2015).
119. Cichocki,F. etal. Cutting edge: microRNA181
promotes human NK cell development by regulating
Notch signaling. J.Immunol. 187, 61716175 (2011).
120. Bezman,N.A., Chakraborty,T., Bender,T. &
Lanier,L. L. miR150 regulates the development of
NK and iNKT cells. J.Exp. Med. 208, 27172731
(2011).
121. Beaulieu,A.M. etal. MicroRNA function in NKcell
biology. Immunol. Rev. 253, 4052 (2013).
122. Xu,X. etal. Systematic analysis of microRNA
fingerprints in thrombocythemic platelets using
integrated platforms. Blood 120, 35753585
(2012).
123. Lu,J. etal. MicroRNA-mediated control of cell fate in
megakaryocyte-erythrocyte progenitors. Dev. Cell 14,
843853 (2008).
124. Garzon,R. etal. MicroRNA fingerprints during human
megakaryocytopoiesis. Proc. Natl Acad. Sci. USA 103,
50785083 (2006).
125. Rasmussen,K.D. etal. The miR144/451 locus is
required for erythroid homeostasis. J.Exp. Med. 207,
13511358 (2010).
126. Lu,T.X. etal. MiR223 deficiency increases
eosinophil progenitor proliferation. J.Immunol. 190,
15761582 (2013).
127. Mayoral,R.J. etal. MicroRNA221222 regulate the
cell cycle in mast cells. J.Immunol. 182, 433445
(2009).
128. Marques,S.C. etal. MicroRNAs in Bcells: from
normal differentiation to treatment of malignancies.
Oncotarget 6, 725 (2015).
129. Podshivalova,K. & Salomon,D.R. MicroRNA
regulation of Tlymphocyte immunity: modulation of
molecular networks responsible for Tcell activation,
differentiation, and development. Crit. Rev. Immunol.
33, 435476 (2013).
130. Dooley,J., Linterman,M.A. & Liston,A. MicroRNA
regulation of Tcell development. Immunol. Rev. 253,
5364 (2013).
131. de Yebenes,V.G., Bartolome-Izquierdo,N. &
Ramiro,A.R. Regulation of Bcell development and
function by microRNAs. Immunol. Rev. 253, 2539
(2013).
132. Li,J., Wan,Y., Ji,Q., Fang,Y. & Wu,Y. The role of
microRNAs in Bcell development and function.
Cell. Mol. Immunol. 10, 107112 (2013).
133. Jeker,L.T. & Bluestone,J.A. MicroRNA regulation of
Tcell differentiation and function. Immunol. Rev. 253,
6581 (2013).
www.nature.com/nri
.
d
e
v
r
e
s
e
r
s
t
h
g
i
r
l
l
A
.
d
e
t
i
m
i
L
s
r
e
h
s
i
l
b
u
P
n
a
l
l
i
m
c
a
M
6
1
0
2
REVIEWS
134. Baumjohann,D. & Ansel,K.M. MicroRNA-mediated
regulation of Thelper cell differentiation and plasticity.
Nat. Rev. Immunology 13, 666678 (2013).
135. Nutt,S.L. & Kee,B.L. The transcriptional regulation
of Bcell lineage commitment. Immunity 26, 715725
(2007).
136. Matthias,P. & Rolink,A.G. Transcriptional networks
in developing and mature Bcells. Nat. Rev. Immunol.
5, 497508 (2005).
137. Igarashi,H., Gregory,S.C., Yokota,T., Sakaguchi,N.
&Kincade,P.W. Transcription from the RAG1 locus
marks the earliest lymphocyte progenitors in bone
marrow. Immunity 17, 117130 (2002).
138. ORiordan,M. & Grosschedl,R. Coordinate regulation
of Bcell differentiation by the transcription factors
EBF and E2A. Immunity 11, 2131 (1999).
139. Cobaleda,C., Schebesta,A., Delogu,A. &
Busslinger,M. Pax5: the guardian of Bcell identity
and function. Nat. Immunol. 8, 463470 (2007).
140. Souabni,A., Cobaleda,C., Schebesta,M. &
Busslinger,M. Pax5 promotes B lymphopoiesis and
blocks Tcell development by repressing Notch1.
Immunity 17, 781793 (2002).
141. Sun,B. etal. Sox4 is required for the survival of
proBcells. J.Immunol. 190, 20802089 (2013).
142. Mallampati,S. etal. Integrated genetic approaches
identify the molecular mechanisms of Sox4 in early
Bcell development: intricate roles for RAG1/2 and
CK1. Blood 123, 40644076 (2014).
143. Chen,C.Z., Li,L., Lodish,H.F. & Bartel,D.P.
MicroRNAs modulate hematopoietic lineage
differentiation. Science 303, 8386 (2004).
This is the first study to show that miRNAs can
modulate immune cell development.
144. Basso,K. etal. Identification of the human mature
Bcell miRNome. Immunity 30, 744752 (2009).
145. Tan,L.P. etal. miRNA profiling of Bcell subsets:
specific miRNA profile for germinal center Bcells
withvariation between centroblasts and centrocytes.
Lab. Invest. 89, 708716 (2009).
146. Zhang,J. etal. Patterns of microRNA expression
characterize stages of human Bcell differentiation.
Blood 113, 45864594 (2009).
147. Koralov,S.B. etal. Dicer ablation affects antibody
diversity and cell survival in the B lymphocyte lineage.
Cell 132, 860874 (2008).
This is an early study that details the impact of
miRNA deletion on Bcell development and function.
148. Zhou,B., Wang,S., Mayr,C., Bartel,D.P. &
Lodish,H. F. miR150, a microRNA expressed in
mature B and Tcells, blocks early Bcell development
when expressed prematurely. Proc. Natl Acad. Sci.
USA 104, 70807085 (2007).
149. Xiao,C. etal. MiR150 controls Bcell differentiation
by targeting the transcription factor cMyb. Cell 131,
146159 (2007).
150. Thompson,C.B., Challoner,P.B., Neiman,P.E. &
Groudine,M. Expression of the cmyb proto-oncogene
during cellular proliferation. Nature 319, 374380
(1986).
151. Lahortiga,I. etal. Duplication of the MYB oncogene in
Tcell acute lymphoblastic leukemia. Nat. Genet. 39,
593595 (2007).
152. Rao,D.S. etal. MicroRNA34a perturbs B
lymphocyte development by repressing the forkhead
box transcription factor Foxp1. Immunity 33, 4859
(2010).
153. Ventura,A. etal. Targeted deletion reveals essential
and overlapping functions of the miR17 through 92
family of miRNA clusters. Cell 132, 875886 (2008).
154. McHeyzer-Williams,M., Okitsu,S., Wang,N. &
McHeyzer-Williams,L. Molecular programming of
Bcell memory. Nat. Rev. Immunol. 12, 2434 (2012).
155. Ding,B.B., Bi,E., Chen,H., Yu,J.J. & Ye,B.H.
IL21 and CD40L synergistically promote plasma cell
differentiation through upregulation of Blimp1 in
human Bcells. J.Immunol. 190, 18271836 (2013).
156. Nutt,S.L., Hodgkin,P.D., Tarlinton,D.M. &
Corcoran,L.M. The generation of antibody-secreting
plasma cells. Nat. Rev. Immunol. 15, 160171 (2015).
157. Barnes,N.A., Stephenson,S., Cocco,M., Tooze,R.M.
& Doody,G.M. BLIMP1 and STAT3 counterregulate
microRNA21 during plasma cell differentiation.
J.Immunol. 189, 253260 (2012).
158. Lu,D. etal. The miR155PU.1 axis acts on Pax5
to enable efficient terminal Bcell differentiation.
J.Exp. Med. 211, 21832198 (2014).
159. Porstner,M. etal. miR148a promotes plasma cell
differentiation and targets the germinal center
transcription factors Mitf and Bach2. Eur. J.Immunol.
45, 12061215 (2015).
160. Yin,Q., Wang,X., McBride,J., Fewell,C. &

Flemington,E. Bcell receptor activation induces
BIC/miR155 expression through a conserved AP1
element. J.Biol. Chem. 283, 26542662 (2008).
161. Gerloff,D. etal. NFB/STAT5/miR155 network
targets PU.1 in FLT3ITD-driven acute myeloid
leukemia. Leukemia 29, 535547 (2015).
162. Gonzalez-Martin,A. etal. The microRNA miR148a
functions as a critical regulator of Bcell tolerance
and autoimmunity. Nat. Immunol. http://dx.doi.org/
10.1038/ni.3385 (2016).
163. Gururajan,M. etal. MicroRNA 125b inhibition of
Bcell differentiation in germinal centers. Int. Immunol.
22, 583592 (2010).
164. Montecino-Rodriguez,E. & Dorshkind,K. B-1 Bcell
development in the fetus and adult. Immunity 36,
1321 (2012).
165 Zhou,Y. etal. Lin28b promotes fetal B lymphopoiesis
through the transcription factor Arid3a. J.Exp. Med.
212, 569580 (2015).
166. Palsson-McDermott,E.M. etal. Altered lymphopoiesis
and immunodeficiency in miR142 null mice. Proc. Natl
Acad. Sci. USA 125, 37203730 (2015).
167. Boldin,M.P. etal. miR146a is a significant brake on
autoimmunity, myeloproliferation, and cancer in mice.
J.Exp. Med. 208, 11891201 (2011).
This study describes how the loss of an antiinflammatory miRNA can lead to autoimmunity
andcancer.
168. Rodriguez,A. etal. Requirement of bic/microRNA155
for normal immune function. Science 316, 608611
(2007).
This is one of the first studies to demonstrate the
role of an inflammatory miRNA in the germinal
centre response.
169. Vigorito,E. Kohlhaas,S., Lu,D. & Leyland,R.
miR155: an ancient regulator of the immune system.
Immunol. Rev. 253, 146157 (2013).
170. Vigorito,E. etal. microRNA155 regulates the
generation of immunoglobulin class-switched plasma
cells. Immunity 27, 847859 (2007).
171. Xu,Z., Zan,H., Pone,E.J., Mai,T. & Casali,P.
Immunoglobulin class-switch DNA recombination:
induction, targeting and beyond. Nat. Rev. Immunol.
12, 517531 (2012).
172. Teng,G. etal. MicroRNA155 is a negative regulator
of activation-induced cytidine deaminase. Immunity
28, 621629 (2008).
This is one of the first studies to demonstrate a role
for an inflammatory miRNA in Bcell class-switching
recombination and somatic hypermutation.
173. Okazaki,I.M. etal. Constitutive expression of
AID leads to tumorigenesis. J.Exp. Med. 197,
11731181 (2003).
174. de Yebenes,V.G. etal. miR181b negatively regulates
activation-induced cytidine deaminase in Bcells.
J.Exp. Med. 205, 21992206 (2008).
175. Mok,Y. etal. MiR210 is induced by Oct2, regulates
Bcells, and inhibits autoantibody production.
J.Immunol. 191, 30373048 (2013).
176. de Yebenes,V.G. etal. miR217 is an oncogene that
enhances the germinal center reaction. Blood 124,
229239 (2014).
177. Germain,R.N. Tcell development and the CD4CD8
lineage decision. Nat. Rev. Immunol. 2, 309322
(2002).
178. Yui,M.A. & Rothenberg,E.V. Developmental gene
networks: a triathlon on the course to Tcell identity.
Nat. Rev. Immunol. 14, 529545 (2014).
179. Monticelli,S. etal. MicroRNA profiling of the murine
hematopoietic system. Genome Biol. 6, R71 (2005).
180. Wu,H. etal. miRNA profiling of naive, effector and
memory CD8 Tcells. PLoS ONE 2, e1020 (2007).
181. Cobb,B.S. etal. Tcell lineage choice and
differentiation in the absence of the RNase III enzyme
Dicer. J.Exp. Med. 201, 13671373 (2005).
182. Muljo,S.A. etal. Aberrant Tcell differentiation in the
absence of Dicer. J.Exp. Med. 202, 261269 (2005).
References179 and 180 demonstrate the impact
of miRNA deletion on Tcell development.
183. Ghisi,M. etal. Modulation of microRNA expression
inhuman Tcell development: targeting of NOTCH3
bymiR150. Blood 117, 70537062 (2011).
184. Li,Q.J. etal. miR181a is an intrinsic modulator of
Tcell sensitivity and selection. Cell 129, 147161
(2007).
This interesting study demonstrates how a miRNA
can serve as a rheostat for signalling.
185. McGeachy,M.J. & Cua,D.J. Th17 cell differentiation:
the long and winding road. Immunity 28, 445453
(2008).
186. Hu,R. etal. MicroRNA155 confers encephalogenic

potential to Th17 cells by promoting effector gene
expression. J.Immunol. 190, 59725980 (2013).
187. Yao,R. etal. MicroRNA155 modulates Treg and
Th17 cells differentiation and Th17 cell function by
targeting SOCS1. PLoS ONE 7, e46082 (2012).
188. Murugaiyan,G. etal. MicroRNA21 promotes
Th17 differentiation and mediates experimental
autoimmune encephalomyelitis. J.Clin. Invest. 125,
10691080 (2015).
189. Mycko,M.P. etal. MicroRNA301a regulation of a
Thelper 17 immune response controls autoimmune
demyelination. Proc. Natl Acad. Sci. USA 109,
E1248E1257 (2012).
190. Du,C. etal. MicroRNA miR326 regulates TH17
differentiation and is associated with the pathogenesis
of multiple sclerosis. Nat. Immunol. 10, 12521259
(2009).
191. Zhu,E. etal. miR20b suppresses Th17 differentiation
and the pathogenesis of experimental autoimmune
encephalomyelitis by targeting RORt and STAT3.
J.Immunol. 192, 55995609 (2014).
192. Nakahama,T. etal. Aryl hydrocarbon receptormediated induction of the microRNA132/212 cluster
promotes interleukin17producing Thelper cell
differentiation. Proc. Natl Acad. Sci. USA 110,
1196411969 (2013).
193. Han,Y.C. & Vidigal,J.A. An allelic series of miR17
approximately 92mutant mice uncovers functional
specialization and cooperation among members of a
microRNA polycistron. Nat. Genet. 47, 766775
(2015).
194. Jiang,S. etal. Molecular dissection of the miR1792
clusters critical dual roles in promoting Th1 responses
and preventing inducible Treg differentiation. Blood
118, 54875497 (2011).
195. Stittrich,A.B. etal. The microRNA miR182 is
induced by IL2 and promotes clonal expansion of
activated helper T lymphocytes. Nat. Immunol. 11,
10571062 (2010).
196. Jindra,P.T., Bagley,J., Godwin,J.G. & Iacomini,J.
Costimulation-dependent expression of
microRNA214 increases the ability of Tcells to
proliferate by targeting Pten. J.Immunol. 185,
990997 (2010).
197. Cho,S. etal. miR23 approximately 27 approximately
24 clusters control effector Tcell differentiation and
function. J.Exp. Med. 213, 235249 (2016).
198. Pua,H.H. etal. MicroRNAs 24 and 27 suppress
allergic inflammation and target a network of
regulators of T helper 2 cell-associated cytokine
production. Immunity http://dx.doi.org/10.1016/
j.immuni.2016.01.003 (2016).
199. Hu,R. etal. miR155 promotes T follicular helper cell
accumulation during chronic, low-grade inflammation.
Immunity 41, 605619 (2014).
200. Huffaker,T.B. etal. Epistasis between microRNAs
155 and 146a during Tcell-mediated antitumor
immunity. Cell Rep. 2, 16971709 (2012).
201. Yang,L. etal. miR146a controls the resolution
of Tcell responses in mice. J.Exp. Med. 209,
16551670 (2012).
202. Lu,L.F. etal. Function of miR146a in controlling
Treg cell-mediated regulation of Th1 responses.
Cell 142, 914929 (2010).
This is one of the first papers describing the role
of miRNAs in Treg cell function.
203. Kang,S.G. etal. MicroRNAs of the miR17
approximately 92 family are critical regulators of
TFH differentiation. Nat. Immunol. 14, 849857
(2013).
204. Calin,G.A. & Croce,C.M. MicroRNA signatures in
human cancers. Nature reviews. Cancer 6, 857866
(2006).
205. Calin,G.A. etal. MicroRNA profiling reveals distinct
signatures in Bcell chronic lymphocytic leukemias.
(2004).
206. de Leeuw,D.C. etal. MicroRNA profiling can classify
acute leukemias of ambiguous lineage as either acute
myeloid leukemia or acute lymphoid leukemia.
Clin. Cancer Res. 19, 21872196 (2013).
207. Lu,J. etal. MicroRNA expression profiles classify
human cancers. Nature 435, 834838 (2005).
208. Schotte,D., Pieters,R. & Den Boer,M.L.
MicroRNAs in acute leukemia: from biological
players to clinical contributors. Leukemia 26, 112
(2012).
209. Garzon,R. etal. MicroRNA signatures associated with
cytogenetics and prognosis in acute myeloid leukemia.
Blood 111, 31833189 (2008).
VOLUME 16 | MAY 2016 | 293

.
d
e
v
r
e
s
e
r
s
t
h
g
i
r
l
l
A
.
d
e
t
i
m
i
L
s
r
e
h
s
i
l
b
u
P
n
a
l
l
i
m
c
a
M
6
1
0
2
REVIEWS
210. Simpson,L.J. & Ansel,K.M. MicroRNA regulation of
lymphocyte tolerance and autoimmunity. J.Clin. Invest.
125, 22422249 (2015).
211. Singh,R.P. etal. The role of miRNA in inflammation
and autoimmunity. Autoimmun. Rev. 12, 11601165
(2013).
212. Bousquet,M., Harris,M.H., Zhou,B. & Lodish,H.F.
MicroRNA miR125b causes leukemia. Proc. Natl
Acad. Sci. USA 107, 2155821563 (2010).
213. Enomoto,Y. etal. Emu/miR125b transgenic mice
develop lethal Bcell malignancies. Leukemia 25,
18491856 (2011).
214. Schneider,C. etal. MicroRNA 28 controls cell
proliferation and is down-regulated in Bcell
lymphomas. Proc. Natl Acad. Sci. USA 111,
81858190 (2014).
215. Sandhu,S.K. etal. Bcell malignancies in microRNA
Emu-miR17~92 transgenic mice. Proc. Natl Acad.
Sci. USA 110, 1820818213 (2013).
216. Wong,P. etal. The miR1792 microRNA polycistron
regulates MLL leukemia stem cell potential by
modulating p21 expression. Cancer Res. 70,
38333842 (2010).
217. He,L. etal. A microRNA polycistron as a potential
human oncogene. Nature 435, 828833 (2005).
218. Xiao,C. etal. Lymphoproliferative disease and
autoimmunity in mice with increased miR1792
expression in lymphocytes. Nat. Immunol. 9,
405414 (2008).
This is the first study to demonstrate that aberrant
miRNA expression can lead to autoimmune
disease.
219. Mansour,M.R. etal. The TAL1 complex targets the
FBXW7 tumor suppressor by activating miR223 in
human Tcell acute lymphoblastic leukemia.
J.Exp. Med. 210, 15451557 (2013).
220. Iliopoulos,D., Hirsch,H.A. & Struhl,K. An epigenetic
switch involving NFB, Lin28, Let7 MicroRNA, and
IL6 links inflammation to cell transformation.
Cell 139, 693706 (2009).
221. Xiang,M. etal. STAT3 induction of miR146b forms a
feedback loop to inhibit the NFB to IL6 signaling
axis and STAT3driven cancer phenotypes. Sci. Signal.
7, ra11 (2014).
222. OConnell,R.M. etal. MicroRNA155 promotes
autoimmune inflammation by enhancing
inflammatory Tcell development. Immunity 33,
607619 (2010).
223. Kurowska-Stolarska,M. etal. MicroRNA155 as a
proinflammatory regulator in clinical and
experimental arthritis. Proc. Natl Acad. Sci. USA 108,
1119311198 (2011).
224. Chevillet,J.R. etal. Quantitative and stoichiometric
analysis of the microRNA content of exosomes.
(2014).
225. Chen,Y., Gao,D.Y. & Huang,L. Invivo delivery of
miRNAs for cancer therapy: challenges and strategies.
Adv. Drug Delivery Rev. 81, 128141 (2015).
226. Janssen,H.L. etal. Treatment of HCV infection by
targeting microRNA. New Engl. J.Med. 368,
16851694 (2013).
227. Li,Z. & Rana,T.M. Therapeutic targeting of

microRNAs: current status and future challenges.
Nat. Rev. Drug Discov. 13, 622638 (2014).
228. Ling,H., Fabbri,M. & Calin,G.A. MicroRNAs and
other non-coding RNAs as targets for anticancer drug
development. Nat. Rev. Drug Discov. 12, 847865
(2013).
229. Kim,Y.K. etal. TALEN-based knockout library for
human microRNAs. Nat. Struct. Mol. Biol. 20,
14581464 (2013).
230. Uhde-Stone,C. etal. A TALEN-based strategy for
efficient biallelic miRNA ablation in human cells.
RNA 20, 948955 (2014).
231. Hu,R., Wallace,J., Dahlem,T.J., Grunwald,D.J. &
OConnell,R.M. Targeting human microRNA genes
using engineered Tal-effector nucleases (TALENs).
PLoS ONE 8, e63074 (2013).
This paper describes an approach to genetic
deletion of miRNAs in human cells using
TALENs.
232. Ho,T.T. etal. Targeting non-coding RNAs with
theCRISPR/Cas9 system in human cell lines.
Nucleic Acids Res. 43, e17 (2015).
233. Zhao,Y. etal. Sequence-specific inhibition of
microRNA via CRISPR/CRISPRi system. Scientif. Rep.
4, 3943 (2014).
234. Chi,S.W., Zang,J.B., Mele,A. & Darnell,R.B.
Argonaute HITS-CLIP decodes microRNA-mRNA
interaction maps. Nature 460, 479486 (2009).
This study describes a high-throughput approach
to identify miRNA targets by looking directly at the
binding of miRNAs to mRNAs.
235. Friedman,R.C., Farh,K.K., Burge,C.B. &
Bartel,D.P. Most mammalian mRNAs are conserved
targets of microRNAs. Genome Res. 19, 92105
(2009).
236. Guo,H., Ingolia,N.T., Weissman,J.S. & Bartel,D.P.
Mammalian microRNAs predominantly act to
decrease target mRNA levels. Nature 466, 835840
(2010).
237. Ha,M. & Kim,V.N. Regulation of microRNA
biogenesis. Nat. Rev. Mol. Cell Biol. 15, 509524
(2014).
238. He,L. & Hannon,G.J. MicroRNAs: small RNAs
with a big role in gene regulation. Nat. Rev. Genet.
5, 522531 (2004).
239. Agarwal,V., Bell,G.W., Nam,J.W. & Bartel,D.P.
Predicting effective microRNA target sites in
mammalian mRNAs. eLife 4, http://dx.doi.org/
10.7554/eLife.05005 (2015).
This paper describes the algorithm used by
Targetscan, a popular miRNA target prediction
software.
240. Liu,G. etal. miR147, a microRNA that is induced
upon Toll-like receptor stimulation, regulates
murine macrophage inflammatory responses.
(2009).
241. Nahid,M.A. etal. Regulation of TLR2mediated
tolerance and cross-tolerance through IRAK4
modulation by miR132 and miR212. J.Immunol.
190, 12501263 (2013).
294 | MAY 2016 | VOLUME 16
242. Davis,B.N., Hilyard,A.C., Lagna,G. & Hata,A.

SMAD proteins control DROSHA-mediated microRNA
maturation. Nature 454, 5661 (2008).
This study demonstrates that extracellular
signalling through growth factors can alter miRNA
processing.
243. Trabucchi,M. etal. The RNA-binding protein KSRP
promotes the biogenesis of a subset of microRNAs.
Nature 459, 10101014 (2009).
244. Heo,I. etal. TUT4 in concert with Lin28 suppresses
microRNA biogenesis through pre-microRNA
uridylation. Cell 138, 696708 (2009).
245. OCarroll,D. etal. A Slicer-independent role for
Argonaute 2 in hematopoiesis and the microRNA
pathway. Genes Dev. 21, 19992004 (2007).
246. Orom,U.A., Nielsen,F.C. & Lund,A.H.
MicroRNA10a binds the 5UTR of ribosomal protein
mRNAs and enhances their translation. Mol. Cell 30,
460471 (2008).
247. Place,R.F., Li,L.C., Pookot,D., Noonan,E.J. &
Dahiya,R. MicroRNA373 induces expression of
genes with complementary promoter sequences.
248. Vasudevan,S., Tong,Y. & Steitz,J.A. Switching from
repression to activation: microRNAs can upregulate
translation. Science 318, 19311934 (2007).
249. Ciafre,S. A. & Galardi,S. microRNAs and RNAbinding proteins: a complex network of interactions
and reciprocal regulations in cancer. RNA Biol. 10,
935942 (2013).
250. Heo,I. etal. Mono-uridylation of pre-microRNA as a
key step in the biogenesis of group II let7 microRNAs.
Cell 151, 521532 (2012).
251. Nam,Y., Chen,C., Gregory,R.I., Chou,J.J. & Sliz,P.
Molecular basis for interaction of let7 microRNAs
with Lin28. Cell 147, 10801091 (2011).
252. van Kouwenhove,M., Kedde,M. & Agami,R.
MicroRNA regulation by RNA-binding proteins and
its implications for cancer. Nat. Rev. Cancer 11,
644656 (2011).
253. Pasquinelli,A.E. MicroRNAs and their targets:
recognition, regulation and an emerging reciprocal
relationship. Nat. Rev. Genet. 13, 271282 (2012).
254. Salmena,L., Poliseno,L., Tay,Y., Kats,L. &
Pandolfi,P.P. A ceRNA hypothesis: the Rosetta Stone
of a hidden RNA language? Cell 146, 353358
(2011).
255. Tay,Y., Rinn,J. & Pandolfi,P.P. The multilayered
complexity of ceRNA crosstalk and competition.
Nature 505, 344352 (2014).
Acknowledgements
The preparation of this review was supported by the US

National Institute of Health (RO1AI079243 to D.B.),
theNational Research Service Award (CA183220 to A.M.)
and the University of California, Los Angeles/California
Institute of Technology Medical Scientist Training Program
(A.M.). The authors also thank J. Zhao, D. Rao and M. Mann
for their comments in preparation of this manuscript.
Competing interests statement
The authors declare no competing interests.
www.nature.com/nri
.
d
e
v
r
e
s
e
r
s
t
h
g
i
r
l
l
A
.
d
e
t
i
m
i
L
s
r
e
h
s
i
l
b
u
P
n
a
l
l
i
m
c
a
M
6
1
0
2

MiRNAs and Immune System

Diunggah oleh

Informasi Dokumen

Hak Cipta

Format Tersedia

Bagikan dokumen Ini

Bagikan atau Tanam Dokumen

Opsi Berbagi

Apakah menurut Anda dokumen ini bermanfaat?

Apakah konten ini tidak pantas?

Hak Cipta:

Format Tersedia

MiRNAs and Immune System

Diunggah oleh

Hak Cipta:

Format Tersedia

REVIEWS

MicroRNAs as regulatory elements

Abstract | MicroRNAs (miRNAs) are crucial post-transcriptional regulators of haematopoietic cell

Division of Biology and

Mammalian haematopoiesis has conventionally been

and differentiation (FIG.1b). Appropriate and balanced

NATURE REVIEWS | IMMUNOLOGY

VOLUME 16 | MAY 2016 | 279

b Bone marrow niche signals

Figure 1 | Overview of immune system development and the regulatory

and outcome of cell fate in a context-dependent man

Mechanisms of miRNA regulation of cell fate

280 | MAY 2016 | VOLUME 16

Protein expression noise

The coherent and incoherent feed-forward motifs

occurs (FIG.2g). In the haematopoietic system, these

Regulation of HSC function by miRNAs

NATURE REVIEWS | IMMUNOLOGY

VOLUME 16 | MAY 2016 | 281

The complex of two enzymes,

Buffering protein expression

Maintaining the expression of a

(ceRNA). RNAs that bind

Noisy protein expression from

2. Negative feedback can provide

A collection of microRNAs that

3. Buering protein concentration to within a narrow range

Figure 2 | The different roles of miRNAs in network motifs

mice deficient in the essential miRNA-processing pro

failure71. This is possibly due to an altered proliferation

282 | MAY 2016 | VOLUME 16

WNT1 and TGF signalling

Cell cycling and self-renewal

SMAD2 and SMAD4

Small PI3K signal

Large PI3K signal

Buered FOXO3 range

Nature Reviews | Immunology

miR29a is also enriched in LT-HSCs 81, but its

Figure 3 | Overview of miRNAs that alter HSC

TET2, which catalyses the oxidation of 5methylcyto

NATURE REVIEWS | IMMUNOLOGY

VOLUME 16 | MAY 2016 | 283

miR193b and miR132 are both induced in LTHSCs

(REF.107). Thus, TLR4 activation initiates an incoherent

feed-forward loop that drives macrophage activation

inflammatory response. In addition to its function in

NATURE REVIEWS | IMMUNOLOGY

VOLUME 16 | MAY 2016 | 285

including RAS-related C3 botulinum substrate 1

CD4+ Treg cell

Buered MYB range

Nature Reviews | Immunology

A subset of Bcells expressing

KIP1)127. A deeper understanding of miRNA-mediated

NATURE REVIEWS | IMMUNOLOGY

VOLUME 16 | MAY 2016 | 287

loop that allows for early expansion of cells that are

cancers173, which may be why negative feedback regu

Tcell development. The bulk of Tcell development

288 | MAY 2016 | VOLUME 16

TH17 lineage commitment by targeting ETS1 (REF.190).

a dominant role200. Of note, miR146a has an additional

Tcell immune function. The regulated activation of